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    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
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    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
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    10 |   \item{semilandmark.pattern}{a regular expression pattern passed to \code{sub()} for identifying and grouping curve points. The default is landmark names ending in one or more numbers. To disable grouping, set to code{''}.}
       |                                                                                                                                                                                                                           ^
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    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("config")}
       | ^
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    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_container")}
       | ^
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       | ^
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       | ^
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       | ^
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    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_task")}
       | ^
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    14 | \code{$demographic.coord}{
       |                          ^
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    18 | \code{$genetic.coord}{
       |                      ^
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    22 | \code{$demographic.measures}{
       |                             ^
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    26 | \code{$genetic.frequencies}{
       |                            ^
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    70 | {Basic model operations:} \cr
       | ^
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    79 | {Parameter estimation:} \cr
       | ^
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    88 | {Sensitivity and Monte Carlo analyses:} \cr
       | ^
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    98 | {Compare model runs:} \cr
       | ^
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   105 | {Fishery yield analysis:} \cr
       | ^
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   111 | {Visualize model inputs:} \cr
       | ^
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   117 | {Visualize model outputs:} \cr
       | ^
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    38 | \code{\link[streamDAG]{stream.order}}, \code{\link[igraph]{delete.vertices}}, code{\link[igraph]{add.vertices}}, code{\link[igraph]{add.edges}}
       |                                                                                   ^
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    38 | \code{\link[streamDAG]{stream.order}}, \code{\link[igraph]{delete.vertices}}, code{\link[igraph]{add.vertices}}, code{\link[igraph]{add.edges}}
       |                                                                                                                      ^
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efpFunctional: multiple local function definitions for ‘plotProcess’
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    22 | \item{quant}{numeric quantile to calculate {0,1}, default 0.95.}
       |                                            ^
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    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                        ^
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    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                            ^
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    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                        ^
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    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                            ^
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    18 |  used for this will be 1.00*10^{-PoissonThreshold}.}
       |                                ^
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    14 | {suggests} aims to make that workflow as minimal and painless as possible,
       | ^
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    30 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{csvdata}
       |                                ^
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    88 | \item{jsondata}{\code{deprecated} use data argument instead; data in nested d3 JSON hierarchy with `{name:...,  children:[];}`}
       |                                                                                                     ^
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    22 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{list}, \code{character},
       |                                ^
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    19 |     \item{\code{Number}:}{code{"numeric"}, number of biclusters in the set}
       |                               ^
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    42 |  \item{color.off}{color code; specifying the color for set(s) which are "{absent}" for an intersection.}
       |                                                                          ^
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--- re-building ‘suppdata-intro.Rnw’ using knitr

Quitting from lines 40-42 [unnamed-chunk-2] (suppdata-intro.Rnw)
Error: processing vignette 'suppdata-intro.Rnw' failed with diagnostics:
SI number '2' greater than number of detected SIs (1)
--- failed re-building ‘suppdata-intro.Rnw’

SUMMARY: processing the following file failed:
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     6 | getFittedValues <- function(object) {
       |                                     ^
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    14 | getFittedValues <- function(object) {
       |                                     ^
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Auto-generated content requiring editing in Rd file 'suRtex.Rd':
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  \keyword: ‘~kwd2’
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    24 | \item{mpl_h0t}{MPL estimates of the baseline hazard for T, i.e. h_{0T}(x_i)}
       |                                                                   ^
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    25 | \item{mpl_h0c}{MPL estimates of the baseline hazard for C, i.e. h_{0C}(x_i)}
       |                                                                   ^
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    26 | \item{mpl_H0t}{MPL estimates of the baseline cumulative hazard for T, i.e. H_{0T}(x_i)}
       |                                                                              ^
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    27 | \item{mpl_H0c}{MPL estimates of the baseline cumulative hazard for C, i.e. H_{0c}(x_i)}
       |                                                                              ^
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    28 | \item{mpl_S0t}{MPL estimates of the baseline survival for T, i.e. S_{0T}(x_i)}
       |                                                                     ^
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    29 | \item{mpl_S0c}{MPL estimates of the baseline survival for C, i.e. S_{0C}(x_i)}
       |                                                                     ^
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    66 | A {data.table} which is stored as an attribute of
       |   ^
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    76 | The estimation procedure here is performed using coxph {survival} and inserting these estimated
       |                                                        ^
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    24 | set, svKomodo loads {svSocket}, starts the socket server listening to the
       |                     ^
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    18 | Komodo and (2) the present {svKomodo} R package that work hand in hand to
       |                            ^
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    28 | Nevertheless, the SciViews-K Komodo addin and the {svKomodo} R package
       |                                                   ^
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    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                          ^
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    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                                         ^
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    37 | Both SciViews-K and {svKomodo} should be considered archived items. I keep
       |                     ^
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    32 | \code{\link[survey:surveysummary]{survey::svymean()}} and related functions from the {survey}
       |                                                                                      ^
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    28 | numeric (scalar or vector): Relative treatment effect upon crossing over from control. Note that this is not the treatment effect (the treatment effect is specified in the call to other functions such as \code{swPwr} or \code{swSim})!  If \code{tx.effect.frac} is set to a scalar with value of 1, the standard SW CRT treatment effect will be presumed. If code{tx.effect.frac} is set to a scalar with a fractional value between 0 and 1, then only the first time point upon crossing over from control will have fractional relative treatment effect; the remaining exposure times will have a relative treatment effect of 1. If a vector of fractional treatment effect is specified, each element of the vector corresponds to the (fractional) treatment effect upon crossing over from control; if the length of the vector is less than total number of exposure times, the remaining time points will have a relative treatment effect value of 1; if the length of the vector is greater than total number of time points after crossing over, not all elements of \code{tx.effect.frac} will be used. The default value is (scalar) 1.
       |                                                                                                                                                                                                                                                                                                                                                                        ^
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Problems with news in ‘NEWS.md’:
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    Additional functions and data sets
    Amendments to functions
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    18 |   \item{epsilon}{positive convergence tolerance \emph{e}; the iterations converge when |fit - fit_{old}|/|fit| < \emph{e}. Default is \emph{e=1e-04}.}
       |                                                                                                   ^
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    14 | \code{n} x 4 matrix of coordinates consisting of {lat or y, lon or x} pairs for each each site
       |                                                  ^
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    28 | before plotting {ex: \code{trans = c(s = "exp", d = "exp")}}/}
       |                 ^
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    68 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
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    67 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
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    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |   ^
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    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |                      ^
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   119 | Brownlees, C. T., and Gallo, G. M. (2006). Financial Econometric Analysis at Ultra{--}High Frequency: Data Handling Concerns, \emph{Computational Statistics and Data Analysis} \bold{51}, 2232--2245.
       |                                                                                   ^
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    59 | Brownlees, C. T., and Gallo, G. M. (2006). Financial Econometric Analysis at Ultra{--}High Frequency: Data Handling Concerns, \emph{Computational Statistics and Data Analysis} \bold{51}, 2232--2245.
       |                                                                                   ^
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    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
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    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
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    35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
       |                                                                                                                                                                                                                                                                                                                                                  ^
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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    32 | link{squaredError}
       |     ^
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checkRd: (-1) Tendril.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
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    19 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
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    23 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
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    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
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    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
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    10 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
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    16 | \item{\code{func}}{prepared for objective functions like SYS_LSF$func <- function(x){return(x[1] + x[2])}}
       |                                                                                     ^
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Package suggested but not available for checking: ‘gurobi’
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    37 |  {The 2 in the first row means there are two cycles;}
       |  ^
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    38 |   {The second row means there is a cycle of length 2, with members  (1,3);}
       |   ^
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    39 |  {The third row means  there is a cycle of length 1, with member  (2);}
       |  ^
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    40 |  {The fourth row is redundant for this specific case.}
       |  ^
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    41 |  {One can read from the output of permucycle() to obtain cycle notation (13)(2) of the permutation, and other information.}
       |  ^
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    16 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variatioanl approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
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    26 | It is recommended to use link{sibp_param_search} instead of this function to search over multiple configurations of the most important parameters.  So long as only the training data is used, the analyst can freely experimient with as many parameter configurations as he likes without corrupting his causal inferences.  Once a parameter configuration is chosen, the user can then use \link{sibp_amce} on the test set to estimate the average marginal component effect (AMCE) for each treatment.}
       |                              ^
checkRd: (-1) sibp.Rd:28: Lost braces; missing escapes or markup?
    28 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variational approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
checkRd: (-1) sibp_amce.Rd:19: Lost braces
    19 |   \item{sibp.amce}{The table returned by code{sibp_amce}.}
       |                                              ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) make.phrase.matrix.Rd:20: Lost braces
    20 |  \\tabular{rrrrr}{
       |           ^
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    20 |  \\tabular{rrrrr}{
       |                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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    63 | NOTE: Currently only n in {2, 3, 4, 5} are supported. For n=5 some numerical
       |                           ^
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    31 | The teigen family. Stat Comput 22:1021{1029. <doi.org/10.1007/
       |                                       ^
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
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    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                    ^
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                           ^
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                                          ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
checkRd: (-1) single_imputation.Rd:21-22: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
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     5 | \title{Install {timeseriesdb} System Functions}
       |                ^
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    17 | Installs functions needed to operated {timeseriesdb} in
       |                                       ^
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     5 | \title{Grant execute on {timeseriesdb} functions}
       |                         ^
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    17 | Grant execute on {timeseriesdb} functions
       |                  ^
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     5 | \title{Install {timeseriesdb} System Tables}
       |                ^
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    17 | Installs tables needed to operated {timeseriesdb} in
       |                                    ^
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     5 | \title{Install {timeseriesdb} Triggers}
       |                ^
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   247 |   do any conversion on the POSIX{l,c}t objects).
       |                                 ^
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    10 | \item{body}{an XML object generated via {tinkr}}
       |                                         ^
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    13 | The {commonmark} package is used to translate markdown to XML, but it does
       |     ^
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    14 | not assign a namespace prefix, which means that {xml2} will auto-assign a
       |                                                 ^
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     5 | \title{The {tinkr} stylesheet}
       |            ^
checkRd: (-1) stylesheet.Rd:14: Lost braces; missing escapes or markup?
    14 | This function returns the path to the {tinkr} stylesheet
       |                                       ^
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    11 | stylesheet used by {tinkr}.
       |                    ^
'LazyData' is specified without a 'data' directory
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
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    20 | \item{cutoff}{Numeric. The value max(0, g_{i,j} - cutoff) so that there are <\code{.num_components}> components in the graph.}
       |                                           ^
GNU make is a SystemRequirements.
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   332 |   If the input argument code{boxes} is \code{F}, the \code{lBox},
       |                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
Auto-generated content requiring editing in Rd file 'effect.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'effectInfo.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Specified C++14: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the episode_id value found in the change entries.
       |                                                 ^
checkRd: (-1) tv_season_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the season_id value found in the change entries.
       |                                                 ^
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checkRd: (-1) pvalEffectPlot.Rd:94: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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     5 | \title{Format data as a JSON object (like this: {"x": "120"}).}
       |                                                 ^
checkRd: (-1) jsonStr.Rd:18: Lost braces; missing escapes or markup?
    18 | Format data as a JSON object (like this: {"x": "120"}).
       |                                          ^
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checkRd: (-1) Data.Rd:17: Lost braces in \itemize; meant \describe ?
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    21 | Recommended range is in {5, ..., 20}.}
       |                         ^
checkRd: (-1) getSegsExtra.Rd:14: Lost braces
    14 | \item{data}{data.table returned from function /code{tdtr}}
       |                                                    ^
checkRd: (-1) ETM.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ETM.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ETM.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ETM.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ETM.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Package suggested but not available for checking: ‘gurobi’
Package suggested but not available for checking: ‘toscaData’
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
'LazyData' is specified without a 'data' directory
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    23 |     item{\code{estimates}: parameter estimates}
       |         ^
checkRd: (-1) parse_beast_output_files.Rd:24-28: Lost braces
    24 |     item{
       |         ^
checkRd: (-1) parse_beast_output_files.Rd:29-31: Lost braces
    29 |     item{\code{operators}: the BEAST2 MCMC operator
       |         ^
checkRd: (-1) parse_beast_posterior.Rd:28: Lost braces
    28 |     item{\code{estimates}: parameter estimates}
       |         ^
checkRd: (-1) parse_beast_posterior.Rd:29-33: Lost braces
    29 |     item{
       |         ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) Sim-Functions.Rd:100-102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:108: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) trait_missing.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘taxidata’
Error(s) in re-building vignettes:
  ...
--- re-building ‘mtram.Rnw’ using knitr
** Processing: figure/mtram-toenail_OR_2-1.png
1800x1200 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 260592 bytes
Input file size = 261042 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 234718
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 234718

Output IDAT size = 234718 bytes (25874 bytes decrease)
Output file size = 234796 bytes (26246 bytes = 10.05% decrease)


Quitting from lines 1329-1334 [mtram-toenail_glmer_RS] (mtram.Rnw)
Error: processing vignette 'mtram.Rnw' failed with diagnostics:
PIRLS loop resulted in NaN value
--- failed re-building ‘mtram.Rnw’

--- re-building ‘tram.Rnw’ using knitr

warning: solve(): system is singular; attempting approx solution

warning: solve(): system is singular (rcond: 1.92626e-18); attempting approx solution
--- finished re-building ‘tram.Rnw’

SUMMARY: processing the following file failed:
  ‘mtram.Rnw’

Error: Vignette re-building failed.
Execution halted
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    69 | numeric with two values {0,1} and gaussian(link = "identity") otherwise.
       |                         ^
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    31 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
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    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
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    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
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    24 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
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    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
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    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
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    18 | data.frame with "{var_name}" column for the mean and
       |                  ^
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    19 | "{var_name}_{prob}" columns for each probability.
       |  ^
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    19 | "{var_name}_{prob}" columns for each probability.
       |             ^
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  almost never needs to use ::: for its own objects:
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    16 | \item{matrix.logical}{With matrix=TRUE, the matrix is logical TRUE/FALSE or string "*"/code{" "}}
       |                                                                                            ^
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    39 | If \code{order.x} or {order.y} are \code{NULL}, their respective series will be fitted automatically using a AR model.
       |                      ^
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    31 | If \code{order.x} or {order.y} are \code{NULL}, their respective series will be fitted automatically using a AR model. If \code{permissive} is \code{TRUE} and no AR order is found automatically, an AR order of 1 will be imposed, if this case fails, then no order can be found and the function produces an error.
       |                      ^
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    16 | Converts any variable with two possible values to a {0,1} binary
       |                                                     ^
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    13 | A vector with values in {0,1}.
       |                         ^
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    28 | The final representation has length equal to floor(n / 2^{level}), where n is a length of original time series.
       |                                                          ^
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    74 |         doi{10.1093/biomet/74.2.221}
       |            ^
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    25 | \item{xcov}{Either a \[stats]{formula} with an empty left-hand side specifying external covariates
       |                              ^
Auto-generated content requiring editing in Rd file 'retweets.Rd':
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    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |     ^
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    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |                                  ^
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    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |  ^
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    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |               ^
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    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |                                ^
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    47 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
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    33 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
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   111 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
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    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
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    42 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
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    33 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
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    45 | link[dlogitnorm]{dlogitnorm}for the normal density.
       |                 ^
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    59 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}
       |                                  ^
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    60 | \item{\code{sim_CI}}: {vector containing the cluster indices for each generated unimodal reference distribution}
       |                       ^
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    61 | \item{\code{pvalue_emp}}: {the empirical p-value:  the proportion of times the cluster index from the reference
       |                           ^
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    63 | \item{\code{pvalue_norm}}: {the normalized p-value: the simulated p-value based on comparison to a standard normal distribution }
       |                            ^
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    58 | \item{\code{BestK}}: {A matrix with 1 row and 4 columns named: "Max_CI","Max_CI_wi_1SE","Max_scaled_CI" and "Max_logWCSS_wi_1SE".
       |                      ^
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    63 | \item{\code{full_process}}: {A matrix containing the number of clusters, K, evaluated, the CI from the data, the average CI from the null
       |                             ^
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    66 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}}
       |                                  ^
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    21 |    \code{train}{The mldr dataset with train examples, that includes all
       |                ^
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    23 |    \code{test}{The mldr dataset with test examples, defined by the
       |               ^
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    25 |    \code{validation}{Optionally, only if \code{has.validation = TRUE}.
       |                     ^
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    18 | Generate \code{n} random samples from multivariate Gaussian distribution N(0, (L^TL)^{-1})
       |                                                                                      ^
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    97 | \item{ID_level2}{Optional}{variable for unit ID codes. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                           ^
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    99 | \item{dataset}{Optional}{survey data object convertible to \code{data.table}.}
       |                         ^
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   122 | \item{ind_gr}{Optional}{variable by which divided independently X matrix of the auxiliary variables for the calibration. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                        ^
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   124 | \item{use.estVar}{Logical}{value. If value is \code{TRUE}, then \code{R} function \code{estVar} is used for the  estimation of covariance matrix of the residuals. If value is \code{FALSE}, then \code{R} function \code{estVar} is not used for the estimation of covariance matrix of the residuals.}
       |                           ^
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    69 | \item{percentratio}{Positive}{numeric value. All linearized variables are multiplied with \code{percentratio} value, by default - 1.}
       |                              ^
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   121 | \item{month_at_work}{Variable}{for total number of month at work (sum of the number of months spent at full-time work as employee, number of months spent at part-time work as employee, number of months spent at full-time work as self-employed (including family worker), number of months spent at part-time work as self-employed (including family worker)).  One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                               ^
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     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Burr distribution due to Parana\'{i}ba et al. (2011) given by
       |                                                                                                                        ^
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     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Fr\'{e}chet distribution due to Barreto-Souza et al. (2011) given by
       |                                                                                           ^
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     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                      ^
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     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                                                      ^
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     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Kumaraswamy Burr XII distribution due to Parana\'{i}ba et al. (2013) given by
       |                                                                                                                                   ^
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    40 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + exp(2*X22)*e
       |                                ^
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    42 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + 6*X22 + e
       |                                ^
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    15 | \item{file.suffix}{Regex expression for end of file name. For example, `file.suffix = '_S\\d{1,2}_.*_R1_.*'` will match R1 files.1 files.}
       |                                                                                             ^
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    23 | The function returns the K-by-K matrices {A_1, ..., A_p} as a list object.
       |                                          ^
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    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                    ^
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    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                                        ^
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    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |      ^
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    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |          ^
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    15 | and dimension information (\code{dim} or code{length}) of each item,
       |                                              ^
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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     6 | \title{Indexing to extract subsets of a 'code{\link[via:XArray-class]{VirtualArray}}'-class object}
       |                                              ^
checkRd: (-1) subset.Rd:20: Lost braces
    20 | \item{drop}{\code{logical} in case the result of subsetting is a single element, should the \\code{\link[via:XArray-class]{VirtualArray}} wrapper be dropped?}
       |                                                                                                   ^
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   311 | albedo must be supplied in code{forcing_veg}. Default = 1.}
       |                                ^
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   323 | supplied in code{forcing_veg}. Default = 1.}
       |                 ^
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   341 | be supplied in code{forcing_veg} Default = 0.}
       |                    ^
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'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("vines")
  Loading required package: copula
  > 
  > test_check("vines", reporter = "summary")
  h: 
  h: 1
  hinverse: 
  hinverse: 2
  
  ══ Failed ══════════════════════════════════════════════════════════════════════
  ── 1. Error ('test-h.R:3:1'): (code run outside of `test_that()`) ──────────────
  Error in `testthat:::test_code(new_desc, substitute(code), env = env)`: argument "reporter" is missing, with no default
  Backtrace:
      ▆
   1. └─vines:::test_that_for_each_copula(...) at test-h.R:3:1
   2.   └─testthat:::test_code(new_desc, substitute(code), env = env) at tests/testthat/helper-copulas.R:37:13
  
  ── 2. Error ('test-hinverse.R:3:1'): (code run outside of `test_that()`) ───────
  Error in `testthat:::test_code(new_desc, substitute(code), env = env)`: argument "reporter" is missing, with no default
  Backtrace:
      ▆
   1. └─vines:::test_that_for_each_copula(...) at test-hinverse.R:3:1
   2.   └─testthat:::test_code(new_desc, substitute(code), env = env) at tests/testthat/helper-copulas.R:37:13
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
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    75 |   \item \strong{Pollen productivity}: In each time step the model computes the pollen productivity (in relative values) of the population using the equation \eqn{P_{t} = \sum x_{it} \times max(S_{t}, B)}, where \emph{t} is time (a given simulation time step), \emph{P} is the pollen productivity of the population at a given time, \emph{x_{i}} represents the biomass of every adult individual, \emph{S} is the environmental suitability at the given time, \emph{B} is the contribution of biomass to pollen productivity regardless of environmental suitability (\emph{pollen.control} parameter in the simulation, 0 by default). If \emph{B} equals 1, \emph{P} is equal to the total biomass sum of the adult population, regardless of the environmental suitability. If \emph{B} equals 0, pollen productivity depends entirely on environmental suitability values.
       |                                                                                                                                                                                                                                                                                                                                                    ^
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    16 |   ...{currently not used}
       |      ^
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    32 | A call to {new} returns a newly allocated object from the class identified by the first argument.
       |           ^
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Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) ViSiElse.Rd:101-107: Lost braces in \itemize; meant \describe ?
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) aminoAcidFun.Rd:37: Lost braces
    37 | \item{ownVLFreduced}{ownVLFMatrix}{A matrix containing only those specimen that have VLFs as well as the amino acids at the positions that contain VLFs and NAs in all other positions of the sequence.  Only appears if own is not NULL.}
       |                                   ^
checkRd: (-1) vlfFun.Rd:36: Lost braces
    36 | \item{ownVLFreduced}{ownVLFMatrix}{A matrix containing only those specimen that have VLFs as well as the nucleotides at the positions that contain VLFs and NAs in all other positions of the sequence.  Only appears if own is not NULL.}
       |                                   ^
Specified C++11: please drop specification unless essential
checkRd: (-1) getTurnType.Rd:38: Lost braces; missing escapes or markup?
    38 | Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
       |               ^
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Data-Examples.Rd:39: Lost braces in \itemize; meant \describe ?
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Specified C++11: please drop specification unless essential
checkRd: (-1) WACS.Rd:18: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) WACSreadAgroclim.Rd:16-17: Lost braces in \itemize; \value handles \item{}{} directly
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) anchor_points_grey.Rd:9: Lost braces
     9 | Zeeden et al., (2013) and anchored to the code{\link{astrosignal_example}} \cr
       |                                               ^
checkRd: (-1) retrack_wt_MC.Rd:206: Lost braces
   206 | be off in certain intervals. the link[WaverideR]{retrack_wt_MC} mitigates
       |                                                 ^
checkRd: (-1) retrack_wt_MC.Rd:40: Lost braces
    40 | link[WaverideR]{analyze_wavelet} wavelet function
       |                ^
checkRd: (-1) retrack_wt_MC.Rd:41: Lost braces
    41 | To create a list use the link[base]{list} function}
       |                                    ^
checkRd: (-1) retrack_wt_MC.Rd:44: Lost braces
    44 | To create the matrix use the link[base]{cbind} function and only add the
       |                                        ^
Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
Specified C++11: please drop specification unless essential
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: ‘prepr’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) get_cid.Rd:58-59: Lost braces
    58 | <structure search> is assembled as "{\code{substructure} |
       |                                     ^
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    59 | \code{superstructure} | \code{similarity} | \code{identity}} / {\code{smiles}
       |                                                                ^
checkRd: (-1) get_cid.Rd:70-71: Lost braces
    70 | "{\code{fastidentity} | \code{fastsimilarity_2d} | \code{fastsimilarity_3d} |
       |  ^
checkRd: (-1) get_cid.Rd:71-72: Lost braces
    71 | \code{fastsubstructure} | \code{fastsuperstructure}}/{\code{smiles} |
       |                                                      ^
checkRd: (-1) Session.Rd:146: Lost braces
   146 | sQuote{page load} timeout specifies a time to wait for the page loading
       |       ^
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'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
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    15 | /href{https://crawdad.org/coppe-ufrj/RioBuses/20180319/}
       |      ^
Specified C++11: please drop specification unless essential
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    10 | integer/numeric with values all in {0=negative,1=positive} or
       |                                    ^
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    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       | ^
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    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       |                            ^
checkRd: (-1) CLIC.Rd:149: Lost braces
   149 | Composite likelihood {E}{M} algorithm with applications to
       |                         ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
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
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'LazyData' is specified without a 'data' directory
checkRd: (-1) secondDerivative.Rd:14: Lost braces
    14 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
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checkRd: (-1) windAC.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) windAC.Rd:33: 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
checkRd: (-1) word2vec_similarity.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) word2vec_similarity.Rd:31: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘wordnetDicts’
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checkRd: (-1) wordpiece_cache_dir.Rd:20-21: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘wmtsa’
Auto-generated content requiring editing in Rd file 'wqs.est.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Malformed Title field: should not end in a period.
checkRd: (-1) createDemandSite.Rd:26: Lost braces
    26 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
checkRd: (-1) createDemandSite.base.Rd:26: Lost braces
    26 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
checkRd: (-1) createDemandSite.default.Rd:32: Lost braces
    32 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) wtest.Rd:61-64: Lost braces
    61 | {When \code{w.order} =2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
checkRd: (-1) wtest.high.Rd:61-64: Lost braces
    61 | {When \code{w.order} > 2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
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checkRd: (-1) wvar_cpp.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) exploreSignatures.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) generateData.Rd:47: Lost braces
    47 | \bold{code{data}} \tab the generated data \cr
       |           ^
checkRd: (-1) generateData.Rd:53: Lost braces
    53 | Refer to \bold{\emph{code{\link{retrieveDataFactory}}}} and to
       |                          ^
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    14 | A emph{\code{list}} with following names
       |       ^
checkRd: (-1) qualifyFunctionArguments.Rd:26: Lost braces
    26 | \item{code{arguments}}{a \code{pairList} of argument names and values.
       |           ^
checkRd: (-1) completeManualPage.Rd:12: Lost braces
    12 | See \emph{\bold{code{\link{ProcessingContext}}}}. Only
       |                     ^
checkRd: (-1) produceAllManualPagesFromObject.Rd:14: Lost braces
    14 | See \emph{\bold{\\code{\link{ProcessingContext}}}}.}
       |                       ^
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checkRd: (-1) knecht.Rd:105: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xgb.txt’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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checkRd: (-1) xml_to_df.Rd:144: Lost braces; missing escapes or markup?
   144 | Default {NULL} means the workbook will not be protected with a password}
       |         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
checkRd: (-1) xwfGridsearch.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{iter}{Number of levels in the adaptive grid search. The resolution in b obtained is 2^{-1-iter}.}
       |                                                                                             ^
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   110 | \code{min} and {max} are mandatory for setting limits on the test length. User-defined
       |                ^
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     3 | \title{Bootstrap metrics produced from /code{calc.yhat}}
       |                                             ^
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    19 |     Ouput of /code{lm}
       |                   ^
checkRd: (-1) boot.yhat.Rd:22: Lost braces
    22 |     Output of /code{calc.yhat}
       |                    ^
checkRd: (-1) booteval.yhat.rd:3: Lost braces
     3 | \title{Evaluate bootstrap metrics produced from /code{calc.yhat}}
       |                                                      ^
checkRd: (-1) booteval.yhat.rd:5: Lost braces
     5 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
checkRd: (-1) combCI.rd:26: Lost braces
    26 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
checkRd: (-1) commonality.rd:12: Lost braces
    12 |     Output from /code{aps}
       |                      ^
checkRd: (-1) dombin.rd:12: Lost braces
    12 |     Output from /code{dominance}
       |                      ^
checkRd: (-1) dominance.rd:12: Lost braces
    12 |     Output from /code{aps}
       |                      ^
checkRd: (-1) plotCI.yhat.rd:5: Lost braces
     5 |   This function plots CIs that have been produced from /code{booteval.yhat}.
       |                                                             ^
checkRd: (-1) plotCI.yhat.rd:32: Lost braces
    32 |   This function plots CIs that have been produced from /code{booteval.yhat}.   
       |                                                             ^
checkRd: (-1) plotCI.yhat.rd:35: Lost braces
    35 | This returns a plot of CIs that have been produced from /code{booteval.yhat}.
       |                                                              ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'RNRCS', 'metScanR', 'rnoaa'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) glm.cons.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{method}{the method used in fitting the model. The default method "\code{glm.fit.cons}" uses function {nnnpls} from package nnls instead of \code{lm.fit} to impose the sign of the coefficients. As in \code{glm}, the alternative method "\code{model.frame}" returns the model frame and does no fitting.}
       |                                                                                                            ^
'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: ‘pct’
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:74: Escaped LaTeX specials: \_
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checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:182: Lost braces
   182 |   dQuote{tab-delimited text file} when you have done and close the spreadsheet
       |         ^
checkRd: (-1) in.zoom.Rd:34: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) zm.Rd:30: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) update_ztable.Rd:75: Lost braces; missing escapes or markup?
    75 | must be NULL or contain only elements of {"h","t","b","p","!","H"}.}
       |                                          ^
checkRd: (-1) ztable_sub.Rd:78: Lost braces; missing escapes or markup?
    78 | must be NULL or contain only elements of {"h","t","b","p","!","H"}.
       |                                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) abclass.Rd:133: Lost braces; missing escapes or markup?
   133 |     \code{abclass.control()} returns an object of class {abclass.control}
       |                                                         ^
checkRd: (-1) supclass.Rd:109: Lost braces; missing escapes or markup?
   109 | to solve the equivalent linear programming problem via the package {Rglpk}.
       |                                                                    ^
checkRd: (-1) supclass.Rd:110: Lost braces; missing escapes or markup?
   110 | It is recommended to use a recent version of {GLPK}.
       |                                              ^
Auto-generated content requiring editing in Rd file 'ABC_P2_gamma.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'ABC_P2_norm.Rd':
  \keyword: ‘~kwd1’
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Auto-generated content requiring editing in Rd file 'ABC_P2_pois.Rd':
  \keyword: ‘~kwd1’
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Auto-generated content requiring editing in Rd file 'fit_dist_gamma.Rd':
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Auto-generated content requiring editing in Rd file 'fit_dist_norm.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'fit_dist_pois.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_ex_data.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_ex_data.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_ex_data.Rd:34-35: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) tidy_results.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_results.Rd:30: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) bind_tweets.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bind_tweets.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) accelimp.Rd:15: Lost braces
    15 | \item[]{...}
       |        ^
Found the following files/directories:
  ‘acceldata2.RData’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) overstallwoods.Rd:184-185: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:186-187: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:188-189: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:190-191: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Ehrenfest.Rd:19: Lost braces
    19 | In this experiment there are i balls in Urn I, and remaining 2n-i balls in Urn II. Then at any instance, the probability of selecting a ball from Urn I and placing it in Urn II is i/2n, and the other way of placing a ball from Urn II to Urn I is (2n-i)/2n. At each instant we let the number i of balls in the Urn I to be the state of the system. Thus, the state space is S = { 0, 1, 2, \ldots, 2n }. Then we can pass from state i only to either of the states i-1 or i+1.
       |                                                                                                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) Ehrenfest.Rd:20: Lost braces
    20 | Here, S = {0, 1, \ldots, 2n}. 
       |           ^
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
checkRd: (-1) est_S_Plus_Plus_MethodA.Rd:31: Lost braces; missing escapes or markup?
    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
checkRd: (-1) est_S_Plus_Plus_MethodB.Rd:31: Lost braces; missing escapes or markup?
    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method B}
       |                                                          ^
checkRd: (-1) est_S_Star_Plus_MethodA.Rd:29: Lost braces; missing escapes or markup?
    29 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
checkRd: (-1) est_S_Star_Plus_MethodB.Rd:29: Lost braces; missing escapes or markup?
    29 |   \item{trt_diff}{Estimate of treatment difference for S_{*+} using Method B}
       |                                                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) adana.Rd:25: Lost braces; missing escapes or markup?
    25 |   \item{gatype}{Type of GA. \itemize{\item{"gga": generational GA}  \item{"ssga": steady state GA} } {Default value is "gga"}}
       |                                                                                                      ^
checkRd: (-1) adana.Rd:26: Lost braces; missing escapes or markup?
    26 |   \item{objective}{Type of optimization. \itemize{\item{"min": minimization}  \item{"max": maximization} } {Default value is "max"}}
       |                                                                                                            ^
checkRd: (-1) adana.Rd:34: Lost braces; missing escapes or markup?
    34 |                  {Default value is "initbin"}}
       |                  ^
checkRd: (-1) adana.Rd:56: Lost braces; missing escapes or markup?
    56 |                \itemize{\item{"integer"}  \item{"real"} } {Default value is "real"}}
       |                                                           ^
checkRd: (-1) adana.Rd:185: Lost braces; missing escapes or markup?
   185 |     {Default value is "w"}
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) adapt.Rd:46: Lost braces
    46 | \item{qvals}{a vector of values in [0, 1]U{Inf}. Q-values. See Details}
       |                                           ^
checkRd: (-1) corr_lfdr.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ctgm_lfdr.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ctgm_lfdr.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot_2d.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{plot_2d_lfdr} gives the contour plot of local FDR estimates when all p-values are equal to \code{targetp}. It is recommended to run \code{plot_2d_lfdr} for multiple \code{targetp}'s ranging from {0.001, 0.005, 0.01, 0.05}.
       |                                                                                                                                                                                                          ^
checkRd: (-1) SVMDECON.Rd:23: Lost braces; missing escapes or markup?
    23 | and the best result from three values of v = {0.25, 0.5, 0.75}
       |                                              ^
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
'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
Auto-generated content requiring editing in Rd file 'dea.fast.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'dea.gem.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'dea.sbm.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
'LazyData' is specified without a 'data' directory
checkRd: (-1) varipart.Rd:19: Lost braces
    19 | \item{type}{a character specifying the algorithm which should be used to adjust R-squared (either \code{"simulated"} or \ code{"parametric"}).}
       |                                                                                                                               ^
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) med.groups.Rd:20: Lost braces; missing escapes or markup?
    20 | medication groups using the construction \emph{"{NAME}"}.
       |                                                 ^
checkRd: (-1) med.groups.Rd:26: Lost braces; missing escapes or markup?
    26 | Another example is "NotVita" defined as "(!{Vitamines})", which selects all
       |                                            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Amatdual.Rd:15: Lost braces
    15 |   \item{removelist}{a vector of indices into env{X} of the lifted coefficients during the transform (in the order of removal). }
       |                                                 ^
checkRd: (-1) fwtnp.Rd:30: Lost braces
    30 | Given \eqn{n} points on a line, \env{input}, each with a corresponding env{f} value this algorithm computes a lifting transform of the (\env{input},\env{f}) data. If lengths are inputted (\env{inputtype="lengths"}), then the gridpoints are taken to be the left endpoints of the intervals defined by the lengths inputted. 
       |                                                                           ^
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lintr’ ‘pharmaversesdtm’ ‘pkgdown’ ‘testthat’
A package should be listed in only one of these fields.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) count_cases.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) enrich.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitaep.Rd:14: Lost braces
    14 | \item A sequence of goodness-of-fit measures consist of Akaike Information Criterion (\code{AIC}), Consistent Akaike Information Criterion (\code{CAIC}), Bayesian Information Criterion (\code{BIC}), Hannan-Quinn information criterion (\code{HQIC}), Anderson-Darling (\code{AD}), Cram\'{e}er-von Misses (\code{CVM}), Kolmogorov-Smirnov (\code{KS}), and log-likelihood (\code{log-likelihood}) statistics.
       |                                                                                                                                                                                                                                                                                              ^
Found the following files/directories:
  ‘table_AeRobiology’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) estimate.affinity.matrix.Rd:31: Lost braces; missing escapes or markup?
    31 | than \code{Y}, then those variables that appear in \code{X} but no in {Y}
       |                                                                       ^
checkRd: (-1) estimate.affinity.matrix.lowrank.Rd:36: Lost braces; missing escapes or markup?
    36 | \code{Y}, then those variables that appear in \code{X} but no in {Y} should
       |                                                                  ^
checkRd: (-1) show.correlations.Rd:47: Lost braces
    47 | code{ndims} dimensions. Defaults to all dimensions unless the latter are
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) getNetworkGridLayout.Rd:6-11: Lost braces
     6 | getCoordinatesFromVertexId2<-function(AFMImage, vId) {
       |                                                      ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package which this enhances but not available for checking: ‘asreml’
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AEHMLE.Rd:42-45: Lost braces
    42 | \item{basehaz}{: {baseline hazard structure including baseline
       |                  ^
checkRd: (-1) AHMLE.Rd:41-43: Lost braces
    41 | \item{basehaz}{: {baseline hazard structure including baseline
       |                  ^
checkRd: (-1) CalOptimalDecision.Rd:45: Lost braces; missing escapes or markup?
    45 | A \code{data.frame} of (1) the probability that the optimal decision for each observation being d in {0,1,...,k}, (2) expected utility of binary version of judge's decision (g_d), (3) expected utility of binary DMF recommendation, and (4) the difference between (2) and (3). If \code{include.utility.diff.mcmc = TRUE}, returns a list of such \code{data.frame} and a \code{data.frame} that includes the result for mean and quantile of \code{Utility.diff.control.mcmc} and \code{Utility.diff.treated.mcmc} across mcmc samples.
       |                                                                                                      ^
checkRd: (-1) aimPlot.Rd:39: Lost braces; missing escapes or markup?
    39 |  \item \code{Variable} {1st column: The various aims to be completed}
       |                        ^
checkRd: (-1) aimPlot.Rd:40: Lost braces; missing escapes or markup?
    40 |  \item \code{Percentage} {2nd column: The percentage of completeness}
       |                          ^
checkRd: (-1) CreateInputsPert.Rd:65: Lost braces
    65 | \emph{InputsPert}{[list] object of class \emph{InputsModel} containing the ensembles of perturbed model inputs required to perform data assimilation:}
       |                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_airnow_area.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{parameters}{Parameter(s) to return data for. Choices are PM_{2.5}
       |                                                                   ^
Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.dke.fun.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item{las}{ Numeric in {0,1,2,3}; the style of axis labels. 
       |                          ^
checkRd: (-1) interpp.Rd:119: Lost braces
   119 |   If \code{linear} is \\code{TRUE}, linear
       |                             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) buildPhylipLineage.Rd:61: Lost braces; missing escapes or markup?
    61 |                                      names with the format {"Inferred1", "Inferred2", ...}.
       |                                                            ^
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) APEXMS.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) APEXMS.Rd:15: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) allestimates.Rd:25: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) compare_cohorts.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_cohorts.Rd:36: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
checkRd: (-1) altopt.ic.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) altopt.rc.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) convertCoord.Rd:32: Lost braces
    32 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) convertCoord.individual.Rd:33: Lost braces
    33 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) getCoord.Rd:39: Lost braces
    39 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) getCoord.individual.Rd:39: Lost braces
    39 | here{https://lbs.amap.com/faq/account/key/72}}
       |     ^
checkRd: (-1) getLocation.Rd:60: Lost braces; missing escapes or markup?
    60 | {https://lbs.amap.com/faq/account/key/72}}
       | ^
checkRd: (-1) getLocation.individual.Rd:60: Lost braces
    60 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) aMNLFA.prune.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) AmpliconDuo-package.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:40-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:43-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:53-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:56-58: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
checkRd: (-1) EKF_1d_interp_joint.Rd:55: Lost braces; missing escapes or markup?
    55 | Prior 1x1 covariance matrix for predicting x_t from x_{t-1}.
       |                                                       ^
checkRd: (-1) EKF_interp_joint.Rd:65: Lost braces; missing escapes or markup?
    65 | Prior 2x2 covariance matrix for predicting x_t from x_{t-1}.
       |                                                       ^
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) animate.Rd:625-627: Lost braces
   625 | group = function(...) {
       |                       ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) concat.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                     ^
checkRd: (-1) concat.Rd:35: Lost braces
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                               ^
checkRd: (-1) concat.Rd:35: Lost braces
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                                             ^
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) PS-methods.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:65-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Sim-Functions.Rd:126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:127-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:138-140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:141-143: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) apc.indiv.est.model.Rd:142: Lost braces
   142 | For model testing: \code{\link{apc.indiv.model.table}}, code{\link{apc.indiv.compare.direct}}, \code{\link{waldtest}}, \code{\link{linearHypothesis}}
       |                                                             ^
Packages suggested but not available for checking:
  'clusterProfiler', 'DOSE'
Note: skipping ‘aPEAR-vignette.Rmd’ due to unavailable dependencies:
  'clusterProfiler'
Specified C++11: please drop specification unless essential
checkRd: (-1) predict_adjust.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iconplot.Rd:172: Lost braces
   172 |     the height of the area containing the panels and a margin of size code{100 * 0.1} 
       |                                                                           ^
Found the following calls to attach():
File ‘apollo/R/apollo_attach.R’:
  attach(as.list(apollo_beta), warn.conflicts = FALSE)
  attach(database, warn.conflicts = FALSE)
  attach(draws, warn.conflicts = FALSE)
  attach(randcoeff, warn.conflicts = FALSE)
  attach(lcpars, warn.conflicts = FALSE)
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘APBinary_PPV.csv’ ‘APBinary_TPF.csv’
  ‘APBinary_ap_summary(method=perturbation,B=1500).csv’
  ‘APBinary_auc_summary(method=perturbation,B=1500).csv’
  ‘APSurv_PPV.csv’ ‘APSurv_TPF.csv’
  ‘APSurv_ap_summary(method=bootstrap,B=500).csv’
  ‘APSurv_auc_summary(method=bootstrap,B=500).csv’
  ‘CompareAP_Binary_dap_summary(method=none).csv’
  ‘CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv’
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                              ^
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                                            ^
Package suggested but not available for checking: ‘arcgisbinding’
Package suggested but not available for checking: ‘ArchaeoData’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘TDA’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) estimate_t0.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_t0.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_t0.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       | ^
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       |                                 ^
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       |                                                ^
checkRd: (-1) uecm.Rd:76: Lost braces; missing escapes or markup?
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |   ^
checkRd: (-1) uecm.Rd:76: Lost braces; missing escapes or markup?
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                  ^
checkRd: (-1) uecm.Rd:76-77: Lost braces
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘TDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) convertAlgoPerfToWideFormat.Rd:28: Lost braces
    28 | code{NA} means the performance value is not available, possibly because the algorithm run was aborted.
       |     ^
checkRd: (-1) parseASScenario.Rd:40: Lost braces
    40 |   code{NA} means the cost is not available, possibly because the feature computation was aborted.
       |       ^
checkRd: (-1) parseASScenario.Rd:47: Lost braces
    47 |   code{NA} means the cost is not available, possibly because the feature computation was aborted.
       |       ^
checkRd: (-1) parseASScenario.Rd:55: Lost braces
    55 |   code{NA} means the feature is not available, possibly because the feature computation was aborted.
       |       ^
checkRd: (-1) parseASScenario.Rd:62: Lost braces
    62 |   code{NA} means the feature is not available, possibly because the feature computation was aborted.
       |       ^
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.AssetPricing.Rd:199-200: Lost braces
   199 |   yakka. (Note that \code{flap} stands for dQuote{function list
       |                                                  ^
Auto-generated content requiring editing in Rd file 'Wcorrected.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'Wqls.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Package suggested but not available for checking: ‘asteRiskData’
Specified C++11: please drop specification unless essential
checkRd: (-1) readOEM.Rd:34: Lost braces
    34 |   always, the identifier has the format YYYY-NNNP{PP}, where YYYY is the year
       |                                                  ^
checkRd: (-1) readOEM.Rd:36: Lost braces
    36 |   during year YYYY and P{PP} is a part specifier comprising 1 to 3 capital letters
       |                         ^
checkRd: (-1) readOEM.Rd:74-75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readOEM.Rd:76-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readOEM.Rd:80-86: Lost braces in \itemize; \value handles \item{}{} directly
GNU make is a SystemRequirements.
checkRd: (-1) ataCoKriging.Rd:52: Lost braces; missing escapes or markup?
    52 | only one contrained condition for all points and all variables, \\sum_{i=1}^n\\lambda_i +\\sum_{j=1}^m\\beta_j =1, assuming expected means of variables known and constant with the study area.
       |                                                                       ^
checkRd: (-1) ataCoKriging.Rd:52: Lost braces; missing escapes or markup?
    52 | only one contrained condition for all points and all variables, \\sum_{i=1}^n\\lambda_i +\\sum_{j=1}^m\\beta_j =1, assuming expected means of variables known and constant with the study area.
       |                                                                                                ^
checkRd: (-1) simulation_dgp.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{x_discrete}{TRUE if the distribution of the covariate is uniform on {-3.0, -2.9, ..., 3.0} and
       |                                                                           ^
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    23 | \item{att_oracle}{the sample analog of E[D{Y(1) - Y(0)}|D=1]}
       |                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) audioSample.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) audioSample.Rd:21: Lost braces in \itemize; meant \describe ?
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
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    50 | \item \code{covars_data}   {The \code{data.frame} that is filtered out of \code{df} with only the selected \code{covars}}. The values of the
       |                            ^
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    53 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
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    40 | \item \code{multiplicative_bias}{The absolute log of the multiplicative bias term for each of the auto-selected prioritised covariates}
       |                                 ^
checkRd: (-1) get_recurrence_covariates.Rd:34: Lost braces
    34 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
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
Packages required but not available: 'fgsea', 'clusterProfiler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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    27 | code{\link{help}}
       |     ^
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    25 | code{\link{help}}
       |     ^
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    22 | code{\link{help}}
       |     ^
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    29 | code{\link{help}}
       |     ^
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    32 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
Specified C++11: please drop specification unless essential
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checkRd: (-1) noauto_scorecard.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{fit}{See glm {stats}.}
       |                    ^
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    21 | \item{fit}{See glm {stats}.}
       |                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) avar_mo_cpp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_mo_cpp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) avar_to_cpp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) avar_to_cpp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
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    21 | \item{host}{For \code{cosmos_mongo_endpoint}, the URL of the Cosmos DB MongoDB endpoint. Usually of the form "https://{account-name}.mongo.cosmos.azure.com:443/".}
       |                                                                                                                       ^
Package suggested but not available for checking: ‘lixoftConnectors’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘fdpbandsdata’
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
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    27 | read.dna() from package {ape} was used to obtain DNAbin object for unaligned non-coding barcodes.
       |                         ^
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    30 | the {dplyr}'s verbs and thus use it in local memory completely.
       |     ^
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    52 | Writes a remote table to disk that was called via {bdplyr}.
       |                                                   ^
checkRd: (-1) bdplyr.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Compatibility with {dplyr} verbs without using SQL language}
       |                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Earlier versions
checkRd: (-1) BasicTable.Rd:659: Lost braces; missing escapes or markup?
   659 | `function(v, cell) { if(isTRUE(v>0.8)) return("green") }`.\cr
       |                    ^
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   151 | The CSS style rule, e.g. { text-align: center; color: red; }
       |                          ^
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   172 | The CSS style rule, e.g. cell { text-align: center; color: red; }
       |                               ^
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   209 | The CSS style rule, e.g. { text-align: center; color: red; }
       |                          ^
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   232 | The CSS style rule, e.g. cell { text-align: center; color: red; }
       |                               ^
checkRd: (-1) nfiMetrics.Rd:23: Lost braces
    23 | code{(4)} the number of
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) ExperimentJob.Rd:14: Lost braces
    14 |   \item{\code{algo.id} [\code{character(1)}]:}{algo.id}{Algorithm ID.}
       |                                                        ^
checkRd: (-1) getAlgorithmIds.Rd:13: Lost braces
    13 | \item{ids}{[code{integer}]\cr
       |                 ^
checkRd: (-1) getProblemIds.Rd:13: Lost braces
    13 | \item{ids}{[code{integer}]\cr
       |                 ^
checkRd: (-1) makeExperimentRegistry.Rd:28: Lost braces
    28 | Default is dQuote{<name of registry>_files} in current working directory.}
       |                  ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doMPI’
checkRd: (-1) JobCollection.Rd:41: Lost braces
    41 |  \item{namespaces}{code{character} with required packages to load via \code{\link[base]{requireNamespace}}.}
       |                        ^
checkRd: (-1) addAlgorithm.Rd:31: Lost braces
    31 | Algorithms are functions which get the code{data} part as well as the problem instance (the return value of the
       |                                            ^
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
GNU make is a SystemRequirements.
checkRd: (-1) plotDistributions.Rd:32: Lost braces
    32 | plot{...} functions are generated programmatically so the function calls in
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) coupledMetropolis.Rd:83-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:86-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:89-91: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) coupledMetropolis.Rd:104-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:107-109: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) coupledMetropolis.Rd:113-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:116-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:119-121: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:122-124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:125-127: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
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checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) bayesDccGarch.Rd:91: Lost braces; missing escapes or markup?
    91 | \item{$H_n1 }{ Bayesian prediction of volatilities and co-volatilities for y_{n+1}.}
       |                                                                              ^
checkRd: (-1) bayesDccGarch.Rd:92: Lost braces; missing escapes or markup?
    92 | \item{$R_n1 }{ Bayesian prediction of coditional correlation for y_{n+1}.}
       |                                                                    ^
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) GroupSingleVoxelFETS.Rd:53: Lost braces
    53 | online trajectories related to the state parameter, the simulated BOLD responses, \mjseqn{\hat{Y}}{ascii}.
       |                                                                                                   ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
checkRd: (-1) gMLE.bb.Rd:18: Lost braces
    18 |   \item{optim.method}{optimization method in \code{optim()}{stats}.}
       |                                                            ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) bma.bx.cy.Rd:69: Lost braces
    69 | the initial values for parameters in models. For example, inits<-function(){list(alpha=0,beta=0,c=0,var1=0.5,r=1,lamda=0.01)}.
       |                                                                            ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) DE.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DE.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DE.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DE.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:58: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) DEzs.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:61: Lost braces in \itemize; meant \describe ?
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.bayeslm.fit.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{X         }{ If call \code{bayeslm} with matrices input \code{x} and {y} but not formula, pass new matrix to predict here. See example for details.}
       |                                                                              ^
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  Warning: namespace ‘rstanarm’ is not available and has been replaced
  Warning: namespace ‘rstan’ is not available and has been replaced
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bayesMeanScale.Rcheck/00install.out’ for details.
Auto-generated content requiring editing in Rd file 'BayesMixSurv.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'BayesMixSurv_CrossVal.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'plot_BayesMixSurv.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'predict_BayesMixSurv.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'summary_BayesMixSurv.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
checkRd: (-1) insert_NAs.Rd:22: Lost braces; missing escapes or markup?
    22 | A data frame where new rows have been inserted to regularize the \code{date} column. This results in values provided for \code{id}, \code{date}, and {dt} while inserting NAs for all other columns. Additionally, observations with duplicate date-times are removed.
       |                                                                                                                                                      ^
'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.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
checkRd: (-1) BayesTreePrior.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:41: Lost braces in \itemize; meant \describe ?
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) runUI.Rd:11: Lost braces
    11 | Runs a \bold{Shiny} application. This function normally does not return; interrupt bold{R} to stop the application (usually by pressing Ctrl+C or Esc).
       |                                                                                        ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) getOperatingSystem.Rd:30: Lost braces in \itemize; meant \describe ?
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData’
'LazyData' is specified without a 'data' directory
checkRd: (-1) goftype1.Rd:4: Lost braces
     4 | \description{The goodness-of-fit (GOF) measures consist of Anderson-Darling (\code{AD}) and Cram\'{e}er-von Misses (\code{CVM}) statistics for progressive type-I interval censoring scheme are given, respectively, by
       |                                                                                                   ^
Found the following files/directories:
  ‘fabiabreast.txt’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BchronDensity.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) BchronDensity.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
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    34 | itemize{
       |        ^
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) WindowSweep.Rd:32: Lost braces
    32 | `code{\link{GetVT}}`.   Otherwise, any column (e.g. \code{"Depth"}) in the 
       |      ^
checkRd: (-1) WindowSweep.Rd:36: Lost braces
    36 | \code{T.mid}  from the output of the `code{\link{GetVT}}`.}
       |                                           ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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    17 | giving the virus access to the cell and thus facilitating the COVID-19 disease. The gene sequence is mapped to the alphabet {0,1,2,3} via the obvious map A->0, C->1, G->2, T->3.
       |                                                                                                                             ^
checkRd: (-1) sars_cov_2.Rd:16: Lost braces; missing escapes or markup?
    16 | It consists of n = 29903 base pairs. The gene sequence is mapped to the alphabet {0,1,2,3} via the obvious map A->0, C->1, G->2, T->3.
       |                                                                                  ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) bde.Rd:22: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) bde.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:56: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘dump.txt’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘beast_plot_toy.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) sockeye.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sockeye.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hill.Rd:39: Lost braces; missing escapes or markup?
    39 | \code{a} in {0, 1, 2} (see details))}
       |             ^
checkRd: (-1) read_ambi.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_ambi.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) gen.data.Rd:42: Lost braces
    42 | code{cortype = 2} denotes the constant structure, where the \eqn{(i,j)} entry of covariance
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) BETSsearch.Rd:56: Lost braces
    56 |        \item{To exclude whole expressions from the search, surround them with code{' '} and insert a \code{~} before each of them.
       |                                                                                   ^
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    23 | \item{date}{a \code{list}. The periods for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                               ^
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    25 | \item{from}{An \code{integer vector} The starting period of a sequence of perids for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                                                                         ^
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    27 | \item{to}{The ending period of a sequence of perids for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                                            ^
'LazyData' is specified without a 'data' directory
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    42 | \item{c.star}{The threshold for computing posterior tail probabilities p_{ij} for Bayesian FDR as defined in Section 3.2 of  Song, Ge et al.(2019). If not specified the default is to set this threshold as the minimum posterior standard deviation, where the minimum is taken over all regression coefficients in the model.}
       |                                                                          ^
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
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checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
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    29 | \item \code{euclidean.df1, affine.df1} -  degrees of freedom of the nominator used for the F-statistics propagated by Nakaya (1997); df1 = p-2, with p is the number of elements  needed to calculate the referring model: p=4 for the Euclidean and p=6 for the affine geometry {Nakaya, 1997, Table 1}.
       |                                                                                                                                                                                                                                                                                  ^
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Package suggested but not available for checking: ‘ffbase’
Package suggested but not available for checking: ‘INLA’
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following calls to data() loading into the global environment:
File ‘biglm/R/bigglm.R’:
  data(reset = TRUE)
  data(reset = FALSE)
See section ‘Good practice’ in ‘?data’.
Specified C++14: please drop specification unless essential
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    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                         ^
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    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                                                                                   ^
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) pQF.Rd:30: Lost braces; missing escapes or markup?
    30 | When \code{M} is not square, a randomised estimator for the trace of \code{crossprod(M)^2} is used. This is the sample size. When \code{M} is of \code{"matrixfree"} and does not include the trace of {crossprod(M)} as a component, this sample size will also be used to compute that. See Hutchinson reference. }
       |                                                                                                                                                                                                        ^
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checkRd: (-1) VARXFit.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘ccf_ccf_ID31_ID32_res.jpg’ ‘ccf_ccf_ID31_ID32_res.pdf’
  ‘output_ENSO_NHSST.tmp’ ‘plot_plot_ts_RAW_BIN_enso_sst.pdf’
  ‘plot_plot_ts_RAW_BIN_enso_sst01.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst02.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst03.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst04.png’ ‘plot_ts_ACER_ABRUPT.pdf’
  ‘plot_ts_ACER_ABRUPT01.png’ ‘plot_ts_ACER_ABRUPT02.png’
  ‘plot_ts_ACER_ABRUPT03.png’ ‘plot_ts_ACER_ABRUPT04.png’
  ‘salida_ACER_ABRUPT.tmp’ ‘scaterplot_scatterplot_ENSO_SST.jpg’
  ‘scaterplot_scatterplot_ENSO_SST.pdf’
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checkRd: (-1) binom.confint.Rd:32-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:39-40: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) binom.confint.Rd:45: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) ringApply.Rd:9: Lost braces; missing escapes or markup?
     9 |   \item{lv}{{numeric} position, or {character} name, of an
       |                                    ^
checkRd: (-1) calc_ed.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_pi.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_si.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) cluster_reg_exp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
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'LazyData' is specified without a 'data' directory
checkRd: (-1) ROC.Rd:55: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:56: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:57: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:58: Lost braces in \enumerate; \value handles \item{}{} directly
Package which this enhances but not available for checking: ‘asreml’
checkRd: (-1) mmds.2D.multi.Rd:118: Lost braces
   118 |   a numeric value in inches indicating the height of graph outfile. Default differs by outfile.type. The resolution for tiff and png figures is 150 dpi. See \code{pdf}, code{tiff}, \code{png}, \code{postscript}.
       |                                                                                                                                                                              ^
checkRd: (-1) mmds.2D.plot.Rd:134: Lost braces
   134 |   a numeric value in inches indicating the height of graph outfile. Default differs by outfile.type. The resolution for tiff and png figures is 150 dpi. See \code{pdf}, code{tiff}, \code{png}, \code{postscript}.
       |                                                                                                                                                                              ^
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
Compilation used the following non-portable flag(s):
  ‘-multi_normal_suff(’
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) RLdata500.Rd:8: Lost braces
     8 | A data frame with five variables: \code{fname_c1},\code{lname_c1},  \code{by}, code{bm}, \code{bd}.
       |                                                                                    ^
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    15 | format A vector that contains the code{id}
       |                                       ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) durban.Rd:16: Lost braces; missing escapes or markup?
    16 | This data set was obtained from the durban.rowcol {agridat} example in package 'agridat' 
       |                                                   ^
checkRd: (-1) fraction.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fraction.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fraction.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_density.Rd:25: Lost braces; missing escapes or markup?
    25 | evenly spaced points between \code{min} and {max}.
       |                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bluebike.Rd:17: Lost braces
    17 | \item{\code{import_month_data}}\cr {Takes in numeric year/month values and imports data from \href{https://www.bluebikes.com/system-data}{Blue Bikes System Data} for the specified time}
       |                                    ^
checkRd: (-1) bluebike.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{\code{station_distance}}\cr {Returns stations with distance in ascending order given the user's current location}
       |                                   ^
checkRd: (-1) bluebike.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{\code{station_radius}}\cr {Plots the position of the stations within walking distance (500 m), and present the basic information about the stations via leaflet}
       |                                 ^
checkRd: (-1) bluebike.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{\code{trip_distance}}\cr {Computes the geographical distance between the start and end stations}
       |                                ^
checkRd: (-1) bluebike.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{\code{trip_history_sample}} \cr {A sample of 1000 trip data entries from February 2022}
       |                                       ^
checkRd: (-1) bluebike.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{\code{station_data}} \cr {A dataset that includes identification, position, and other basic information about bluebike stations}
       |                                ^
Specified C++11: please drop specification unless essential
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    20 | Helper function for as.data.frame.{fitted, forecast}. Converts predictive array to data.frame.
       |                                   ^
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BMSC_pareto_k_table.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:57-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:60-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:64-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:67-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
checkRd: (-1) autoplot.tsregime.Rd:20: Lost braces
    20 | Graph for the stochastic processes of the object \ dQuote {\ code {tsregime}} for: Output process and if they exist for: Threshold process and Covariates process. In the case that there are missing data, a red line is drawn at the indicated time.
       |                                                           ^
checkRd: (-1) autoplot.tsregime.Rd:20: Lost braces; missing escapes or markup?
    20 | Graph for the stochastic processes of the object \ dQuote {\ code {tsregime}} for: Output process and if they exist for: Threshold process and Covariates process. In the case that there are missing data, a red line is drawn at the indicated time.
       |                                                                   ^
checkRd: (-1) MvInv.Rd:23-35: Lost braces
    23 | function(eps, u = 0.5, alpha = 1, kappa = 1, gama = 1 / 2, N = 3001) {
       |                                                                      ^
checkRd: (-1) dt_.Rd:19-21: Lost braces
    19 | function(x, df, mean, sd) {
       |                           ^
Specified C++11: please drop specification unless essential
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checkRd: (-1) strength.viewer.Rd:148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:152: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |               ^
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |                                             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) refAnnots.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) refAnnots.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:13-14: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking:
  'adiposerefdata', 'musclerefdata'
checkRd: (-1) Extractor.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:16: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) Extractor.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:19: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) bootSVD.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{Y}{initial data sample, which can be either a matrix or a \code{\link{ff}} matrix. \code{Y} can be either tall (\eqn{p} by \eqn{n}) or wide (\eqn{n} by \eqn{p}). If \code{Y} is entered and \code{V}, \code{d} and \code{U} (see definitions below) are not entered, then \code{bootSVD} will also compute the SVD of \code{Y}. In this case where the SVD is computed, \code{bootSVD} will assume that the larger dimension of \code{Y} is \eqn{p}, and the smaller dimension of code {Y} is \eqn{n} (i.e. \code{bootSVD} assumes that (\eqn{p>n}). This assumption can be overriden by manually entering \code{V}, \code{U} and \code{d}.\cr
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
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    75 | $$SV = sqrt(sum(x_{i+1} - x_i)^2/n-1)$$
       |                   ^
checkRd: (-1) bp_sv.Rd:80: Lost braces; missing escapes or markup?
    80 | $$SD = sqrt(sum(x_{i+1} - xbar)^2/n-1)$$
       |                   ^
checkRd: (-1) sv.Rd:78: Lost braces; missing escapes or markup?
    78 | $$SV = sqrt(sum(x_{i+1} - x_i)^2/n-1)$$
       |                   ^
checkRd: (-1) sv.Rd:82: Lost braces; missing escapes or markup?
    82 | $$SD = sqrt(sum(x_{i+1} - xbar)^2/n-1)$$
       |                   ^
'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
checkRd: (-1) brglm.Rd:173: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:174: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:175-176: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:177-178: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) profile.brglm.Rd:56: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) printHands.Rd:42: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) assertall.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) assertall.Rd:46: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) builders.Rd:51: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) builders.Rd:54: Lost braces in \itemize; meant \describe ?
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Package suggested but not available for checking: ‘cmdstanr’
Package suggested but not available for checking: ‘glmmADMB’
Package suggested but not available for checking: ‘orcutt’
Unknown package ‘orcutt’ in Rd xrefs
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
checkRd: (-1) bscontrol.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{opt.solver}{a character string in the set {'enum', 'enum_c', 'gurobi', 'cplex', 'lpSolve', 'greedy'} indicating the optimization solver to be used in the program. The choice of 'cplex' requires the package \code{cplexAPI}, 'gurobi' requires the package \code{gurobi}, and 'lpSolve' requires the package \code{lpSolve}. These solver options are only available in the full version at \url{https://github.com/profyliu/bsnsing/}. The default (and the best) is 'enum_c'.}
       |                                                 ^
checkRd: (-1) bscontrol.Rd:45: Lost braces; missing escapes or markup?
    45 | \item{opt.model}{a character string in the set {'gini','error'} indicating the optimization model to solve in the program. The default is 'gini'. The 'error' option is not available in the current version.}
       |                                                ^
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
GNU make is a SystemRequirements.
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checkRd: (-1) terms.BTM.Rd:23-25: Lost braces in \itemize; \value handles \item{}{} directly
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    42 | function. If {sizeBreaks} vector is supplied then this will be ignored and
       |              ^
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    96 | function. If {sizeBreaks} vector is supplied then this will be ignored and
       |              ^
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   117 | \code{unitBase}. This will be supplied to pretty function. If {sizeBreaks} is
       |                                                               ^
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GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
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    24 | functions, and often the /code{cut()} function are relatively slow when working with tens of millions of rows or more.
       |                               ^
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    19 | \item{y}{response variable (in {0,1}).}
       |                                ^
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   112 | Stop recording images with {camcorder}.
       |                            ^
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Unknown package ‘taxize’ in Rd xrefs
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  ‘MDA231_tree.pdf’
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    31 |      {RRD = ln(N_1/N_2)}
       |      ^
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    34 |      {PDI = (N_1/(N_1 + N_2))-0.5}
       |      ^
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    33 |   \item{Length of tip branch lengths (TIPS)}{Length of tip branch lengths (TIPS)}{Unlike UEH, this measure does not use the unique paths to each tips on the \strong{subtree} and instead gives the sum of the unique branches leading to the tips on the \strong{complete tree}.}
       |                                                                                  ^
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  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
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    13 | The exit status code{R CMD build}, invisibly.
       |                     ^
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   130 | \code{x1, x2, x3, \dots}- {input to the model, there must be one column
       |                           ^
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Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
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Running examples in ‘CauchyCP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CauchyCP
> ### Title: A robust test under non-proportional hazards using Cauchy
> ###   combination of change-point Cox regressions.
> ### Aliases: CauchyCP
> 
> ### ** Examples
> 
> data(gast)
> CauchyCP(time=gast$time, status=gast$status, x=gast$trt)
Error in anova.coxphlist(object, test = test) : 
  models do not have the same strata
Calls: CauchyCP -> anova -> anova.coxph -> anova.coxphlist
Execution halted
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    71 |   \item{states.samples}{(\code{niter}- \code{burn}) draws from p(alpha_t | Y_{1:T}).}
       |                                                                              ^
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    61 |   \item{states.samples}{(\code{niter}- \code{burn}) draws from p(alpha_t | Y_{1:T}).}
       |                                                                              ^
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   160 | see \code{?DoE.base::fac.design} as well as the JSS article on the {DoE.base}
       |                                                                    ^
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   174 | well as the JSS article on the {DoE.base} package (Grömping, 2018).
       |                                ^
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   197 | {idefix} package (Traets et al, 2020).
       | ^
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    70 | estimation. See the {logitr} documentation for details about other
       |                     ^
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    25 | The number of low-dimension of C (J1 < {N,M}).
       |                                        ^
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    29 | The number of low-dimension of R (J2 < {N,M}).
       |                                        ^
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    23 | The number of low-dimension (J < {N,M}).
       |                                  ^
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  ‘hotcold.csv’
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    57 | \code{RU}: {Referent units}
       |            ^
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    59 | \code{PI}: {Partitioning and iterating attribute}
       |            ^
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    61 | \code{APP}: {Appropriateness attribute}
       |             ^
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    63 | \code{MC}: {Multiplicative Comparison attribute}
       |            ^
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
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Unexported objects imported by ':::' calls:
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  See the note in ?`:::` about the use of this operator.
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    10 | Scrapes {https://api.census.gov/data.json} and returns a dataframe
       |         ^
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    36 | A code{data.frame} with the requested variables at the requested
       |       ^
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    22 | Centroid value C_{cen}(v) for node v defined as:
       |                  ^
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    23 | where the term f(c_{i}) accounts for the effect of i's local clustering and the term '+1' results from the contribution of \eqn{j}{j} itself. \cr
       |                    ^
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    31 |   {epsi}^{# regression coefficients} times the initial value,
       |   ^
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    31 |   {epsi}^{# regression coefficients} times the initial value,
       |          ^
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    23 | Assuming one-dimensional \code{p1} and \code{p2} for clarity, the algorithm calculates cumulative incidence function for cuase 1 using a recursive formula: \code{ci1[n+1] = ci1[n] + dci1[n]}, where \code{dci1[n] = 0.5*(p2[n] + p2[n+1])*(p1[n] - p1[n+1])}. The increment in cumulative incidence function for cause 2 is similarly calculated, \code{dci2[n] = 0.5*(p1[n] + p1[n+1])*(p2[n] - p2[n+1])}. These equations guarantee that \code{dci1[n] + dci2[n] = p1[n]*p2[n] - p1[n+1]*p2[n+1]}. Event-free probability is simply calculated as code{efp[n] = p1[n]*p2[n]}. Taken together, this numerical integration ensures that \code{efp[n+1] - efp[n] + dci1[n] + dci2[n] = 0}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           ^
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    47 |         call (see {\dots } section below.)
       |                   ^
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    10 | \item{vec1}{A \code{integer} vector forms a subset of {1, 2, ..., n}.}
       |                                                       ^
checkRd: (-1) Hausdorff.dist.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{vec2}{A \code{integer} vector forms a subset of {1, 2, ..., n}.}
       |                                                       ^
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    47 | online.univar.one2 = function(y_vec, gamma, tau_gamma, ...){
       |                                                            ^
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    50 |   while(FLAG == 0 & t <= length(y_vec)){
       |                                        ^
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    71 | online.univar.one3 = function(y_vec, tau_vec, ...){
       |                                                   ^
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    72 |   if(length(y_vec) != length(tau_vec)){
       |                                       ^
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    77 |   while(FLAG == 0 & t <= length(y_vec)){
       |                                        ^
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    81 |     while(j < J & FLAG == 0){
       |                             ^
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    28 | {X} \code{<x_var>, <(x_facet)>}: \tab\tab\tab\tab  X-axis variable. May include a second categorical\cr
       | ^
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    30 | {Y} \code{<y_var>}: \tab\tab\tab\tab Y-axis variable. *Not used for \code{hist}.\cr
       | ^
checkRd: (-1) cql.Rd:38: Lost braces; missing escapes or markup?
    38 | {Y_label} \code{'<ylab>'}: \tab\tab\tab\tab  Y-axis custom label. Defaults to <y_var>\cr
       | ^
checkRd: (-1) cql.Rd:39: Lost braces; missing escapes or markup?
    39 | {Legend} \code{'<legend>'}: \tab\tab\tab\tab  Legend custom label. Defaults to <x_category>\cr
       | ^
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    40 | {Colorset} \code{'<clist>'}: \tab\tab\tab\tab  Custom set of colors for <x_category> levels.\cr
       | ^
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    42 | {AggFunc} \code{'<func>'}: \tab\tab\tab\tab Summary function for \code{bar} type.\cr
       | ^
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    45 | {Fit} \code{'<show_se>'}: \tab\tab\tab\tab Valid types: \code{true|false}. Fit quadratic line.\cr
       | ^
checkRd: (-1) cql.Rd:47: Lost braces; missing escapes or markup?
    47 | {ConfInt} \code{'<interval>'}: \tab\tab\tab\tab  Show error bars. Value is confidence interval value. E.g. '.95'
       | ^
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    17 | Create `{testthat}` test cases for the code.
       |         ^
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    43 | \item \code{type}, the type of the detected entity, either \code{"global"} or {"import"}.
       |                                                                               ^
checkRd: (-1) as.matrix.checkglobals.Rd:32: Lost braces; missing escapes or markup?
    32 | \item \code{type}, the type of the detected entity, either \code{"global"} or {"import"}.
       |                                                                               ^
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  \keyword: ‘~kwd2’
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    28 |     40 x {
       |          ^
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    28 |     40 x {
       |          ^
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    63 |     40 x {
       |          ^
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     5 | \title{prepares Dy y_1 Dy_1 ... Dy_{nlag-1} for estimation}
       |                                    ^
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    15 | ymat contains the folloiwing columns {Dy y_1 Dy_1 ... Dy_{nlag-1}}
       |                                      ^
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    15 | ymat contains the folloiwing columns {Dy y_1 Dy_1 ... Dy_{nlag-1}}
       |                                                          ^
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    21 |              REM: alternative to "lead-lag" {dplyr} which applies to vector y
       |                                             ^
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Packages required but not available: 'ChIPseeker', 'fgsea'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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checkRd: (-1) CIplot.Rd:58: Lost braces; missing escapes or markup?
    58 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.
       |                       ^
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    42 | Lo\"{g}ae\"{v}e, M. (1977). Probability Theory I. (fourth edition) Springer-Verlag, New York.
       |     ^
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    42 | Lo\"{g}ae\"{v}e, M. (1977). Probability Theory I. (fourth edition) Springer-Verlag, New York.
       |            ^
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    93 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                     ^
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    93 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                             ^
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    95 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++}, S_{*+}
       |                                                                 ^
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    95 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++}, S_{*+}
       |                                                                         ^
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    96 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                     ^
checkRd: (-1) data_generator_loop.Rd:96: Lost braces; missing escapes or markup?
    96 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                             ^
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    98 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++},
       |                                                                 ^
checkRd: (-1) data_generator_loop.Rd:99: Lost braces; missing escapes or markup?
    99 |   S_{*+} and PP estimands}
       |     ^
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checkRd: (-1) ciu.ggplot.col.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
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    27 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
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    30 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
checkRd: (-1) ciu.textual.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
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    13 | character vector listing all the languages that tag API call supports. See \code{\link{tag_images}} and code{\link{tag_image_urls}}
       |                                                                                                             ^
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
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    68 | \code{\link{cf_find_station}} and code{vignette("choose-station")} for
       |                                       ^
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   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                   ^
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   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                                 ^
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    13 | \item{query}{A phenotype query defined using the code{\link{phenotype}} function and logic operators (see example below)}
       |                                                      ^
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    10 | \item{id}{A single phenotype id. Possible phenotyoes can be explored using the code{\link{cb_search_phenotypes}} function}
       |                                                                                    ^
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    24 | the sense that its Karhunen-Lo\`{e}ve decomposition has qx terms only.}
       |                                 ^
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  ‘clusterhap_reports’
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    62 | \item{centers }{A matrix of cluster centres.}
       |      ^
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    62 | \item{centers }{A matrix of cluster centres.}
       |                ^
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    63 | \item{cluster }{A vector of integers (from 1:\code{k}) indicating the cluster to which each point is allocated.}
       |      ^
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    63 | \item{cluster }{A vector of integers (from 1:\code{k}) indicating the cluster to which each point is allocated.}
       |                ^
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    64 | \item{itnb }{The number of iterations executed until convergence}
       |      ^
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    64 | \item{itnb }{The number of iterations executed until convergence}
       |             ^
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    65 | \item{converged }{Whether the algorithm stopped by converging or through reaching the maximum number of itertions.}
       |      ^
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    65 | \item{converged }{Whether the algorithm stopped by converging or through reaching the maximum number of itertions.}
       |                  ^
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    10 | \item \code{train}{ a list of class "hhsmm.data" as the train dataset}
       |                   ^
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    11 | \item \code{test}{ a list of class "hhsmm.data" as the test dataset}
       |                  ^
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    12 | \item \code{subsets}{ a matrix containig the number of units in each subset of the CMAPSS data set (FD001-FD004) for the train and test datasets}
       |                     ^
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    50 |   \item{order}{applied conditioning order {length p}}
       |                                           ^
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    20 | The list \code{l.v} is created by \code{makedistlist()} from a {n x p} design matrix on which to generate the unconditional GP realization.  The correlation parameters take on values in \code{(0,1)} and use the Gaussian correlation model, calculated as \code{rho^d(xi,xj)^2}.  This helper function is used to create the demonstration data used in the example for \code{calibrate()}.
       |                                                                ^
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    24 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
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    38 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
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    29 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
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    43 | \emph{Technometrics}, bold{60} (1), 48-60, DOI 10.1080/00401706.2017.1281846.\cr\cr
       |                           ^
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    35 | Given \eqn{n} points on a line, \env{x}, each with a corresponding env{f} value this function computes
       |                                                                       ^
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Auto-generated content requiring editing in Rd file 'COCONUT.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
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    32 | ({FALSE})? If a bin is empty, the center of the bin is returned as the
       |  ^
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    82 | of the bin ({FALSE})? If a bin is empty, the center of the bin is returned
       |             ^
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Unexported object imported by a ':::' call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
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     6 |              Generates all points on a {p,n} simplex lattice (i.e. a p-part
       |                                        ^
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  ‘cometExactTest_plot.pdf’
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    36 | {0, 1}.
       | ^
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    40 | values in {0, 1}.
       |           ^
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    10 | \item{item}{factor}{200 levels - which item the measurements came from}
       |                    ^
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    11 | \item{fragment}{factor}{4 levels - which of the four fragments from each item the observations were made
       |                        ^
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    13 | \item{logNaO}{numeric}{log of sodium concentration to oxygen concentration}
       |                       ^
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    14 | \item{logMgO}{numeric}{log of magnesium concentration to oxygen concentration}
       |                       ^
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    15 | \item{logAlO}{numeric}{log of aluminium concentration to oxygen concentration}
       |                       ^
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    16 | \item{logSiO}{numeric}{log of silicon concentration to oxygen concentration}
       |                       ^
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    17 | \item{logKO}{numeric}{log of potassium concentration to oxygen concentration}
       |                      ^
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    18 | \item{logCaO}{numeric}{log of calcium concentration to oxygen concentration}
       |                       ^
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    19 | \item{logFeO}{numeric}{log of iron concentration to oxygen concentration}
       |                       ^
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     9 |  \item{"tangle"}: {Dihedral angle defined by atoms A-B-C-D as described below. \code{NA}'s represent the free side chain dihedral angles \emph{chi} for that amino acid.}
       |                   ^
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    10 |  \item{"names"}: {The component atoms of the amino acid side chain.  Represents atom D in the dihedral.}
       |                  ^
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    11 |  \item{"matx"}: {The names of atoms A,B,C in the dihedral, with rows corresponding to the atoms in "names".}
       |                 ^
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    12 |  \item{"bangle"}: {Planar bond angle formed between B-C-D}
       |                   ^
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    13 |  \item{"blength"}: {Bond length between C-D}
       |                    ^
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    82 | a_{ij} = (S_ij + 1) / (S_ij + S_ji + 2). This step should make comparing
       |   ^
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Auto-generated content requiring editing in Rd file 'OptimPriceStorage.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'cplfunction.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'cplfunctionvec.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'cpqfunction.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'cpqfunctionvec.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
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    13 | value is required. Ranges from {0, 1} and often used for comparison over
       |                                ^
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    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                ^
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    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                      ^
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    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                                    ^
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Found the following files/directories:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
Specified C++11: please drop specification unless essential
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    69 | To obtain the preference rankings from the paired comparisons the procedure has been the following: the first row of the raw data is [1  3  2   1   2   1  1  2  1   1   1   2   1    1   2]. London is preferred to Paris, St. Gallen, Barcelona Stockholm (LP, LM, LSg, LB and LSt are always equal to 1), and there is no preference between London and Milan (they are tied); Milan is preferred to Paris (PM = 2), St. Gallen, Barcelona and Stockholm; and so on. The first ordering is then <{L M} Sg St B P> corresponding to a ranking [1,5,1,2,4,3], where the columns indicate L  P  M Sg  B St.  
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ^
GNU make is a SystemRequirements.
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    28 | \item{plotCI}{a vector of up to 4 numbers out of the set {1,2,3,4}, corresponding to which
       |                                                          ^
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    40 |        item{\code{maxit}}{the maximum number of iterations to be used by \code{\link{optim}} when optimizing the objective function. Defaults to \code{1000}.}
       |            ^
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    40 |        item{\code{maxit}}{the maximum number of iterations to be used by \code{\link{optim}} when optimizing the objective function. Defaults to \code{1000}.}
       |                          ^
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    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                          ^
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    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                                      ^
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    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                  ^
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    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                              ^
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     5 | \title{Draws the contour {f=c}.}
       |                          ^
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    20 | Draws the contour {f=c}.
       |                   ^
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    22 | value \code{getSurface} shortens the output of \code{conv} to remove artificial surface layers. The output is thus a subset of the input, and identical in structure to the /code{conv} output.
       |                                                                                                                                                                                  ^
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    18 |     \item{\code{killip}}{Killip level of cardiac event severity (1-4)age75}{1= Age>75; 0=Age<=75}
       |                                                                            ^
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  ‘covfefe_inauguration.txt’
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checkRd: (-1) coxph.RT.Rd:59-71: Lost braces in \itemize; \value handles \item{}{} directly
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'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
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    23 | \doi{10.7910/DVN/YXMQZM}{Harvard dataverse}
       |                         ^
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    54 | \item("predTime"){
       |                  ^
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    59 |  no longer the default (see \item{return.type}). If the original data were 
       |                                  ^
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Problems with news in ‘NEWS.md’:
No news entries found.
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    39 | {analytes}}
       | ^
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    27 | ode{standards}, \code{analytes}}
       |    ^
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    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                                                                                    ^
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    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                                                                                      ^
checkRd: (-1) confRegUCRandUCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
Package suggested but not available for checking: ‘INLA’
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    21 | section{Dependencies}{
       |        ^
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    21 | section{Dependencies}{
       |                      ^
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    26 | section{Citation}{
       |        ^
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    26 | section{Citation}{
       |                  ^
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    30 | references{
       |           ^
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    16 | V A real number. The volume (in angstroms^3 or angstroms^{-3})
       |                                                          ^
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    24 | equals (I-B)^{-1}Gamma. The indirect effect equals the difference between
       |              ^
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    81 |   beta ~ N( 0 , tau^2 * QQ^{-1} )
       |                            ^
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  ‘Hello.csv’
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File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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'LazyData' is specified without a 'data' directory
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  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
Specified C++11: please drop specification unless essential
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Package which this enhances but not available for checking: ‘RGtk2’
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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Packages which this enhances but not available for checking:
  'gurobi', 'rcbc'
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) fit.Rd:37: Lost braces in \itemize; meant \describe ?
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    55 |     \code{tol}{  A small, positive scalar that determines when iterations
       |               ^
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    60 |     \code{maxiter}{  An integer denoting the maximum limit on the number of
       |                   ^
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    63 |     \code{trace}{  A logical variable denoting whether some of the intermediate
       |                 ^
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checkRd: (-1) formatScientificTeX.Rd:33: Lost braces; missing escapes or markup?
    33 | function will return  " 3.0\\\\times 10^{2}"
       |                                         ^
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     7 |  {adegenet} object}
       |  ^
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    68 | The function is essentially a wrapper for glPca {adegenet} or pcoa \{ape\}
       |                                                 ^
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    17 | code{x2@other$history[c(1,4,5)]}). [optional].}
       |     ^
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    49 | bold{Note} that when n is very small, jackknife resampling is not recommended.
       |     ^
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    51 | Parallel computation is implemented. The argument code{n.cores} indicates the 
       |                                                       ^
GNU make is a SystemRequirements.
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--- re-building ‘accessing-data.Rmd’ using rmarkdown

Quitting from lines 115-116 [unnamed-chunk-11] (accessing-data.Rmd)
Error: processing vignette 'accessing-data.Rmd' failed with diagnostics:
object 'format_name' not found
--- failed re-building ‘accessing-data.Rmd’

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--- finished re-building ‘authorized-users.Rmd’

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

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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checkRd: (-1) StartEnd.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) StartEnd.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processFlow.Rd:14: Lost braces
    14 | \item{roundDigits}{Integer. If NA, numerics are not rounded before comparison. If /code{roundDigits} is specified, numerics are 
       |                                                                                        ^
checkRd: (-1) processFlow.Rd:15: Lost braces
    15 | rounded to /code{roundDigits} decimal places using \link[base]{round}.}
       |                 ^
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checkRd: (-1) data_edit.Rd:137: Lost braces
   137 | code{data_edit} is a shiny application built on \code{rhandsontable} that is
       |     ^
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    29 | code{\link{variableType}}, \code{\link{countMissing}}, \code{\link{uniqueValues}},
       |     ^
Found the following files/directories:
  ‘my new data set.rds’
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    15 | Map a vector of dates to a factor at one of these levels {"yearmonth", "yearquarter", "quarter", "month"}
       |                                                          ^
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    12 | \item{type}{One of {"year", "yearquarter", "yearmonth", "quarter", "month"}}
       |                    ^
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    29 | code{\link{variableType}}, \code{\link{countMissing}}, \code{\link{uniqueValues}},
       |     ^
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    48 |   \ code{size} is extracted from argument \code{x}.
       |         ^
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    10 | \item{i}{the row index of the interest entry X_{i,j}}
       |                                                ^
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    12 | \item{j}{the row index of the interest entry X_{i,j}}
       |                                                ^
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    11 | \doi{10.1007/s40258-021-00647-3}{DOI}
       |                                 ^
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    36 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
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    37 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
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    49 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
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    50 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
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    60 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
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    61 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
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    34 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
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    35 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
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    27 |  {q = [0, 1]}. Kernels are of the Müller-Wang type ("MW"), Müller type ("M")
       |  ^
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    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Age}, or code{age}.}
       |                                                                              ^
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    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Sex}, or code{sex}.}
       |                                                                              ^
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    28 | code{\link{ggbChooseAges}}
       |     ^
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    85 |     \code{tg}, std. error of \eqn{g}, \eqn{G} (the cdf of {g}),
       |                                                           ^
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    18 | section{Dependencies}{
       |        ^
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    18 | section{Dependencies}{
       |                      ^
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    23 | section{Citation}{
       |        ^
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    23 | section{Citation}{
       |                  ^
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    27 | references{
       |           ^
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    28 |  \item{purify}{logical: should item purification be performed? (Default is code{FALSE}). See \bold{Details}.}
       |                                                                                ^
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    53 | {\itemize{
       | ^
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    59 | {\itemize{
       | ^
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     9 | \code{conifersIP} {has following variables:}
       |                   ^
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    68 |         response.  See code{\link{makeDepmix}} for an example of how to use
       |                            ^
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.N’ ‘.Nmiss’ ‘.Q1’ ‘.Q3’ ‘.factorN’ ‘.factorNmiss’ ‘.factorQ1’
  ‘.factorQ3’ ‘.factormax’ ‘.factormean’ ‘.factormedian’ ‘.factormin’
  ‘.factorsd’ ‘.max’ ‘.mean’ ‘.median’ ‘.min’ ‘.sd’
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    21 | \item{r}{vector for the proportion for each sub-population, r_1 is 1, r_i>r_{i+1}}
       |                                                                             ^
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    25 | \item{r_set}{the matrix of proportion for each sub-population, r_1 is 1, r_i>r_{i+1}}
       |                                                                                ^
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    21 | \item{r}{vector for the proportion for each sub-population, r_1is 1, r_i>r_{i+1}}
       |                                                                            ^
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    26 | \item{expr}{an expression that generates a {detourr} widget}
       |                                            ^
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    80 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
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    67 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
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    65 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
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    76 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
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    11 | Variables are evaluated using {tidyselect} syntax.}
       |                               ^
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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    47 | \item{comp}{the measures of model complexity used to compute the measure of goodness-of-fit. It is equal to \code{npar} when code{complexity = "df"};}
       |                                                                                                                                  ^
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   258 |                 \item{\code{7}}{maximum number of solution points ('code{np}') reached.}
       |                                                                         ^
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--- re-building ‘dhis2r.Rmd’ using rmarkdown

Quitting from lines 48-50 [unnamed-chunk-3] (dhis2r.Rmd)
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Error: Vignette re-building failed.
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    32 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dHSIC-package.Rd:36: Lost braces
    36 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dHSIC-package.Rd:36: Lost braces
    36 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
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    84 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
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    88 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
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    88 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
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   124 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
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   128 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
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   128 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
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    40 |  {Paul Schneider <paul.schneider@usi.ch>}{}
       |  ^
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    74 | form average treatment effects for groups of {it}.
       |                                              ^
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    25 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
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    25 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
checkRd: (-1) sensitivitySamplerManual.Rd:22: Lost braces
    22 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
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    72 |   {The Sharma-Song test} {\code{\link[DiffXTables]{sharma.song.test}}}
       |   ^
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    74 |   {The comparative chi-squared test} {\code{\link[DiffXTables]{cp.chisq.test}}}
       |   ^
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    76 |   {The heterogeneity test} {\code{\link[DiffXTables]{heterogeneity.test}}}
       |   ^
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   185 |  \code{\link[deltaPlotR]{deltaPlot}}, code{\link[deltaPlotR]{diagPlot}}, \code{\link{dichoDif}}
       |                                           ^
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   272 | \item{name}{the name of the model {"GNG", "iNUDGE","NUDGE"} where
       |                                   ^
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    79 | n^{1/3} up to sacrificing some accuracy, for details see
       |   ^
Unknown package ‘loe’ in Rd xrefs
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    10 | \item{input, output, session}{Internal parameters for `{shiny}`.
       |                                                        ^
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    52 | P\'{a}ez, A. (2013). Mapping travelers’ attitudes: does space matter?. Journal of Transport Geography, 26, 117-125. (https://doi.org/10.1016/j.jtrangeo.2012.09.002)
       |    ^
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    49 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
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    74 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
checkRd: (-1) mc_commute_wide.Rd:87: Lost braces
    87 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
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    50 | Lavery, T., P\'{a}ez, A., & Kanaroglou, P.S. (2013). Driving out of choices: An investigation of transport modality in a university sample. Transportation Research Part A: Policy and Practice, 57:37-46 (https://doi.org/10.1016/j.tra.2013.09.010)
       |                ^
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    32 | [a_{q-1}, a_q) are available.
       |    ^
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    31 | [a_{q-1}, a_q) are available.
       |    ^
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    23 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
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    24 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
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    23 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
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    24 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
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    21 | [a_0, a_1), [a_1, a_2), ..., [a_{q-1}, a_q) ("character vector")}
       |                                 ^
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    56 | strings, and you are encouraged to use {fasttime} to convert the strings to
       |                                        ^
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    10 | \item{.f}{a normal function or purrr syntax function i.e. `~{ ...code...}`}
       |                                                             ^
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    89 | link{read_from_DB} function. Those parameters define rows and columns that will be returned.
       |     ^
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    46 | \code{data1.shared.var} and {data2.shared.var} must contain unique values within its own data frame.
       |                             ^
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    27 | udf <- function(x){
       |                   ^
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    37 |   {M(theta)=-(log(y_1-y_0)+log(y_2-y_1)+...+log(y_m-y_m-1))}
       |   ^
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--- re-building ‘newDistributions-knitr.Rnw’ using knitr
Warning in doTryCatch(return(expr), name, parentenv, handler) :
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! LaTeX Error: Command \textquotedbl unavailable in encoding OT1.

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! Emergency stop.
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l.281 Let \code{N} an object of class \code{"
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    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
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    47 | When y_t is controlled, only y_{t-delay-1} and before 
       |                                ^
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    64 |                  estimate of theta_{j-1} for model k at t}
       |                                    ^
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    66 |                  variance of theta_{j-1} for model k at t}
       |                                    ^
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    68 |                  estimate of theta_{j-1} at t}
       |                                    ^
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    70 |                  variance of thetahat_{j-1} at t}
       |                                       ^
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    24 | \eqn{neglinks_{ij} = 1} means chunklet \code{i} and chunklet {j}
       |                                                              ^
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    26 | \eqn{neglinks_{ij} = 0} means chunklet \code{i} and chunklet {j}
       |                                                              ^
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    57 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |            ^
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    57 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |                          ^
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    10 | \item{...}{arguments goint to code{scale_color_manual()}}
       |                                   ^
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    10 | \item{...}{arguments goint to code{scale_color_manual()}}
       |                                   ^
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   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                 ^
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   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                             ^
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   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                                             ^
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   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                                                         ^
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   143 |   where g_{y,i} and g_{x,i} are the two groups involved in the merge at
       |           ^
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   143 |   where g_{y,i} and g_{x,i} are the two groups involved in the merge at
       |                       ^
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   144 |   step i, and g_{x,i} is the group which X belongs to. Note that if X
       |                 ^
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    85 | statespace {0,1,2}, which this is *not* checked anywhere. Thus, if
       |            ^
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Auto-generated content requiring editing in Rd file 'DNLC_statistics.Rd':
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    13 |     \item{\code{x}}{dose (log base 10 CS2mgl^{-1})}
       |                                              ^
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    96 |       URL{http://www.jstatsoft.org/v32/i07/}.
       |          ^
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     5 | \title{Tell {reticulate} to use Python Conda version available on Domino Data Lab.}
       |             ^
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
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See section ‘Good practice’ in ‘?attach’.
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    56 | You can increase it by including a {timeout=n} argument value.
       |                                    ^
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    54 | You can increase it by including a {timeout=n} argument value.
       |                                    ^
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File ‘doSNOW/R/doSNOW.R’:
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See section ‘Good practice’ in ‘?attach’.
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     9 | \item{occupancies}{Either a data frame containing two columns or an object of class \code{"upgrain"} from the \code{\link{upgrain}} function. If using a data frame the first column must be the grain sizes (cell area in squared units e.g. km^{2}). The second column is the proportion of occupancies at each grain size.}
       |                                                                                                                                                                                                                                                  ^
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    13 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
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    13 | \item{new.areas}{vector of grain sizes as cell area (in same units as cell.width but squared e.g. km^{2}) at fine scales for model prediction.}
       |                                                                                                      ^
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    10 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
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    43 |   emph{Generalized Linear Models}, 
       |       ^
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    18 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
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    16 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
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    11 | code{\link[DrDimont]{compute_correlation_matrices}}}
       |     ^
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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    67 | parameter uncertainty. See Wood, Pya & S{\"a}fken (2016) for more
       |                                         ^
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   100 | Wood, S.N., Pya, N. and S{\"a}fken, B. (2016) Smoothing parameter and model
       |                          ^
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    22 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
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    21 |    \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                                ^
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    24 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
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    64 | The empiric model is specified as F(d, beta) = d^{exp(beta)}. The logistic model is
       |                                                  ^
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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    27 |      For example, the order {a, b, c} implies that a > b, a  > c, and b > c.
       |                             ^
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    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                          ^
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    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                                                     ^
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    19 | \item{log_style}{is a {crayon::style()} that will colorize
       |                       ^
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    22 | \item{msg_style}{is a {crayon::style()} style that will gray scale the
       |                       ^
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    22 | \item{"sysname"} : {The operating system name.}
       |                    ^
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    23 | \item{"release"} : {The OS release.}
       |                    ^
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    24 | \item{"version"} : {The OS version.}
       |                    ^
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    25 | \item{"nodename"} : {A name by which the machine is known on the network (if any).}
       |                     ^
checkRd: (-1) sys_context.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{"machine"} : {A concise description of the hardware, often the CPU type.}
       |                    ^
checkRd: (-1) sys_context.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{"login"} : {The user's login name, or "unknown" if it cannot be ascertained.}
       |                  ^
checkRd: (-1) sys_context.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{"user"} : {The name of the real user ID, or "unknown" if it cannot be ascertained.}
       |                 ^
checkRd: (-1) sys_context.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{"r-ver"} : {R Version in (major).(minor) format.}
       |                  ^
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 ?
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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: \&
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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}}
       |                                                                                                                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘fgsea’
Package unavailable to check Rd xrefs: ‘fgsea’
'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
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) OCC1950.Rd:64: Lost braces
    64 |     \doi{10.18128/D010.V10.0}{IPUMS USA: Version 10.0 [dataset]. Minneapolis, MN: IPUMS}. 
       |                              ^
checkRd: (-1) Oil.Rd:45: Lost braces
    45 |       code{pt-pt-1} on a constant
       |           ^
checkRd: (-1) breaches.Rd:70-74: Lost braces
    70 |     \code{breach_end}{
       |                      ^
checkRd: (-1) breaches.Rd:75-78: Lost braces
    75 |     \code{year}{
       |                ^
checkRd: (-1) nuclearWeaponStates.Rd:82-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:93-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:104-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:128-140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:141-150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:151-161: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:162-172: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:173-191: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:192-219: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'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}`.
       |  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taxize’
'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
The following files should probably not be installed:
  ‘econet.tex’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) transformFitness.Rd:25: Lost braces; missing escapes or markup?
    25 | minimization (most others). This function computes a factor from {-1, 1} for
       |                                                                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) read.edf.Rd:30: Lost braces
    30 | Kemp B., V\"{a}rri, A., Rosa, A.C., Nielsen, K.D. and Gade, J. (1992).
       |             ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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
'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.
Problems with news in ‘NEWS.md’:
No news entries found.
'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: \_
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
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
       |                         ^
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
checkRd: (-1) macacaModels.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) macacaModels.Rd:10-11: Lost braces in \itemize; meant \describe ?
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) 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
'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.}
       |               ^
Auto-generated content requiring editing in Rd file 'validate-methods.Rd':
  \keyword: ‘~~ other possible keyword(s) ~~’
Package suggested but not available for checking: ‘Rmpi’
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
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
'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},
       |                                                        ^
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
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   111 | \ifelse{html}{\out{<i>r</i><sub>1</sub> = 1}}{{\eqn{r_1 = 1}}{r_1 = 1}} while the individual with the lowest phenotypic value
       |                                                              ^
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   112 | is given the rank \ifelse{html}{\out{<i>r<sub>n</sub></i> = <i>n</i>}}{{\eqn{r_n = n}}{r_n = n}}), the probability of an individual
       |                                                                                       ^
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   120 | }{
       |  ^
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    16 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then Sigma^{-1} 
       |                                                                         ^
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    17 | has the corresponding q-factor decomposition Sigma^{-1}=diag(phi)(I-theta theta')diag(phi), where theta is a mxq matrix and phi the vector of 
       |                                                    ^
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    21 | \item{iSB}{m x q matrix (diag(Psi)+BB')^{-1}B.}
       |                                         ^
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    15 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then the function returns a matrix Omega such that Sigma^{-1} = Omega Omega'. Equivalently,
       |                                                                                                                       ^
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    80 | \item{XtXlamIinv}{explicit value of (X'X + diag(penalty))^{-1}.  Useful
       |                                                           ^
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    12 | \item{orden}{Es un valor numérico que representa el orden del momento central (orden = {1,2,3,4,...})}
       |                                                                                        ^
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   138 | $j^{th}$ for all the observations.
       |    ^
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Package required but not available: ‘TDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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    15 | A list of cluster labels and a R object of class "fcm {ppclust}"
       |                                                       ^
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    15 | A list of cluster labels and a R object of class "pam {cluster}"
       |                                                       ^
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    26 | the \code{names} column in {data} as labels. If \code{NULL} (default),
       |                            ^
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    52 | \item{legend}{should a legend be added? Defaults to code{FALSE}}
       |                                                         ^
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    56 | \item{legend.pretty}{logical: should the legend values produced by \[base]{pretty}? Othewrwise they are exact. Defaults to \code{TRUE}}
       |                                                                           ^
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     5 |   Conducts a generalized likelihood ratio test testing whether {\eqn{\beta \in}  (-\code{c},\code{c})}. Covariates can be accommodated.
       |                                                                ^
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    34 |   This is a similar function to the main function \code{evian}. Instead of testing H0: \eqn{\beta}=0, it tests for whether H0:{\eqn{\beta \in} (-\code{c},\code{c})}.
       |                                                                                                                               ^
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   183 |  \item {nlumgammagpd} and {proflumgammagpd} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], sigmau, xi)}
       |                           ^
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   181 |  \item {nlumgammagpdcon} and {proflumgammagpdcon} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], xi)}
       |                              ^
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    87 | code{\link[evmix:kernels]{kd*}}  and \code{\link[evmix:kernels]{kp*}} give the
       |     ^
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    18 | Procrustes distance provides a measure of coincidence of two point sets {xi} and {yi}, i=1..N. For this purpose the variance of point deviations is calculated at the optimal superposition of the sets. It allows to characterize the shape proximity of a given simplex to shape of a reference one.
       |                                                                         ^
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    18 | Procrustes distance provides a measure of coincidence of two point sets {xi} and {yi}, i=1..N. For this purpose the variance of point deviations is calculated at the optimal superposition of the sets. It allows to characterize the shape proximity of a given simplex to shape of a reference one.
       |                                                                                  ^
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    42 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
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    41 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
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     6 | Computation of aggregation matrices for generalized interactions that are used in code{\link{extRC}} to estimate extended RC models.
       |                                                                                       ^
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     5 | \description{It plots the output of code{\link{extRC}} function for a vector of lambda values.}
       |                                         ^
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     5 | \description{Given the output of code{\link{extRC}} function, it is written in a readable form.}
       |                                      ^
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     5 | \description{Summary method for the output of code{\link{extRC}} function.}
       |                                                   ^
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    80 | \doi{10.1016/s0002-9394(02)01825-1}{Beck et al.}, and
       |                                    ^
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    37 | where, \code{alpha(i)} is the intercept, \code{f(t)} is a {K x 1} vector of 
       |                                                           ^
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    82 | \item{las}{one of {0, 1, 2, 3} to set the direction of axis labels, same as
       |                   ^
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    39 | Returned object is of class {summary.ffm}.
       |                             ^
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    75 | (2001) proposed: "the smallest k such that gap(k) >= gap(k+1) - s_{k+1}". 
       |                                                                   ^
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    77 | SE.factor*s_{k+1}" where SE.factor is a numeric value which can be 1
       |             ^
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    14 |                  code{Pretty happy} <  \code{Very happy}}
       |                      ^
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    22 | A map of France as {sf} object. Can be used as dataset or for maps
       |                    ^
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    18 | \code{pi0}{The estimated proportion \code{pi0} of null hypotheses.}}
       |           ^
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Auto-generated content requiring editing in Rd file 'net.edges.Rd':
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Auto-generated content requiring editing in Rd file 'net.hubs.Rd':
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    36 |  \item{trait}{One of {'c','d','s',NULL} indicating the type
       |                      ^
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    51 |  \item{trait}{One of {'c','d','s',NULL} indicating the type
       |                      ^
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    19 |                 Must be one of {'ibs', 'linear', 'quadratic'}.
       |                                ^
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    31 |                      {'add', 'dom', 'rec'} indicating additive,
       |                      ^
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    14 |                 Must be one of {'interactive', 'linear', 'quadratic'}.
       |                                ^
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    17 | The value of m^{-1}_{j,j}
       |                ^
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    17 | The value of m^{-1}_{j,j}
       |                     ^
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.run: no visible binding for global variable ‘init’
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.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
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Note: information on .o files is not available
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   107 |   \item \code{do_verbose(response, template)} {
       |                                               ^
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    33 |   \item \code{do(response, mssg)} {
       |                                   ^
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    25 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
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    27 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
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    34 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
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    36 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
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    31 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
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    33 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
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     5 | \title{Plots function for object of class{fbroc.conf}}
       |                                          ^
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    15 | Let $y_{ij}$ denote some outcome measured at
       |        ^
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    16 | $t_{ij}$ on the functional domain (e.g. time) for subject $i$ at observation
       |    ^
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    29 | Initially, a model is fit without $b_i(t_{ij})$. Using the residuals from this initial fit,
       |                                          ^
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    13 | The formula should only include terms not associated with the random function intercept b_i(t_{ij}). See Examples.}
       |                                                                                               ^
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    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                              ^
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    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                                           ^
GNU make is a SystemRequirements.
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    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
       |    ^
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  ‘vert.txt’
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    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}.}
       |                                                                                                                                                                     ^
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checkRd: (-1) contemParametros.Rd:19: Lost braces
    19 | \item{exclui3pontos}{verify por ... ? in f<-function(a, ...){ }}
       |                                                             ^
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    19 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
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    32 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
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    46 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
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    66 | \code{parA }{vector of the six "ABCDEF" coefficients
       |             ^
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    67 | \code{RSS }{'root sum square' figure of merit describing the relative fit quality}
       |            ^
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    68 | \code{iters }{number of iterations at convergence}
       |              ^
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    69 | \code{exitCode }{1 means ellipse, 2 means hyperbola, 3 means parabola.
       |                 ^
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    59 | For \code{xyrot} {a Nx2 array of the x,y coordinates of the rotated data set. }
       |                  ^
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Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
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    14 | All standard distributions from {stats} package are covered. For a list
       |                                 ^
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    11 | The initial design, consisting of \code{d + 1} columns ({d} dimensions and
       |                                                         ^
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    31 |         \code{smoothed} of class {StatMixHMM}).
       |                                  ^
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    31 |         \code{smoothed} of class {StatMixHMMR}).
       |                                  ^
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     8 | This function summarizes a call to code{\link{flamCV}} and identifies the tuning parameter chosen by cross-validation.
       |                                        ^
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    53 | like those in package {MetricsWeighted}.}
       |                       ^
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    49 | {MetricsWeighted}.}
       | ^
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    45 | Experimental. Uses package {ggpubr} to rearrange the figure.
       |                            ^
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    96 | the `{.storyboard}` attribute to individual pages rather than using the
       |      ^
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    45 | If k = 0: (xi_1, ..., x_{C_i - 1}, omega)
       |                         ^
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    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)
       |                         ^
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    30 | \item Don't forget to add {flow} to Suggests in your DESCRIPTION file.
       |                           ^
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    10 | \item{Flow}{Water flow, in m^{3}/s}
       |                              ^
Malformed Description field: should contain one or more complete sentences.
GNU make is a SystemRequirements.
Running examples in ‘fluxfinder-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ffi_qaqc
> ### Title: Generate a QA/QC document
> ### Aliases: ffi_qaqc
> 
> ### ** Examples
> 
> # Toy data
> cars$Plot <- c("A", "B")
> fd <- ffi_compute_fluxes(cars, "Plot", "speed", "dist")
> x <- ffi_qaqc(fd, group_column = "Plot")


processing file: qaqc.Rmd
Warning in file(con, "w") :
  cannot open file 'qaqc.knit.md': Read-only file system
Error in file(con, "w") : cannot open the connection
Calls: ffi_qaqc ... <Anonymous> -> <Anonymous> -> write_utf8 -> writeLines -> file
Execution halted
Found the following files/directories:
  ‘qaqc_files’
Found the following files/directories:
  ‘flux.CH4.txt’
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    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.
       |                                                                                                   ^
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    40 |   \code{dEstable}{ gives the density function;}
       |                  ^
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    41 |   \code{pEstable}{ gives the distribution function or its complement;}
       |                  ^
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    42 |   \code{qEstable}{ gives quantiles;}
       |                  ^
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    43 |   \code{tailsEstable}{ returns a list with the following components
       |                      ^
checkRd: (-1) FMstable.Rd:50: Lost braces
    50 |   \code{dFMstable}{ gives the density function;}
       |                   ^
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    51 |   \code{pFMstable}{ gives the distribution function or its complement;}
       |                   ^
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    52 |   \code{qFMstable}{ gives quantiles;}
       |                   ^
checkRd: (-1) FMstable.Rd:53-66: Lost braces
    53 |   \code{tailsFMstable}{  returns a list with the following components
       |                       ^
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Malformed Description field: should contain one or more complete sentences.
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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    48 |         The metric MdAE is obtained using code{type = "AE"} and  \code{statistic = "Md"}
       |                                               ^
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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}.
       |                                                   ^
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    28 | \item{pavd}{logical input to include Plant Area Volume Density Plot from {plot_pavd},
       |                                                                          ^
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    17 |   \item {file} : {filename}
       |                  ^
checkRd: (-1) depth.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item {z_depth} : {measured focus range depth (z)}}
       |                     ^
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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: ‘bcp’
Package suggested but not available for checking: ‘RandomFields’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) emfrail_control.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:55-57: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) summary.frbs.Rd:32: Lost braces
    32 |                           \code{"GAUSSIAN"}, code{"TRIANGLE"}, \code{"TRAPEZOID"}, \code{"SIGMOID"}, and \code{"BELL"}.
       |                                                  ^
checkRd: (-1) summary.frbs.Rd:60: Lost braces; missing escapes or markup?
    60 |          {4.0, 0.23, 0.43, 0.53, 0.73} on its column. It means that the label a.2 of variable v.1 
       |          ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) maximin.Rd:197: Lost braces
   197 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
Package suggested but not available for checking: ‘dggrids’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'penalizedLDA',
  'relaxo', 'rrlda'
checkRd: (-1) FSelector-package.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report.Rd:18: Lost braces; missing escapes or markup?
    18 |         \item{las}{numeric in {0,1,2,3}; the style of axis labels (see \code{\link{par}}).}
       |                               ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'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 ?
'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
Found the following files/directories:
  ‘completeTrial_byArm_eventPriorRateC3=0.001_eventPriorRateT1=0_eventPriorRateT2=0_eventPriorWt=0.5.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.2.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.4.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.6.RData’
  ‘completeTrial_pooled_eventPriorRate=0.001_eventPriorWt=0.5.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.2.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.4.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.6.RData’
  ‘rcdf_byArm_arm=T1_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03.pdf’
  ‘rcdf_pooled_eventPriorRate=0.06.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) misspellings.Rd:18: Lost braces
    18 | This is a code{tbl_df} mapping misspellings of their words, compiled by
       |               ^
checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                             ^
checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                                                     ^
checkRd: (-1) genmf.Rd:26: Lost braces; missing escapes or markup?
    26 | \item 'gbellmf' is c(\code{a, b, c}), where \code{a} denotes the width, \code{b} is usually positive and {c} locates the center of the curve.
       |                                                                                                          ^
Specified C++11: please drop specification unless essential
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) 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.  
       |                                                                                                                                                                                                                                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) pc.Rd:17: Lost braces
    17 | The functions \code{gamlss.pcr()} and \code{gamlss.pc()} are supporting functions. The  are not intended to be called directly by users. The function \code{gamlss.pc()} is using the linear model function \code{lm()} to fit the first principal components while the function code{gamlss.pcr()} uses \code{fitPCR()}.
       |                                                                                                                                                                                                                                                                                      ^
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    
       |                                                                       ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘doMPI’
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 ?
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) 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.}
       |                                                                                 ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘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) 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
       |                                                                  ^
Running ‘tinytest.R’ [11s/16s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("gdm")
  + }
  
  test_gdm.R....................    0 tests    terra 1.8.5
  
  test_gdm.R....................    0 tests    
  test_gdm.R....................    0 tests    
  test_gdm.R....................    0 tests    
  test_gdm.R....................    0 tests    
  test_gdm.R....................    1 tests [0;32mOK[0m 
  test_gdm.R....................    1 tests [0;32mOK[0m 
  test_gdm.R....................    2 tests [0;31m1 fails[0m 
  test_gdm.R....................    3 tests [0;31m2 fails[0m 
  test_gdm.R....................    3 tests [0;31m2 fails[0m Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'x' in selecting a method for function 'global': object 'trans_raster' not found
  Calls: <Anonymous> ... eval -> eval -> <Anonymous> -> .handleSimpleError -> h
  Execution halted
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
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}}
       |                                                     ^
'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
Package suggested but not available for checking: ‘genderdata’
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 required but not available: ‘clusterProfiler’

Package suggested but not available for checking: ‘fgsea’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fgsea’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘clusterProfiler’
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 ?
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    36 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
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    49 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
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    59 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
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    51 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
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    58 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
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   125 | "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                                ^
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   125 | "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                                    ^
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   127 | GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                    ^
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   127 | GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                        ^
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   129 | section "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more 
       |                                        ^
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   129 | section "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more 
       |                                            ^
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     8 | A named list containing \code{x} {a vector containing the ages}
       |                                  ^
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     9 |   \code{y} {a matrix where each column is a preshape.} The 23rd, 101st,
       |            ^
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GNU make is a SystemRequirements.
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Package which this enhances but not available for checking: ‘INLA’
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’.
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     8 | Download Google fonts and generate CSS to use in {rmarkdown} documents and
       |                                                  ^
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     9 | {shiny} applications. Some popular fonts are included and ready to use.
       | ^
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     5 | \title{Use a Google Font included in {gfonts}}
       |                                      ^
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Found the following assignments to the global environment:
File ‘ggExtra/R/ggMarginalGadget.R’:
  assign(plotname, eval(parse(text = origPlot)), envir = .GlobalEnv)
Package suggested but not available for checking: ‘CopernicusMarine’
Unknown package ‘CopernicusMarine’ in Rd xrefs
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    42 | \item{xmin, ymin, xmax, ymax}{Boundaries of the area in pixels. {0,0} is the
       |                                                                 ^
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':::' 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.
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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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    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}
       |                                                                           ^
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GNU make is a SystemRequirements.
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Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
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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’:
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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}
       |   ^
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    16 |         \item Now \code{AICc == Inf} when {n <= p + 1}.
       |                                           ^
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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.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
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    16 |                          a factor with levels either \\code{F} (female) or code{M} (male)}
       |                                                            ^
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    16 |                          a factor with levels either \\code{F} (female) or code{M} (male)}
       |                                                                                ^
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     4 | \title{{Gal\'{a}pagos} Island species data}
       |              ^
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     6 |   The number of species on the {Gal\'{a}pagos} Islands
       |                                ^
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     6 |   The number of species on the {Gal\'{a}pagos} Islands
       |                                      ^
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    40 |    {Gal\'{a}pagos} (the endemics). 
       |    ^
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    40 |    {Gal\'{a}pagos} (the endemics). 
       |          ^
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    44 |   Species number and endemism: The {Gal\'{a}pagos} Archipelago revisited.
       |                                          ^
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    14 |   \item{object}{A fitted model object, of class \code{glm}, \code{lm} or code{glm.nb}}
       |                                                                              ^
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    14 | code{glmulti} finds what are the \code{n} best models (the confidence set of models) among all possible models (the candidate set, as specified by the user).
       |     ^
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    35 |   Returns the current scale factor $r_{ii}$ for row \code{i} of the specified
       |                                       ^
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    35 |   Returns the current scale factor $s_{jj}$ for column \code{j} of the
       |                                       ^
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    28 |     Scale factor $r_{ii}$.
       |                     ^
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    28 |     Scale factor $s_{jj}$.
       |                     ^
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    65 | the lag distance to take. \%For other options see code{getEmpVariogramSlice}.}
       |                                                       ^
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   114 | \item{MRB}{obtained from simplifying the major crustal boundaries of {Korsch2015a, Korsch2015b}}
       |                                                                      ^
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GNU make is a SystemRequirements.
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    24 | \item{g}{A formula as \code{y~z}, where code{y} is the response and
       |                                             ^
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No news entries found.
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    54 | of `{sf}` objects).}
       |     ^
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    31 | instance from vertex 1.  Internally, it creates the graph Kn-{v1}
       |                                                              ^
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
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
'LazyData' is specified without a 'data' directory
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
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
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
Packages suggested but not available for checking:
  'clusterProfiler', 'fgsea'
Package unavailable to check Rd xrefs: ‘clusterProfiler’
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
Package suggested but not available for checking: ‘edmcr’
Unknown package ‘edmcr’ in Rd xrefs
Specified C++11: please drop specification unless essential
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.
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 ?
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
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
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)}. }
       |                                                                                                                                                                                 ^
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
Package required but not available: ‘DOSE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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
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 
       |                 ^
Package suggested but not available for checking: ‘taxize’
Unknown package ‘taxize’ in Rd xrefs
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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) 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
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
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
'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’
Package suggested but not available for checking: ‘Rmpi’
'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
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
Package suggested but not available for checking: ‘cmdstanr’
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 ?
'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.}
       |                                                     ^
'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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: ‘Rmpi’
checkRd: (-1) hero.Rd:67-68: Lost braces
    67 | then \code{\link[pbapply]{pblapply}} is used. If code{package ==
       |                                                      ^
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    69 | code{package == "Rmpi"}, then \code{\link[Rmpi]{mpi.applyLB}} is used.}
       |     ^
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    20 | A number in the set {-1, 0, 1}, where 1 means row1 is predicted to
       |                     ^
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    18 | A number in the set {-1, 0, 1}, where 1 means row1 is predicted to
       |                     ^
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    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^
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    28 |     terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |               ^
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    30 |     terms, th_{jj}X_j^2, in the model.  Default TRUE.}  
       |               ^
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    63 | \seealso{\link{predict.hierNet.logistic},link{hierNet.logistic.path}}
       |                                              ^
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    39 |   terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |             ^
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    38 |   terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |             ^
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    45 |   as if code{y} were not of class \code{"multipleHmmDataSets"}.
       |             ^
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    93 |   disable some of them, by adding a \code{$UPDATER_NAME=FALSE} pair to the {updater} argument. Another usage of
       |                                                                            ^
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    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.
       |                        ^
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    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.
       |                                                           ^
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    50 | Uses the {updog} R package for simulating read counts and generating
       |          ^
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    31 | (while using the {hwsdr} package for HWSD v2.0).
       |                  ^
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    57 | NOTE: all the dates in the datalist should follow the format in ?as.Date{base}.
       |                                                                         ^
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    24 | Dan Martin {dpmartin42@gmail.com}
       |            ^
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    28 |  \item{Rm1U}{matrix R^{-1}U (see reference).}
       |                       ^
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    32 |   R^{-1}U (see reference) and \link{smoothCon} for the definition of smoothobject}
       |     ^
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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^
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    39 | stocks. \doi{10.17895/ices.pub.3036}{\emph{ICES Advice
       |                                     ^
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    42 | stocks. \doi{10.17895/ices.pub.3036}{\emph{ICES Advice
       |                                     ^
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    64 | \doi{10.17895/ices.pub.3038}{\emph{ICES Advice Technical
       |                             ^
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    71 | \doi{10.17895/ices.pub.5997}{\emph{ICES Scientific Reports
       |                             ^
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    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.}
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
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Found the following assignments to the global environment:
File ‘IgorR/R/ReadIgorBinary.R’:
  assign(WaveName, rval, envir = .GlobalEnv)
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    35 | distribution; 'd${dis}' gives the density function \eqn{g(\cdot)}.}
       |                  ^
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    24 | It develops an object of \code{lab.qcs}-code{link{class}} to perform statistical quality control.
       |                                             ^
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    24 | It develops an object of \code{lab.qcs}-code{link{class}} to perform statistical quality control.
       |                                                  ^
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    41 | be done either as a single vector of values (e.g. `function(x) { ... }`), or individual inputs for each parameter
       |                                                                ^
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    42 | (e.g. `function(x1, x2) { ... }`). If a single vector is used, all parameters will be passed to the target function as
       |                         ^
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   109 |        \code{response} and it will have the same order of code{x} as \code{data}. 
       |                                                               ^
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    23 | \item{grayscale}{logical. Defines color channels of images: 1 if code{TRUE}, 3 if \code{FALSE}.}
       |                                                                      ^
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    23 | minority examples and majority ones, that is, the quotient {size of
       |                                                            ^
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    24 | minority class}/{size of majority class}. There are methods, such as
       |                 ^
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Packages required but not available: 'clusterProfiler', 'DOSE'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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    22 | using the {{placeholder}} convention.
       |           ^
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    23 | placeholders are marked using the {{placeholder}} convention.
       |                                   ^
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    12 | {{placeholder}} format.}
       | ^
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    27 |   \item{call}{a string containing the matched function call that generates this sQuote{inaparc} object.}
       |                                                                                       ^
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    16 | This function creates a matrix such that P[t, s] = P(C = t | I = s) = theta_{t-s} for s <= t and 0 otherwise.
       |                                                                             ^
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    11 | the {janitor} package}
       |     ^
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    40 | adapted from the package {cowplot} by Claus O.Wilke and reflects the principles
       |                          ^
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    45 | It basically combines the half open theme with a grid background from {cowplot}
       |                                                                       ^
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Problems with news in ‘NEWS.md’:
No news entries found.
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Found the following files/directories:
  ‘c.txt’ ‘rho.txt’ ‘sta.txt’ ‘topo.txt’
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Package suggested but not available for checking: ‘INLA’
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Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
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    44 | menu in the {utils} package, yesno in the {devtools} package.
       |             ^
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    44 | menu in the {utils} package, yesno in the {devtools} package.
       |                                           ^
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    25 | This function is useful for saveVideo() in the {animation} package.
       |                                                ^
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    27 | This function is useful for saveSWF() in the {animation} package.
       |                                              ^
checkRd: (-1) os.shutdown.Rd:25: Lost braces; missing escapes or markup?
    25 | This function is a modified version of Yihui's shutdown function from the {fun} package.
       |                                                                           ^
Malformed Title field: should not end in a period.
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
Package suggested but not available for checking: ‘TDA’
'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, 
       |                                                                                           ^
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd file 'ClusterEntropy.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'ClusterPurity.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'ConsensusMatPlot.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'SilhouettePlot.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'nmf.mnnals.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'nmf.opt.k.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
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
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checkRd: (-1) forecast_volume.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_plots.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_plots.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_plots.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) intRvals-package.Rd:60: Lost braces
    60 | B\'{e}dard, J. & Gauthier, G. 1986. Assessment of faecal output in geese. Journal of Applied Ecology, 23, 77-90.
       |    ^
checkRd: (-1) partition.Rd:64: Lost braces
    64 | Bates, D., M\"{a}chler, M., Bolker, B.M. & Walker, S.C. (2015). Fitting linear mixed-effects models using lme4. Journal of Statistical Software, 67, 1-48.
       |               ^
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
'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 ?
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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
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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
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checkRd: (-1) dls2007.Rd:19: Lost braces
    19 | impact. emph{Journal of Applied Psychology}, 92(5), 1380.
       |             ^
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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
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’, ‘Rf_StringFalse’, ‘Rf_StringTrue’,
    ‘Rf_isBlankString’

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 ?
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checkRd: (-1) init_ipm.Rd:57: Lost braces in \itemize; meant \describe ?
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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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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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
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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: \&
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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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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    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}
       |                                                                ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Auto-generated content requiring editing in Rd file 'IsoWrapper.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'curves.plot.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
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 ?
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checkRd: (-1) is_israd_database.Rd:26: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘RMTplot.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘iucnrdata’
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
       |                                               ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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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.
'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.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘remMap’
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'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 
       |                                                      ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘kanjistat.data’
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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 ?
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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
'LazyData' is specified without a 'data' directory
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    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
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    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) compute_all_tests.Rd:22: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) compute_all_tests.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
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    23 | the scale on which to evaluate each subject. \code{stype = "ObsScore"} uses the subject's total score. \code{stype = "Theta"} uses the subject's rank on the \code{thetadist} scale. \code{stype = "ThetaML"} uses the maximum likelihood estimate for the subject on the \code{thetadist} scale. code{stype = "ScoreML"} uses the maximum likelihood estimate for the subject on the overall test score scale.
       |                                                                                                                                                                                                                                                                                                       ^
'LazyData' is specified without a 'data' directory
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    13 | This function adds the {keys} dependencies to your application
       |                        ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
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
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checkRd: (-1) mount_appdata.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{x}{An object of class \code{KinPairData} or {KinPairSimulation}}
       |                                                   ^
Package which this enhances but not available for checking: ‘rkward’
checkRd: (-1) klausuR.answ-class.Rd:17: Lost braces in \itemize; meant \describe ?
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RGeostats’
'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 } )  
       |                                                                                ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘kadmin’
'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) knockoff.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knockoff.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MapPolygon.Rd:20: Lost braces
    20 |   \item{shape}{If the estimators in the function link[KnowBR]{KnowBPolygon} were calculated using an external shape file, it is necessary to indicate the file in this argument. It is not necessary to select any polygon within the file, just to load the whole shape file.}
       |                                                              ^
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    26 |   \item{shape}{If the estimators in the function link[KnowBR]{KnowBPolygon} were calculated using an external shape file, it is necessary to indicate the file in this argument. It is not necessary to select any polygon within the file, just to load the whole shape file.}
       |                                                              ^
'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:
  '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
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'LazyData' is specified without a 'data' directory
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    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}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    ^
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'LazyData' is specified without a 'data' directory
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    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. 
       |                                    ^
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    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]) }
       |                                                                                                        ^
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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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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    46 | 3) Every coordinate yi of the outcome vector y exists in {-1, 1}^n is sampled 
       |                                                          ^
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'LazyData' is specified without a 'data' directory
checkRd: (-1) CreateDataSet.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
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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
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checkRd: (-1) l1_spectralclustering.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) predict.l2boost.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
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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) 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
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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
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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
'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
       |       ^
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   316 |   Gauss-Hermite quadrature rules. A grid of order eqn{K} provides an
       |                                                      ^
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   214 |   item{nu}{This is the degrees of freedom parameter \eqn{\nu}{nu} for
       |       ^
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   214 |   item{nu}{This is the degrees of freedom parameter \eqn{\nu}{nu} for
       |           ^
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    15 |     code{demonoid.hpc}, \code{iterquad}, \code{laplace}, \code{pmc},
       |         ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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
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 ?
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checkRd: (-1) univ.Rd:41: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:42: Lost braces in \enumerate; meant \describe ?
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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’
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'LazyData' is specified without a 'data' directory
checkRd: (-1) TS_diagnostics_plot.Rd:19: Lost braces
    19 | \item{interactive}{\code{logical} input, should be code{TRUE} unless
       |                                                        ^
checkRd: (-1) plot.TS_fit.Rd:29: Lost braces
    29 | \item{interactive}{\code{logical} input, should be code{TRUE} unless
       |                                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
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
'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
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    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^
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    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'},
       |                                                                                                                                               ^
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    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'},
       |                                                                                                                                               ^
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    24 | \code{approach} indicates the algorithm used to get the value. Possible values: {\code{'MAX'},
       |                                                                                 ^
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    24 | \code{approach} indicates the algorithm used to get the value. Possible values: {\code{'MAX'},
       |                                                                                 ^
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    18 | \code{S2mu} computes a estimation of the variance, given a sample {x} with known population mean (denoted by \code{mu}).
       |                                                                   ^
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    20 | \code{sample.quantile} computes a estimation of different quantiles, given a sample {x}, using order statistics.
       |                                                                                     ^
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    28 | article{DBLP:journals/corr/Wu-etal16,
       |        ^
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    29 |   author    = {Liang Wu and Fred Morstatter and Huan Liu},
       |               ^
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    30 |   title     = {SlangSD: Building and Using a Sentiment Dictionary of Slang 
       |               ^
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    32 |   journal   = {CoRR},
       |               ^
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    33 |   volume    = {abs/1608.05129},
       |               ^
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    34 |   year      = {2016},
       |               ^
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    35 |   url       = {http://arxiv.org/abs/1608.05129},
       |               ^
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    36 |   timestamp = {Wed, 17 Aug 2016 23:32:57 GMT}
       |               ^
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    32 | * Neither the name of the {organization} nor the names of its
       |                           ^
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    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"}.
       |                                            ^
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    30 | Laaha, G. and Bl{\"o}schl, G. (2006), Seasonality indices for regionalizing
       |                 ^
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    34 | Mitteilungen, Inst. f{\"u}r Wasserbau u. Ingenieurhydrologie,
       |                      ^
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    31 | Laaha, G. and Bl{\"o}schl, G. (2006), Seasonality indices for regionalizing low flows. Hydrol. Process., 20
       |                 ^
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    13 |   {'uniform', 'normal', 'student-t', 'gamma', 'inv-gamma', 'log-normal'}
       |   ^
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    14 |     \item{X}{a 5000-by-100 matrix, each entry is in {-1,1}.}
       |                                                     ^
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    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}:
       |        ^
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    41 | directory specified by `rmd_dir`. Note that this is an {{rmarkdown}}
       |                                                        ^
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    29 | directory specified by `rmd_dir`. Note that this is an {{rmarkdown}}
       |                                                        ^
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    17 | Test for natural numbers according to ISO 80000-2, that is the set  {0, 1, 2, ...}
       |                                                                     ^
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    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}.}
       |                                                                                                                             ^
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    16 | \item{AIC(x), BIC(x) }{The \code{AIC} or ]code{BIC} value of the first model object.}
       |                                               ^
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    17 | \item{AIC(y), BIC(y) }{The \code{AIC} or ]code{BIC} value of the second model object.}
       |                                               ^
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    78 | $(n_{extreme} + 1) / (B + 1)$.
       |     ^
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     9 | {\code{\link{cdf}}}{: generic distribution function;  }  
       |                    ^
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    10 | {\code{\link{qua}}}{: generic quantile function;  } 
       |                    ^
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    11 | {\code{\link{pel}}}{: fitting of probability distribution function through L-moments. }
       |                    ^
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    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. 
       |                                                                                                                                                                                                                            ^
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    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}.}
       |                                                                                                                               ^
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   104 |         eqn{(2s+1)^{-2}} (this was the default in versions prior to
       |            ^
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   104 |         eqn{(2s+1)^{-2}} (this was the default in versions prior to
       |                    ^
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    15 |     { } \tab {or \code{FBConcuss}=football player with concussion history} \cr
       |     ^
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    14 |     { } \tab {\code{5}=South Asia, \code{6}=East Asia, \code{7}=former Communist countries}\cr
       |     ^
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    17 |     { } \tab {\code{Lifetime Achievement}, \code{Sideman}} \cr
       |     ^
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    17 |     { } \tab {\code{Lifetime Achievement}, \code{Sideman}} \cr
       |     ^
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    12 |     \item{\code{Sex}}{code {F}=female or \code{M}=male}
       |                            ^
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    16 |     { } \tab {for High/Low Synchronization + High/Low Exertion}\cr
       |     ^
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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}.
       |                                                                                                                                                                                                                                                                                                     ^
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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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    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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   112 | \code{"rows"} and code{"columns"}.}
       |                       ^
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    27 |  code{\link{ACSPlan-class}}, 
       |      ^
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    43 | lucas]{Connect_to_db}
       |       ^
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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}.
       |                                                                                                        ^
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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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   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
       |                                                                                                                         ^
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   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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    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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    45 | Kriston, L., H{\"o}elzel, L., Weiser, A., Berner, M., & Haerter, M. (2008).\dQuote{ Meta-analysis: Are 3
       |               ^
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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.}
       |                                                                                                             ^
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    69 | \seealso{\code{\link{lda}}, \code{\link{qda}}, \code{\link{snda}}, \code{\linkS4class{IData}}, \code{\linkS4class{RobEstControl}},code{\link{ConfMat}} }
       |                                                                                                                                       ^
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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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    30 |   if(requireNamespace("ggplot2")){ 
       |                                  ^
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    19 | \eqn{0} means there exists no path for node \eqn{i} and {j}.
       |                                                         ^
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    Bug Fixes
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GNU make is a SystemRequirements.
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    29 | \code{\link{quickfit}}, code{\link{locator}}
       |                             ^
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    14 | 1. \code{\link{estimate_shift}} {Estimate a range shift process.}
       |                                 ^
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    16 | 2. \code{\link{simulate_shift}} {Simulate a range shift process.}
       |                                 ^
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    18 | 3. \code{\link{plot.shiftfit}} {Visualize a range shift process.}
       |                                ^
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    20 | 4. \code{\link{test_rangeshift}} {Test whether a range shift occurred.}
       |                                  ^
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    22 | 5. \code{\link{test_return}} {Test whether a migration was a return migration.}
       |                              ^
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    24 | 6. \code{\link{test_stopover}} {Test whether a stopover occurred during a migration.}
       |                                ^
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    28 | ( if(is.ts(DATA)) { DATA <- as.matrix(data.frame(DATA)) } and a message
       |                   ^
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    17 | \item{inputId}{The code{input} slot that will be used to access the value.}
       |                        ^
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   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}.
       |                                                                                                                                                                                                                                                                                ^
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    14 | (GH^{-1}G).
       |     ^
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    14 | \item{fun}{The function fun should take multiple numbers, and return a single number. For example mean, modal, min or max. It should also accept a na.rm argument (or ignore it, e.g. as one of the 'dots' arguments. For example, length will fail, but function(x, ...){na.omit(length(x))} works. (Specifications from `raster::focal`)}
       |                                                                                                                                                                                                                                                                          ^
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     9 | kernelBiweight <- function(x, mean = 0, sd = 1) {
       |                                                 ^
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    33 | kernelCosine <- function(x, mean = 0, sd = 1) {
       |                                               ^
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    41 | kernelEpanechnikov <- function(x, mean = 0, sd = 1) {
       |                                                     ^
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    58 | kernelOptCosine <- function(x, mean = 0, sd = 1) {
       |                                                  ^
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    65 | kernelRectangular <- function(x, mean = 0, sd = 1) {
       |                                                    ^
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    72 | kernelSquaredCosine <- function(x, mean = 0, sd = 1) {
       |                                                      ^
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    79 | kernelTriangular <- function(x, mean = 0, sd = 1) {
       |                                                   ^
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    86 | kernelTricube <- function(x, mean = 0, sd = 1) {
       |                                                ^
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    93 | kernelTriweight <- function(x, mean = 0, sd = 1) {
       |                                                  ^
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   100 | kernelUniform <- function(x, mean = 0, sd = 1) {
       |                                                ^
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     8 |   \item{X2}{an optional second variable with same length as \code{X}, should the equation be multiple (see Details) {in mm}}
       |                                                                                                                     ^
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    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}.  
       |                                                                                                                                                                                                                                                                                                                                                                                                                              ^
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    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. 
       |                                                                                                                                                    ^
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    90 | expression in braces. For example, the condition "{[ab]*}" is equivalent
       |                                                   ^
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    31 |     {genepos} in the call of \code{Matrix_eQTL_main} function.
       |     ^
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    35 |     the data frames \code{snpspos} and {genepos}.
       |                                        ^
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    46 | \tab Tyberghein L, Verbruggen H, Pauly K, Troupin C, Mineur F and {De Clerck}, O (2012)\cr
       |                                                                   ^
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    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
       |                                                                                                                                                                                                           ^
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    17 | Sigmahat =  (Y^{T} Y)/n;
       |                ^
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    18 | Sigmahat_fit = (Y^{T}  P_fx  Y)/n;
       |                   ^
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    17 | The function computes M^{power} for a symmetric matrix M. }
       |                         ^
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    28 | Della Valle E (2010) Della Valle E 2010 Analisi Multidimensionale dei Dati: la Qualit\'{a} del Lavoro nelle Cooperative Sociali. 
       |                                                                                        ^
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    29 | Unpublished thesis, Seconda Universit\'{a}  degli Studi di Napoli, Capua Italy.
       |                                        ^
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    14 | \code{g} should take a vector input only. Ifcode{g} is \code{NULL}, \code{g} is set to be identity, which is estimation
       |                                                 ^
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    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^
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    36 | Let {1, ... S} be the states of the forest. the Sth state being the oldest.
       |     ^
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    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.
       |                                                                                                                    ^
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    14 | code{stringPlaceExact}: find location of string, using exact match
       |     ^
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    17 | code{stringPlaceFuzzy}: find location of string, using partial match
       |     ^
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    19 | code{stringPlace}: find location of string, generic
       |     ^
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    21 | code{checkFuzzy}: check for "close" string matches
       |     ^
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    25 | The vector of treatment assignments of length \eqn{n}. Must be coded as \eqn{\{0,1} {{0,1}}.
       |                                                                                     ^
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  ‘Data_Correlation.txt’ ‘correlation_FDR_table.txt’
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    79 | A code{$summary} table giving the results of the variation partitioning.  The following table
       |       ^
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Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Problems with news in ‘NEWS.md’:
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    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"}.
       |                                                                                                                                                                                           ^
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    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"}.
       |                                                                                                                                                                                                                                                                                                                                        ^
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    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
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Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Package suggested but not available for checking: ‘INLA’
Auto-generated content requiring editing in Rd file 'bkp.Rd':
  \keyword: ‘~kwd1’
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Package suggested but not available for checking: ‘mvPot’
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    81 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       | ^
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    81 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       |                                      ^
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    84 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       | ^
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    84 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       |                                      ^
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    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.
       |                                    ^
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    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.
       |                                                                                                                                                                                                                                      ^
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    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
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) VIF.Rd:47: Lost braces; missing escapes or markup?
    47 | vif_corrected = vif_basic^{(1/(2*df))}
       |                           ^
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GNU make is a SystemRequirements.
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Package unavailable to check Rd xrefs: ‘microcontax.data’
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checkRd: (-1) readFastq.Rd:62: Lost braces
    62 | code{\link{readFasta}}.
       |     ^
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   426 | \link{MIIVsem}{miivs}
       |               ^
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    60 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
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    62 | Kelly Sovacool, {sovacool@umich.edu}
       |                 ^
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    30 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
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    58 | Kelly Sovacool, {sovacool@umich.edu}
       |                 ^
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    16 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
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    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}
       |                                ^
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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checkRd: (-1) sumKeepAttr.Rd:19: Lost braces
    19 |       (only relevant if code{x} has only one element).}
       |                             ^
checkRd: (-1) PV.Rd:14: Lost braces
    14 | plausible value in turn; with code{rewrite=FALSE} a new data set is
       |                                   ^
Specified C++11: please drop specification unless essential
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
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checkRd: (-1) ml.igls.Rd:62: Escaped LaTeX specials: \&
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    43 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
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    25 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
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    26 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
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    25 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
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    58 |              Note that code{"XGB"} is only available in Mac OS and Linux. moreover,
       |                            ^
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    44 | using reference based imputation as proposed by \doi{10.1080/10543406.2013.834911}{Carpenter et al (2013)}. This approach
       |                                                                                   ^
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  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
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    23 | \code{groupdiff_tau()} computes \eqn{min(x/y, y/x)}, i.e. the smallest symmetric ratio between \eqn{x} and eqn{y}
       |                                                                                                               ^
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   119 | Notes in Computer Science, ISBN 978-3-642-37139-4, pp. 756{770,
       |                                                           ^
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    21 | \item{fim}{the Fisher Information Matrix estimated by Monolix. fim={"sa", "lin"} (default="sa")}
       |                                                                    ^
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    62 | \item Probability of attribution of each unknown individual to each source $p_{u,s}$
       |                                                                               ^
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    69 |   \item{obj$M}{Number of total observations sum_{i=1}^N(pi)}
       |                                                 ^
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     6 | These function takes the output of pgls.iter and uses its list of objects { model fits, optimzations (e.g.AICc)} and performs a weighted average on the ctoefficients estimated in the former by weighting by the latter. The parameters can also optionally be converted to binary by specifying "binary=FALSE" or just running the alias wraper function for assessing evidence of variable importance (Burnham & Anderson 2000).
       |                                                                           ^
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    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)},
       |                           ^
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    23 | It simulates a multivariate response variable, Y_{ij}, that is jth measurement
       |                                                  ^
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    35 |   \item{cum}{a logical value; if  code{TRUE}  (default value), cumulants 
       |                                       ^
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    43 | The maximal value of {d} is \code{20}. If this threshold is exceeded, \code{NA}s
       |                      ^
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   110 |   and code{tvpack}, downloaded in 2005 and again in 2007 from his webpage, 
       |           ^
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    20 | trafo <- function(x){ return(x^2)}
       |                     ^
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   139 | For binary CF models, if{importance.type = 2}, function uses AUC-based variables importances as described by Janitza et al. (2012). Here, the area under the curve instead of the accuracy is used to calculate the importance of each variable. This AUC-based variable importance measure is more robust towards class imbalance. 
       |                         ^
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    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                       ^
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       |                                               ^
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    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                                                          ^
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    16 |   Calculates the stimulus level(s) for a probit model of a psychometric function for given levels of performance.  For a more general version, see \link[MASS]{dose.p} in pkg{MASS}.
       |                                                                                                                                                                              ^
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    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
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    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
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    60 | \item{lnconst}{When inequality constraints are present, \code{lnconst} serves as an adjustment of code{lnInt}. It estimates the logarithm of the proportion of parameter space [0,1]^S that satisfies those inequality constraints, and the log integral term is given by \code{lnInt+lnconst}.
       |                                                                                                       ^
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    38 | The labels on the x-axis. Default is \code{Tree 1} to code{Tree n}.
       |                                                           ^
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    33 |         \item{LogTimes}{Magnification of {-log10(P-value)}; the default is
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    35 |     \item{LODTimes}{Magnification of {LOD score}; the default is 1.2.}
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    10 |            log E(Y_{t+1} | A_t = 0, I_t = 1) = alpha_0 + alpha_1 * time / total_T
       |                    ^
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    42 |   \item{calibrateIntensity_method}{a \code{character} indicating the intensities calibration method used (\code{"TIC"} method by default).  This calibration method can be remplaced by \code{"PQN"} or {"median"}.See \code{calibrateIntensity-methods} of the \code{MALDIquant} R package for details.}
       |                                                                                                                                                                                                         ^
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       |     ^
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    17 |   \item{type}{: Argument that controls the type of parameters to be returned. If \code{type="persons"} (default), a vector with the person parameters is returned. When \code{type="items"} then a vector with the item ranks obtained by the MUDFOLD item selection algorithm is returned. If {type="all"} then a list with both person and item coefficients is returned to the user.
       |                                                                                                                                                                                                                                                                                                ^
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    14 | \item{bivprob}{Bivariate probabilities, {p00, p01, p10, p11}.}
       |                                         ^
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    35 | Returns an object of class 'pcaRes.'  See documentation in the package code{\link[pcaMethods:pcaMethods]{ pcaMethods}}
       |                                                                            ^
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    17 |           \code{U}        \tab The common latent space vectors. U in R^{n x d}\cr
       |                                                                        ^
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    30 | Makowski, D., Jeuffroy, M.-H., Gu\'{e}rif, M., 2004 Bayesian methods for
       |                                    ^
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       |                                    ^
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    15 |   \item{\dots}{... }{possible fixed parameters of the R-function}
       |                     ^
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    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}
       |                           ^
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    74 | \code{\link{glm1path}}, \\code{\link{glm1}}, \code{\link{glm}}, \code{\link{family}}
       |                               ^
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    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.
       | ^
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    22 | @source {Simulated to serve as an example}
       |         ^
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    49 | Takes one or several dois and extracts information from Crossref, then processes them into visual citations with \code{\link{drop_name}}. Requires {rcrossref} > v1.1, see README for further details.
       |                                                                                                                                                    ^
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    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}.
       |                                                                                                                                                                                 ^
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    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}.
       |                                                                                                                                                                                         ^
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Problems with news in ‘NEWS.md’:
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   108 |   \item{gamma}{extra shrinkage parameter for \code{classo} and {sridge} only.}
       |                                                                ^
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   109 |   \item{gamma}{extra shrinkage parameter for \code{classo} and {sridge} only.}
       |                                                                ^
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    69 | Anderson-Darling test." See url{https://github.com/Lakens/perfect-t-test} for
       |                                ^
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   243 | Anderson-Darling test." See url{https://github.com/Lakens/perfect-t-test} for
       |                                ^
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    17 | code{2016}.}
       |     ^
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    27 | In the resulting netSEM model, time was used as a proxy for damp heat exposure stress (S) variable and $P_{max}$ (maximum power generated by the modules) was used as the performance level response ($R$) variable, several mechanistic variables ($M$) were obtained through chemical evaluation methods, including FTIR and TGA  on EVA encapsulant. 
       |                                                                                                           ^
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    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
       |                                                                                                                     ^
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    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
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    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
       |                                                                                                                                              ^
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    33 | A label vector of size n x 1 with elements in {1,2,...,K}
       |                                               ^
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    20 |  \item{las}{numeric in {0,1,2,3}; the style of chromosome labels. 0, always parallel to the track [default]; 1, always horizontal; 2, always perpendicular to the track; 3, always vertical.}
       |                        ^
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    56 | with a matrix response {y}. \code{x1} and \code{x2} are used as
       |                        ^
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   278 | \code{AgeFirstMarij}{Age participant first tried marijuana. Reported for participants aged 18 to 59 years.}
       |                     ^
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    44 | training sample), psi (the value of this observations Psihat(P_{n,B_n}^0)),
       |                                                                ^
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    49 | training sample), psi (the value of this observations Psihat(P_{n,B_n}^0)),
       |                                                                ^
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    19 |   Returns an object of class code{anova}.  These objects represent
       |                                  ^
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    34 | Given \eqn{n} points on a line, \env{input}, each with a corresponding env{f} value this algorithm computes a lifting transform of the (\env{input},\env{f}) data. If lengths are inputted (\env{inputtype="lengths"}), then the gridpoints are taken to be the left endpoints of the intervals defined by the lengths inputted. 
       |                                                                           ^
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    14 |   \item{shape}{either \code{wide} or {long}. Default \code{wide}. See Details.}
       |                                      ^
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    75 |     \item{\code{GetTrace()}:}{retrieve all traced iterations. Returns a list with all the parameters set using the method SetTrace(). See description of snapshot{reference} method for a description of the parameters.  }
       |                                                                                                                                                                  ^
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    35 |               code{plot.type="circle"} and \code{x} is the output of \code{\link{kern.reg.circ.lin}}) or to \code{\link{lines3d}} (if \code{plot.type="circle"})
       |                   ^
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   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.
       |                                                                                                                           ^
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    73 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
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    14 | {Maintainer}: Saurav Guha \email{saurav.iasri@gmail.com}
       | ^
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    21 | \code{MSM.fit} returns an object of class code{MSM.lm} or \code{MSM.glm}, depending on the input model.
       |                                               ^
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    25 | observation at current time step. It should return {xx} (the samples xt) and
       |                                                    ^
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    26 | {logww} (their corresponding log weight).}
       | ^
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    31 |    \item Finally, code{T} is rotated an angle \code{z} about its NEWEST z-axis.
       |                       ^
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    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                               ^
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    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                                         ^
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    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |        ^
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    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |                  ^
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    35 |  function(x, lambda){const_hazard(x, lambda=100)}
       |                     ^
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    87 |  \item{code{addToGroup(userid, groupid)}}{
       |            ^
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    49 |   \code{\link{oglmx}}, code{\link[lmtest]{lrtest}}, code{\link{formula}}.
       |                            ^
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    49 |   \code{\link{oglmx}}, code{\link[lmtest]{lrtest}}, code{\link{formula}}.
       |                                                         ^
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    15 | \item{service}{One of {"locations", "deployments", "deviceCategories", "devices",
       |                       ^
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    18 | \item{method}{One of {"get", "getTree"}}
       |                      ^
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    19 | (numeric) Result code from {0: done, -1: error, -2: fileExists}
       |                            ^
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GNU make is a SystemRequirements.
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    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).
       |                                                                                       ^
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License stub is invalid DCF.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
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    14 | number of individual records. An \code{n} x code{2} dataframe can
       |                                                 ^
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    23 | N is computed from \code{p} length. M is code{10^4} by default.
       |                                              ^
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  ‘Graph_layout_Doptbd_trtE’
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    30 | List/data frame of dimension (number of evaluations) x (4 + n_par) containing input data and results. Columns \code{size} and \code{cost} are optimal holdout size and cost at this size respectively. Parameters N, k1, theta.1, theta.2,...,theta.{n_par} are input data.
       |                                                                                                                                                                                                                                                     ^
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    24 | [GNU Command Line Standards]{http://www.gnu.org/prep/standards/standards.html}
       |                             ^
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     5 | \title{Helper function to calculate other n's given n_{1,T} and allocation ratios}
       |                                                       ^
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    15 | Helper function to calculate other n's given n_{1,T} and allocation ratios
       |                                                ^
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Running examples in ‘OralOpioids-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Brand
> ### Title: Get the Brand name from Health Canada by using the DIN or NDC
> ### Aliases: Brand
> 
> ### ** Examples
> 
> 
> FDA_Opioid_Table <- load_Opioid_Table(no_download = TRUE, country="US")
No updated files were downloaded. The latest Big_data_from was from 2024-01-09
DISCLAIMER: Not a substitute for medical advise. Please note that the output generated by the package should not be substituted for clinical advise and any medication should be only consumed at the advise of a licensed healthcare provider.

Source url of the data: https://download.open.fda.gov/drug/ndc/drug-ndc-0001-of-0001.json.zip
Source url used for dosing: Von Korff M, Saunders K, Thomas Ray G, et al. De facto long-term opioid therapy for noncancer pain. Clin J Pain 2008; 24: 521-527. 2008/06/25. DOI: 10.1097/AJP.0b013e318169d03b.
> HealthCanada_Opioid_Table <- load_Opioid_Table(no_download = TRUE, country="Canada")
Error in open.connection(x, "rb") : cannot open the connection
Calls: load_Opioid_Table ... load_HealthCanada_Opioid_Table -> <Anonymous> -> read_html.default
Execution halted
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    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’
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    69 |   \code{Véase}{Vease} \enc{también}{tambien} \code{\link{distsummin}}, \code{\link{orloca.es-package}}, \code{\link{loca.p}} y \code{\link{distsum}}.
       |               ^
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    80 | \code{Véase}{Vease} \enc{también}{tambien} \code{\link{orloca.es-package}}, \code{\link{loca.p}} y \code{\link{distsum}}.
       |             ^
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    44 | \item{print}{Level of verbosity in Fortran (may not be visible on all terminals); should be an integer between {range, range}, Default: 3}
       |                                                                                                                ^
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    41 | \item{start}{Starting point generation method, see vignettes for details; should be an integer between {range,range}, Default: 2}
       |                                                                                                        ^
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    90 | \item \link{optimise_OSLintervals}: {Approximates the optimal integration intervals. Uses the global
       |                                     ^
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    92 | \item \link{decompose_OSLcurve}: {Calculates component intensities for \strong{all} \code{record_type} measurements.
       |                                  ^
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    97 | fitting with the \emph{RSS_{K-1}} value of the previous fitting and calculates
       |                            ^
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    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                ^
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    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                                ^
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    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/}
       |                                                                                                                                                                 ^
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    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.
       |                                                                                                                     ^
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    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.
       |                                                                                                                                                   ^
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   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/}
       |                                                                                                                                                                 ^
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    15 | \item outcome: codes {I, P, R, NC, O, UH, UO, eUH, eUO, NE}
       |                      ^
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    24 | The input parameters given by the user are {I, P, R, NC, O, UH, UO} and
       |                                            ^
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    25 | the parameter 'e'. The parameter e is multiplied by {UH, UO} internally so as to
       |                                                     ^
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    26 | produce {eUH, eUO}.
       |         ^
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    14 | \item \strong{code:} one of the outcome codes {I, P, R, NC, O, UH, UO, UH, UO, NE}
       |                                               ^
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    20 | code{\link[lintr:lint_package]{lintr::lint_package}} where we hardcode the
       |     ^
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    22 | Christian Vonderach uses the index thus wants file{inst/NEWS.rd} to
       |                                                   ^
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    23 | automatically be in sync with file{./NEWS.md}.
       |                                   ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
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Package suggested but not available for checking: ‘CorShrink’
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    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.
       |                                                                                                                      ^
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   112 | \item `"{exp(estimate) * std.error}"
       |         ^
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    90 | \item `"{exp(estimate) * std.error}"
       |         ^
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    11 |     \item{\code{roof_tile}}{a numeric vector, roof_tile}{dummy, roof made out of tiles =1}
       |                                                         ^
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    25 |     \item{\code{railways}}{a numeric vector, railways}{distance to nearest railway in meters}
       |                                                       ^
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    26 |     \item{\code{nature_SLD}}{a numeric vector, nature_SLD}{distance to nearest nature area in meters}
       |                                                           ^
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Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘Rmpi’
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    15 | Default is code{FALSE}.}
       |                ^
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    16 | code{TRUE}.}
       |     ^
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    15 | Default is code {FALSE}.}
       |                 ^
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    18 | Default is code {FALSE}.}
       |                 ^
Running ‘run-all.R’ [22s/28s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > library(BBmisc)
  
  Attaching package: 'BBmisc'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  > library(ParamHelpers)
  > 
  > test_check("ParamHelpers")
  [ FAIL 2 | WARN 3 | SKIP 1 | PASS 1047 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test_convertParamSetToIrace.R:4:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_convertParamSetToIrace.R:71:3'): convertParamSetToIrace uses correct boundaries ──
  Error in `params$boundary <- `*vtmp*``: cannot add bindings to a locked environment
  Backtrace:
      ▆
   1. └─ParamHelpers::convertParamSetToIrace(ps) at test_convertParamSetToIrace.R:71:3
  ── Error ('test_convertParamSetToIrace.R:85:3'): convertParamSetToIrace work with vecparam ──
  Error in `params$boundary <- `*vtmp*``: cannot add bindings to a locked environment
  Backtrace:
      ▆
   1. └─ParamHelpers::convertParamSetToIrace(ps) at test_convertParamSetToIrace.R:85:3
  
  [ FAIL 2 | WARN 3 | SKIP 1 | PASS 1047 ]
  Error: Test failures
  Execution halted
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    21 |   \item{...}{Other options including {type} which refers to the
       |                                      ^
Malformed Description field: should contain one or more complete sentences.
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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’
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.}
       |                       ^
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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   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.
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    31 |     \code{pars2[1]} {set the conditioning on non-extinction of the clade (1) or not (0) \cr \cr}
       |                     ^
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    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}
       |                     ^
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    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}
       |                    ^
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    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
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Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) PCM_ABC.Rd:106: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) simulate_phylproc.Rd:58-59: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) simulate_phylproc.Rd:67: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) MiniBenchmarkRvsCpp.Rd:16: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) MiniBenchmarkRvsCpp.Rd:18: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd file 'pedroni99.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'pedroni99m.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
checkRd: (-1) getPCRAData.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getPCRAData.Rd:29: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) pcvpcr.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
checkRd: (-1) pcvpls.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
Package suggested but not available for checking: ‘cmdstanr’
Package suggested but not available for checking: ‘PythonInR’
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: 
       |                                     ^
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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
       |           ^
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checkRd: (-1) embedded.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) embedded.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
checkRd: (-1) ensemble.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) ensemble.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
checkRd: (-1) staged.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) staged.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
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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
       |                                                                     ^
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    98 | \doi{10.1016/j.cageo.2008.10.011}{Hiemstra et al. (2009)}.
       |                                  ^
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   100 | Method \code{"d"} was developed by \doi{10.1007/s11004-012-9434-1}{Desassis & Renard (2012)}.
       |                                                                   ^
GNU make is a SystemRequirements.
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   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: 
       |                 ^
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   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 
       |                      ^
Specified C++11: please drop specification unless essential
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checkRd: (-1) classificationMetrics.Rd:85: Lost braces; missing escapes or markup?
    85 |   will use some extra notation, namely: TP = #{p == + & t == +} ; FP =
       |                                               ^
checkRd: (-1) classificationMetrics.Rd:86: Lost braces; missing escapes or markup?
    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |    ^
checkRd: (-1) classificationMetrics.Rd:86: Lost braces; missing escapes or markup?
    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |                              ^
checkRd: (-1) classificationMetrics.Rd:86: Lost braces; missing escapes or markup?
    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |                                                       ^
checkRd: (-1) classificationMetrics.Rd:87: Lost braces; missing escapes or markup?
    87 |   ; P = #{t == +} ; N = #{t == -}; Finally, for some descriptions
       |          ^
checkRd: (-1) classificationMetrics.Rd:87: Lost braces; missing escapes or markup?
    87 |   ; P = #{t == +} ; N = #{t == -}; Finally, for some descriptions
       |                          ^
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checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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    15 | A code{\link{marked_petrinet}}
       |       ^
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'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘animation.gif’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) PhageCocktail.Rd:100-103: Lost braces
   100 | "Result": {
       |           ^
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   105 | "BacteriaLysed": {
       |                  ^
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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.
       |                            ^
checkRd: (-1) phasePlaneAnalysis.Rd:84: Lost braces; missing escapes or markup?
    84 | identified {see (3) above}, if this point is a saddle then the manifolds are
       |            ^
Found the following files/directories:
  ‘test.pdf’
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checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
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GNU make is a SystemRequirements.
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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
       |     ^
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File 'data/datalist' is out-of-date:
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    eyedata
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    x y
Please re-create using tools::add_datalist(force = TRUE).
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    27 | if (interactive()) {
       |                    ^
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    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                       ^
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    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                                 ^
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    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                                              ^
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   127 | rank skipped. For example {1, 0, 2, 1}, ranks the first and fourth items in
       |                           ^
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
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   125 | function serves for the purpose of spot-testing for any pre-specified {n,
       |                                                                       ^
Package suggested but not available for checking: ‘fgsea’
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    19 |     \item{RNAMES}{code{row.names} if \code{x} is a matrix or data.frame,
       |                       ^
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   103 | {'ALL', 'AFF', 'UNAFF', 'ALL(QT)', 'ALL(NP)'}), A1 (Allele 1; usually minor),
       | ^
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    21 | delta_k = log(a_k - a_{k+1})
       |                       ^
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    29 | logical. If code{TRUE} all the q variable are assumed to have the same mean.
       |                 ^
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    15 | When \\code{y0} is not specified, the lowest value of the y-axis is used.}
       |            ^
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    24 | \\code{\\link[graphics]{par}}.}
       |       ^
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    24 | \\code{\\link[graphics]{par}}.}
       |                        ^
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   129 |  in factors are are shown as a special factor level code{"?"}. They can be
       |                                                         ^
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    29 | code{\link{help}}
       |     ^
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    32 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    20 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘Rmpi’
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    16 | Additional arguments are replaced with "{n} more".
       |                                         ^
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pmartRdata’
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   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                              ^
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   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                                                         ^
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    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                   ^
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    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                              ^
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   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`.}
       |                                                                                     ^
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'LazyData' is specified without a 'data' directory
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Package unavailable to check Rd xrefs: ‘INLA’
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    34 | \item{bw}{function describing bandwidth selection (see ?gmm for alternatives). Standard is that the bandwidth depends on the sample length $T$ by $m(T)=T^{1/5}$.}
       |                                                                                                                                                           ^
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Package suggested but not available for checking: ‘pollimetrydata’
checkRd: (-1) inputData.Rd:94: Lost braces
    94 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
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    95 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
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    81 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
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    82 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
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    14 | Number {25, 50, 75}
       |        ^
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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’
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    31 |   the weight vectors \bold{{w}^{i}} corresponds to class \eqn{i}{i}.
       |                                ^
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    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.
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    17 | objects created using code{tfam_inertia}.}
       |                           ^
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    32 |        code{\link{inertia}} measures asymptotic population density relative to stable
       |            ^
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    33 | item{inertia}{inertias of perturbed matrices}
       |     ^
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    33 | item{inertia}{inertias of perturbed matrices}
       |              ^
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Problems with news in ‘NEWS.md’:
No news entries found.
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Package suggested but not available for checking: ‘faux’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) 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
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    22 | the \code{conflict} argument of {powerjoin}'s join functions. \code{coalesce_xy()} is
       |                                 ^
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    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",
       |                                              ^
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    37 | only be used in the \code{x} and \code{y} arguments of {powerjoin} join functions. No
       |                                                        ^
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    26 | \item{model}{Determines of model fit is such that there are p_{it}s (model=1) or
       |                                                               ^
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   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
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   143 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
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   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
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   145 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
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   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
GNU make is a SystemRequirements.
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
'LazyData' is specified without a 'data' directory
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     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
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    39 | \item wrapping a function argument in two curly braces (e.g. `{{arg}} > 0) means
       |                                                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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    20 | the (pre)registration form specification (in {preregr} format), see the
       |                                              ^
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    23 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
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    26 | For an introduction to working with {preregr} (pre)registrations,
       |                                     ^
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    75 | This function creates an R Markdown template from a {preregr}
       |                                                     ^
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    77 | Sheet holding the (pre)registration form specification (in {preregr}
       |                                                            ^
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    81 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
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Problems with news in ‘NEWS.md’:
No news entries found.
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Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
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    20 | The user does not put these directly into this function, but rather uses code{ode} in the \code{deSolve} package.
       |                                                                              ^
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    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
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    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
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    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
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    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
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    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
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    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
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    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
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    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
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    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
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    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
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    20 | \item{lower.v}{logical, if TRUE the specified percentile.value is the upper limit for the mean (or the median or the mode) at the specified confidence level (percentile). If {FALSE} the specified percentile.value is the lower limit for the mean (or the median or the mode) at the specified confidence level (percentile). The default is FALSE.}
       |                                                                                                                                                                               ^
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    91 |     \code{OSME} \tab Output-oriented scale-mix efficiency score \emph{(code{orientation = "out"})}\cr
       |                                                                            ^
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     9 |                 \item{CD}{}{Character disorder scale score}
       |                            ^
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    40 |   by the code{kcachegrind} program available on some operating
       |              ^
Package required but not available: ‘pathwayTMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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    32 | \item{global}{Logical. If \code{TRUE} ({default}), a global density plot is
       |                                        ^
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    12 | \item{model}{the item model to use. Accepts \code{grm} or {gpcm}.}
       |                                                           ^
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    15 | \item{value}{code{data.frame} or code{data.table}}
       |                  ^
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    15 | \item{value}{code{data.frame} or code{data.table}}
       |                                      ^
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    21 | response variable. Vector of length emph{n}, assumed to be quantitative.
       |                                         ^
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    20 | Implementation of the {SnowballC} stemmer. Note that punctuation and capital letters 
       |                       ^
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    20 | Implementation of the {SnowballC} stemmer. Note that punctuation and capitals letters 
       |                       ^
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     7 | See the {rfeel} package now: http://github.com/ColinFay/rfeel}
       |         ^
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    20 | See the {rfeel} package now: http://github.com/ColinFay/rfeel
       |         ^
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    43 | S{Sulewski, P. (2020). \emph{Normal Distribution with Plasticizing Component,} Communications in Statistics ? Theory and Method 51(11), 3806-3835.}
       |  ^
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    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.}
       |                   ^
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    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.}
       |                                                                                         ^
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    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}
       |                         ^
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    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}
       |                         ^
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    39 |                                                         continuous = function(Xytrain){ #defalt is OLS regression
       |                                                                                       ^
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    43 |                                                         incidence = function(Xytrain){ #default is logistic regression
       |                                                                                      ^
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    48 |                                                         survival = function(Xytrain){ #default is Weibull regression
       |                                                                                     ^
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    66 |                                         function(mod, Xyleftout){
       |                                                                 ^
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    74 |                                         function(results, indices_1_1, indices_0_0, indices_0_1, indices_1_0){
       |                                                                                                              ^
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    20 | @Article{Bloemberg2010,
       |         ^
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    30 | Article{Wehrens2015,
       |        ^
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    62 | \item{yi}{Numeric vector of length code{k} with observed effect size
       |                                        ^
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    65 | \item{vi}{Numeric vector of length code{k} with sampling variances.}
       |                                        ^
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     5 | \title{PubMed wordcloud using function 'wordcloud' of package {wordcloud}}
       |                                                               ^
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    32 | This function just call 'wordcloud' from package {wordcloud}. See package {wordcloud} for more details about the parameters.
       |                                                  ^
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    32 | This function just call 'wordcloud' from package {wordcloud}. See package {wordcloud} for more details about the parameters.
       |                                                                           ^
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    10 | \format{the \code{PvarQuantileDF} is a \code{data.frame} with fields \code{prob} an {Qaunt}. 
       |                                                                                     ^
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    42 | \item{no_zi_idx}{List of pairs {(i, j)} where zero inflation is not allowed. To
       |                                ^
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    35 | \item{no_zi_idx}{List of pairs {(i, j)} where zero inflation is not allowed. To
       |                                ^
Running examples in ‘PvSTATEM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generate_plate_report
> ### Title: Generate a report for a plate.
> ### Aliases: generate_plate_report
> 
> ### ** Examples
> 
> 
> plate_file <- system.file("extdata", "CovidOISExPONTENT_CO_reduced.csv", package = "PvSTATEM")
> # a plate file with reduced number of analytes to speed up the computation
> layout_file <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx", package = "PvSTATEM")
> note <- "This is a test report.\n**Author**: Jane Doe \n**Tester**: John Doe"
> 
> plate <- read_luminex_data(plate_file, layout_file, verbose = FALSE)
> example_dir <- tempdir(check = TRUE) # a temporary directory
> generate_plate_report(plate,
+   output_dir = example_dir,
+   counts_lower_threshold = 40,
+   counts_higher_threshold = 50,
+   additional_notes = note
+ )
Generating report...This will take approximately 30 seconds.
Error in file(con, "w") : cannot open the connection
Calls: generate_plate_report ... <Anonymous> -> <Anonymous> -> write_utf8 -> writeLines -> file
In addition: Warning message:
In file(con, "w") :
  cannot open file 'plate_report_template.knit.md': Read-only file system
Execution halted
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    10 |   \item{listRanef}{{\emph{ranef(model)}} object where {\emph{model}} is an { \emph{lmer}} object.}
       |                                                                            ^
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No news entries found.
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   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}.
       |                                                                                                                                                                                         ^
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   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}.
       |                                                                                                                                                                                                                                                   ^
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    10 | \item{trueLoc}{A vector of one or more numbers in the set {1, 2, ..., nSubjects} whose locations are to be hidden.}
       |                                                           ^
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    12 | \item{nSubjects}{An integer larger than 1 used to define the set {1, 2, ..., nSubjects}.}
       |                                                                  ^
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) IPWE_mean_IndCen.Rd:54-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{case}{string. One of {"a", "b", "c"}, corresponding to three models.}
       |                            ^
checkRd: (-1) simJLSDdata.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:32-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) find_lcp.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:63-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:18-19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:23-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) als_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) qualpal.Rd:22-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) qualpal.Rd:30-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cqs.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cqs.Rd:33-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cqs.Rd:37-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) llqr.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) llqr.Rd:38-41: Lost braces in \itemize; \value handles \item{}{} directly
'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
'LazyData' is specified without a 'data' directory
checkRd: (-1) quarries.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:20-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:26-28: Lost braces in \itemize; meant \describe ?
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) 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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘bootmlm’
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
checkRd: (-1) bugs.Rd:158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:166: Lost braces in \itemize; meant \describe ?
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
Found the following HTML validation problems:
Repository.html:125:1 (Repository.Rd:129): Warning: trimming empty <ul>
checkRd: (-1) post_RA_fits.Rd:61: Lost braces; missing escapes or markup?
    61 |     \item{\code{H(po_{bm_{n.bm}}, po_act)}:}{ last benchmark prior bm_{n.bm} inducing the fit \code{fits.bm[[n.bm]]} and actual prior}
       |                                                                       ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot-methods.Rd:98: Lost braces
    98 |                         The line width, a emph{positive} number, defaulting to \code{1}. The interpretation is device-specific, and some devices do not implement line widths less than one (see the help on the device for details of the interpretation). Note that this paramater can also represent a list of different line widths, with length of the list corresponding to the number of \code{DVH} or \code{DVH.list} objects (if \code{plot.type="individual"}, number of line widths should correspond to number of individual \code{DVH} objects).
       |                                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) DataSet-class.Rd:25: Lost braces; missing escapes or markup?
    25 | Example: {fromField:"val1", toField:"value"}.}
       |          ^
checkRd: (-1) amTimeSeries.Rd:119: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amTimeSeries.Rd:120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amTimeSeries.Rd:121: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amTimeSeries.Rd:122: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getCurrentStockData.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getCurrentStockData.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTransformTS.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTransformTS.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:114: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:156: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:157: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) makeDesignMatrix.Rd:16: Lost braces; missing escapes or markup?
    16 | is randomized to a certain treatment {j}, the entry of \code{(i,j)} of the
       |                                      ^
'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) 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}.}
       |                                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) user_log_dir.Rd:48: Lost braces
    48 | \\env{$XDG_CACHE_HOME} if defined
       |      ^
checkRd: (-1) max.Rd:17: Lost braces
    17 | Returns the maximum of all values in a vector by passing \{code{\link{max}} as \code{fn} argument to \code{\link{univar}} function.
       |                                                                ^
checkRd: (-1) min.Rd:17: Lost braces
    17 | Returns the minimum of all values in a vector by passing \{code{\link{min}} as \code{fn} argument to \code{\link{univar}} function.
       |                                                                ^
checkRd: (-1) rapport.inputs.Rd:26: Lost braces
    26 |     \item \emph{dataset inputs}, i.e. the inputs that refer to named element of an |code{R} object provided in \code{data} argument in \code{rapport} call. Currently, \code{rapport} supports only \code{data.frame} objects, but that may change in the (near) future.
       |                                                                                         ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) RasterList-Package.Rd:20: Lost braces
    20 | {\code{\link{rasterList}}}{: it is the constructor of a  \code{\link{RasterList-class}} object from a generic \code{object}, it also transforms a \code{\link{RasterList-class}} into another one throungh a function argument. }
       |                           ^
checkRd: (-1) RasterList-Package.Rd:22: Lost braces
    22 | {\code{\link{rasterListFun}}}{: it is a function that constructs  a  particular \code{\link{RasterList-class}} object in which the objects are \code{function}-type. }
       |                              ^
checkRd: (-1) RasterList-Package.Rd:24: Lost braces
    24 | {\code{\link{RasterListApply}}}{: it is a function that allows to operate among two or more \code{\link{RasterList-class}} objects defined in the same spatial extent through a generic function \code{fun(x,y,...)} where \code{x} and \code{y} are each cell/element of two \code{\link{RasterList-class}} objects given as arguments \code{x} and \code{y} of \code{\link{RasterListApply}}.}
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) as_mcmc.list.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Convert a rater_fit object to a {coda} \code{mcmc.list} object.}
       |                                        ^
checkRd: (-1) as_mcmc.list.Rd:16: Lost braces; missing escapes or markup?
    16 | Convert a rater_fit object to a {coda} \code{mcmc.list} object.
       |                                 ^
checkRd: (-1) as_mcmc.list.Rd:13: Lost braces; missing escapes or markup?
    13 | A {coda} mcmc.list object.
       |   ^
GNU make is a SystemRequirements.
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:109-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:115-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:121-124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:125-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:128-138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) S1.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{m_bar}{the sample vector of moments for a specified vector $(h_{a,r},y)$}
       |                                                                      ^
checkRd: (-1) S1.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{N_k}{index of the $ h_{a,r}$ function considered}
       |                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) rbm.haplos.power.Rd:35: Lost braces; missing escapes or markup?
    35 |   \item{simus.haplos}{ Which method to simulate the data, if \code{simus.haplos="freqs"}, {rbm.haplos.freqs()} is used, otherwise \code{rbm.haplos.thresholds()} is used.}
       |                                                                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘raybevel’
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) R.cache-package.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) R.cache-package.Rd:31-34: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
checkRd: (-1) mig_calculate_rc.Rd:28: Lost braces; missing escapes or markup?
    28 | \item pre-working age: {a1, alpha1}
       |                        ^
checkRd: (-1) mig_calculate_rc.Rd:29: Lost braces; missing escapes or markup?
    29 | \item working age: {a2, alpha2, mu2, lambda2}
       |                    ^
checkRd: (-1) mig_calculate_rc.Rd:30: Lost braces; missing escapes or markup?
    30 | \item retirement: {a3, alpha3, mu3, lambda3}
       |                   ^
checkRd: (-1) mig_calculate_rc.Rd:31: Lost braces; missing escapes or markup?
    31 | \item post retirement: {a4, lambda4}
       |                        ^
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.RData’
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
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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) RcmdrPlugin.MA-package.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ROpenOffice’
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.
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     8 | of the form z_n = g(z_{n-1}) + epsilon. A normal distribution is assumed for the innovations.
       |                       ^
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Package suggested but not available for checking: ‘fgsea’
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Problems with news in ‘NEWS.md’:
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RcppUUID.Rcheck/00install.out’ for details.
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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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
       |                                      ^
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   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)). }
       |   ^
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    15 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
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    28 | space P = {p_1, ..., p_k}, such that each p_i is the farthest 
       |           ^
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Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
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    15 | line in the file to determine the {code{skip}} value.}
       |                                   ^
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    15 | line in the file to determine the {code{skip}} value.}
       |                                        ^
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    19 | \item{pi}{An estimate of the stationary probabilities of four states {(0,0), (0,1), (1,0), (1,1)}.}
       |                                                                      ^
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    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
File ‘readxl/libs/readxl.so’:
  Found non-API calls to R: ‘Rf_StringFalse’, ‘Rf_StringTrue’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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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.
       |                                                           ^
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    33 | Wikipedia (2018): \dQuote{Automobilindustrie --- Wikipedia{,} Die freie Enzyklopaedie}. \url{https://de.wikipedia.org/wiki/Automobilindustrie} (accessed October 14, 2018). 
       |                                                           ^
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Malformed Description field: should contain one or more complete sentences.
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   112 | and another argument named {zCoef} for covariate coefficient vector.
       |                            ^
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    13 | not that quotes need to be escaped (code{\"}).}
       |                                         ^
'LazyData' is specified without a 'data' directory
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
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    21 | NUTS typologies, defaults to code{"geo_var".}}
       |                                  ^
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    19 | NUTS typologies, defaults to code{"geo_var".}}
       |                                  ^
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    32 | In all base log-likelihood functions, we have dropped any additive terms that are independent of the distribution parameter, e.g. constant terms or those terms that are dependent on the response variable only. This is done for computational efficiency. Therefore, these functions cannot be used to obtain the absolute values of log-likelihood functions but only in the context of optimization and/or sampling. Users can write thin wrappers around these functions to add the constant terms to the function value. (Derivatives do not need correction. For binomial family, all factorial terms are ignored since they only depend on \code{n} and {y}.)
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}} and \code{\link[graphics]{matplot}}). 
       |                                ^
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    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}}.
       |                                ^
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    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}.
       |                                                           ^
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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.
       |                                                                                                                                   ^
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checkRd: (-1) rentrez.Rd:17-21: Lost braces
    17 | /enumerated{
       |            ^
'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.
       |                                          ^
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Found the following files/directories:
  ‘PackageCites.bib’
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    44 | ## chunk "item 1" {
       |                   ^
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checkRd: (-1) repo_dependencies.Rd:51-53: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking:
  'clusterProfiler', 'enrichplot'
'LazyData' is specified without a 'data' directory
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    16 |     \item{\code{Smoker}}{Mother a smoker? code{No}, \code{Yes}}
       |                                               ^
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    35 |      {z_probs2 sqrt((n-1)/n) = t_probs,n-1}
       |      ^
GNU make is a SystemRequirements.
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checkRd: (-1) resistance.Rd:52: Lost braces
    52 |     \item B. Bollob\'{a}s, 1998.  \emph{Modern Graph Theory}.  Springer.
       |                      ^
Package suggested but not available for checking: ‘resourcecodedata’
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    44 | \item{perl}{Use perl-like regex? Defaults to {FALSE}.}
       |                                              ^
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   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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    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
       |                                                                         ^
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    76 | \\code{\link{fs_auth}} \code{\link{fs_browse}}
       |       ^
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'LazyData' is specified without a 'data' directory
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    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
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   450 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
checkRd: (-1) RiemannianMetric.Rd:484-487: Lost braces
   484 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
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   588 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
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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
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    53 | /url{http://www.sawtoothsoftware.com/help/lighthouse-studio/manual/index.html?hid_web_cbc_exporting.html}
       |     ^
'LazyData' is specified without a 'data' directory
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     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’
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    34 | origin, v_1, -v_1, v_2, -v_2, v_3, -v_3,..., v_{(numberOfClusters-1)/2},
       |                                                ^
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    35 | -v_{(numberOfClusters-1)/2} (if \code{numberOfClusters} is odd)
       |    ^
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    36 | origin, v_1, -v_1, v_2, -v_2, v_3, -v_3,..., v_{(numberOfClusters-1)/2}
       |                                                ^
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checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:33-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:35-36: Lost braces
    35 |    \item{pam_cluster_64_7_5715},{N=64, seven clusters with 5715 vectors per
       |                                 ^
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:37-38: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:39-40: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:21-22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:23-24: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Auto-generated content requiring editing in Rd file 'meanridit.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'meanridits.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'riditsrefgroup.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'seridit.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'seridits.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'toridit.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Specified C++11: please drop specification unless essential
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) iex.chart.Rd:23: Lost braces; missing escapes or markup?
    23 | r takes only of of the values accepted IN API request. {"5y", "2y", "1y", "ytd", "6m", "3m", "1m", "1d"}
       |                                                        ^
checkRd: (-1) descrip.Rd:122: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:123: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:124-125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:126-128: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:129-133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:134-135: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:136-138: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:139-140: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:141-144: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:145-146: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:147: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:148: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:149: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following assignments to the global environment:
File ‘rim/R/engine.R’:
  assign(varname, output.data, envir = knitr::knit_global())
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) riskParityPortfolio.Rd:163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:168: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:169: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskPredict.Rd:38: Lost braces
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       | ^
checkRd: (-1) riskPredict.Rd:38: Lost braces
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       |     ^
checkRd: (-1) riskPredict.Rd:38: Lost braces; missing escapes or markup?
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       |             ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       | ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |     ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces; missing escapes or markup?
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |             ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |                      ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces; missing escapes or markup?
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |                              ^
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
'LazyData' is specified without a 'data' directory
checkRd: (-1) RivivcA.Rd:7: Lost braces
     7 | This is the major function to be called where numerical convolution ad/or deconvolution might be used for a linear in vitro in vivo correlation level A. It performes either numerical convolution via /code{NumConv()} or deconvolution via /code{NumDeconv()} and correlates their results with the known.data object via linear regression \code{lm()}. If you just want raw results of convolution/deconvolution then call explicitely \code{\link{NumConv}} or \code{link{NumDeconv}}
       |                                                                                                                                                                                                             ^
checkRd: (-1) RivivcA.Rd:7: Lost braces
     7 | This is the major function to be called where numerical convolution ad/or deconvolution might be used for a linear in vitro in vivo correlation level A. It performes either numerical convolution via /code{NumConv()} or deconvolution via /code{NumDeconv()} and correlates their results with the known.data object via linear regression \code{lm()}. If you just want raw results of convolution/deconvolution then call explicitely \code{\link{NumConv}} or \code{link{NumDeconv}}
       |                                                                                                                                                                                                                                                   ^
Non-standard file/directory found at top level:
  ‘jri’
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
License stub is invalid DCF.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'DoubletFinder', 'fgsea', 'RcppPlanc'
'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
Package suggested but not available for checking: ‘rnaturalearthhires’
'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) 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
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: \&
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)
       |                    ^
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’.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rmpi.Rcheck/00install.out’ for details.
'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}
       |                            ^
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: \_
Package which this enhances but not available for checking: ‘Rmpi’
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
'LazyData' is specified without a 'data' directory
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) 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 ?
Specified C++11: please drop specification unless essential
'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) descriptiveTable.Rd:18: Lost braces
    18 | other object type that does not fail in code{model.frame(object)}.}
       |                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ROI_plugin_build_equality_constraints.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_equality_constraints.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:29: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_solve.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) update_tidy_omic.Rd:16-17: Lost braces
    16 | in \code{updated_tidy_data} (names) and the table {features, samples,
       |                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) read_ascii.Rd:33: Lost braces
    33 | \item{respondent_pattern}{For use when the file does not contain a line for every card for every respondent (or contains extra lines that correspond to no respondent), a regular expression that matches the file's respondent identifier; e.g., if the respondent number is stored in the first four digits of each line, preceded by a space, "(?<=^\\s)\\d{4}".}
       |                                                                                                                                                                                                                                                                                                                                                               ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                ^
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                       ^
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                                  ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RandomFields’
checkRd: (-1) Clyde.Rd:8: Lost braces
     8 | These data record the water quality, in terms of dissolved oxygen (\code{DO}) on a percentage scale, at a number of sampling stations (\code{Station}) on the River Clyde.  The date (\code{Day}, \\code{Month}, \code{Year}) is also available, along with the day of the year (\code{Doy} between 1 and 365) and an identified (\code{id}) of the survey on which each measurement was made.
       |                                                                                                                                                                                                         ^
checkRd: (-1) rp.pos.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:31-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:43: Lost braces in \itemize; meant \describe ?
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) rpivotTable.Rd:60: Lost braces; missing escapes or markup?
    60 | An example is: onRefresh=htmlwidgets::JS("function(config) { Shiny.onInputChange('myPivotData', config); }")
       |                                                            ^
checkRd: (-1) plotImage.blcTree.Rd:17: Lost braces
    17 |   \item{method}{Method to determine width of columns that represent classes: \dQuote{weight} (subject weight in class) or dQuote{binary} (depth in tree).}
       |                                                                                                                                 ^
checkRd: (-1) plotImage.glcTree.Rd:16: Lost braces
    16 |   \item{method}{Method to determine width of columns that represent classes: \dQuote{weight} (subject weight in class) or dQuote{binary} (depth in tree).}
       |                                                                                                                                 ^
checkRd: (-1) get.poetry.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{output}{Can be any or a combination of the input terms {'author', 'title', 'lines', 'linecount'}. If NULL, all
       |                                                              ^
'LazyData' is specified without a 'data' directory
Package required but not available: ‘TDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Auto-generated content requiring editing in Rd file 'PPGrectRightAng4.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'PPGrectRightAng5.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'PPGrectRightAng7.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'PPNestdiv.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'PPdiv.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'PPrect.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'PPrightAng.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'SpaceFilling.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
checkRd: (-1) rpql.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.tg.Rd:18: Lost braces; missing escapes or markup?
    18 | Renames the \code{class(tg)["name"]} attribute and sets {class(tg)["type"] <- "TextGrid"} (if it is not already set)
       |                                                         ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) psel.Rd:83: Lost braces; missing escapes or markup?
    83 | For example, a \code{top=1} preference selection on the tuples {(a=1, b=1), (a=1, b=2)}
       |                                                                ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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) 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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) mrrr.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:69-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:71-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:74: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) landslides.Rd:11-21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) landslides.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) landslides.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) landslides.Rd:22-26: Lost braces
    22 | \item \code{dem} {Digital elevation model given as a .Rd grid, i.e. a list
       |                  ^
checkRd: (-1) landslides.Rd:27-28: Lost braces
    27 | \item \code{study_area} {An \code{sf}-object representing the outlines of
       |                         ^
checkRd: (-1) rsaga.get.modules.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rsaga.get.modules.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rsaga.get.modules.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
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
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-release-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_Outputfile’,
    ‘R_TempDir’, ‘R_Visible’, ‘getInputHandler’, ‘ptr_R_Busy’,
    ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’, ‘ptr_R_ReadConsole’,
    ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’, ‘ptr_R_WriteConsole’,
    ‘ptr_R_WriteConsoleEx’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Package suggested but not available for checking: ‘Vdgraph’
Unknown package ‘Vdgraph’ in Rd xrefs
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: ‘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
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) box_m.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) box_m.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) box_m.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) box_m.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wilcox_test.Rd:91: Lost braces; missing escapes or markup?
    91 |  distribution of \code{(u+v)/2}, where \code{u} and {v} are independent, each
       |                                                     ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                              ^
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
GNU make is a SystemRequirements.
checkRd: (-1) tw_options.Rd:22: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) grapes-.-times-grapes.Rd:6-9: Lost braces
     6 | "round.torch.Tensor" <- function(input) {
       |                                         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) rt_GET.Rd:13: Lost braces
    13 | code{\link[httr]{GET}} (\code{TRUE}) or not (\code{FALSE})}
       |     ^
checkRd: (-1) rt_POST.Rd:13: Lost braces
    13 | code{\link[httr]{POST}} (\code{TRUE}) or not (\code{FALSE})}
       |     ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
checkRd: (-1) rts.Rd:32: Lost braces
    32 | If a name of a raster time series file is provided for the \code{x} argument, it acts the same as code{\link[rts]{read.rts}}.
       |                                                                                                       ^
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘Tsttwalk.dat’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'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
       |                                                                    ^
Package suggested but not available for checking: ‘rxode2et’
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  ‘nimble’ ‘nimbleAPT’
  Please use :: or requireNamespace() instead.
  See section 'Suggested 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) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^
Package which this enhances but not available for checking: ‘glmmADMB’
checkRd: (-1) Valpha.Rd:15: Lost braces; missing escapes or markup?
    15 |   \item{V}{a numeric vector with (i,j) entry: V[i,j] = P(theta_{i} >= theta[alpha_{j}]|data) }
       |                                                                ^
checkRd: (-1) Valpha.Rd:15: Lost braces; missing escapes or markup?
    15 |   \item{V}{a numeric vector with (i,j) entry: V[i,j] = P(theta_{i} >= theta[alpha_{j}]|data) }
       |                                                                                   ^
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'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}).
       |                               ^
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    48 |   -df/2*log|L(2*Sigma)L'| -1/2*tr{ (L(2*Sigma)L')^-1 L(-D)L' }
       |                                  ^
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     9 |   equal to exp{b1*x_1ij + ... + bp*x_pij}, where beta=(b1,b2,...,bp) is
       |               ^
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    10 |   a vector of log-conductance values of the covariates {x_kij}.  Each
       |                                                        ^
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    73 |   a vector of log-conductance values of the covariates {x_kij}.  Each
       |                                                        ^
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    31 | This period can be either {"month", "week", "day"}, 
       |                           ^
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    32 | {"months", "weeks", "days"} or
       | ^
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    33 | {12, 52, 365}. This function creates a new time series with the required 
       | ^
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     6 |  emph{Single Interior Knot} at the MSE Optimal m-Extent of Shrinkage. The
       |      ^
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    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}.}
       |                                                                                                                                                   ^
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    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}.}
       |                                                                                                                                                                 ^
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    13 | \item{dataY}{Vector of length n containing {0, 1}-valued observations of the dependent variable y.}
       |                                            ^
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    10 | \item{fit}{an object of class{lm}, i.e. the output from \code{\link{lm}}.}
       |                              ^
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    37 |         class {StatHMMR}).
       |               ^
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    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.
       |         ^
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    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.}
       |         ^
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    42 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
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    83 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
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    29 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
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    72 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
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    Updated help pages with examples
    Updated conjugate model sampler
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    51 |   code{\link[deSolve]{events}}
       |       ^
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   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       | ^
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   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       |                                              ^
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    29 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
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    30 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
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    32 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
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    33 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
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    35 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
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    36 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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    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}.}
       |                                                                                                    ^
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    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.}
       |                                                                                                                                                                                   ^
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    30 | \item{smoother}{\code{principal_curve} parameter; choice of smoother. Domain: {smooth_spline, lowess, periodic_lowess}. Default: smooth_spline. Format: character.}
       |                                                                               ^
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     5 | \title{Get location of script in a fashion analagous to ${BASH_SOURCE[0]}}
       |                                                          ^
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    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
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    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                                         ^
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     7 | url{https://gist.github.com/dgrtwo/eb7750e74997891d7c20}
       |    ^
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    59 | (including ]code{forcelist} variables) that can be used to form tables.}
       |                 ^
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    17 | \item{c}{denotes the expected range of eqn{f} .}
       |                                           ^
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    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"}.}
       |                                                                                                                                   ^
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checkRd: (-1) test.bootSemNeT.Rd:47: Lost braces in \itemize; meant \describe ?
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.
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
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’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BPCells’
Packages suggested but not available for checking:
  'BPCells', 'enrichR', 'presto'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bisee.Rd:127: Lost braces
   127 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) hisee.Rd:101: Lost braces
   101 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) isee.Rd:116: Lost braces
   116 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) see.Rd:98: Lost braces
    98 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) 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) 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
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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘uchardet’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) shiny_pivot_table.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:64: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) addValidationSuffix.Rd:13: Lost braces; missing escapes or markup?
    13 | A string `"{tagId}-shinyreforms-validation"`.
       |            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
checkRd: (-1) add_class.Rd:18: Lost braces; missing escapes or markup?
    18 | Custom function for adding a CSS class used in {shinysurveys}.
       |                                                ^
checkRd: (-1) disable_element.Rd:16: Lost braces; missing escapes or markup?
    16 | Custom function for disabling an HTML element in {shinysurveys}.
       |                                                  ^
checkRd: (-1) enable_element.Rd:16: Lost braces; missing escapes or markup?
    16 | Custom function for disabling an HTML element in {shinysurveys}.
       |                                                  ^
checkRd: (-1) extendInputType.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{extension}{A shiny input type not natively supported by {shinysurveys}. See the examples section for more information.}
       |                                                               ^
checkRd: (-1) getSurveyData.Rd:15: Lost braces; missing escapes or markup?
    15 | default, and the built-in {shinysurveys} userID will be used.}
       |                           ^
checkRd: (-1) radioMatrixInput.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{...}{Additional arguments specific to {shinysurveys} required questions.}
       |                                             ^
checkRd: (-1) remove_class.Rd:18: Lost braces; missing escapes or markup?
    18 | Custom function for removing a CSS class used in {shinysurveys}.
       |                                                  ^
checkRd: (-1) toggle_element.Rd:18: Lost braces; missing escapes or markup?
    18 | Custom function for toggling enable/disable state of HTML element in {shinysurveys}.
       |                                                                      ^
'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) 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
checkRd: (-1) add_k_mer_state.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) sig.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
Found the following files/directories:
  ‘ExportFigtree1.tre’
checkRd: (-1) siland.Rd:64: Lost braces; missing escapes or markup?
    64 | \item x_{l,i}, local variable l,
       |         ^
checkRd: (-1) siland.Rd:70: Lost braces; missing escapes or markup?
    70 | \item d_{r,i} the distance between the center of pixel r and the observation at site i.
       |         ^
checkRd: (-1) inlandwaters.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_Y_Binary_X.Rd:51: Lost braces
    51 |     \item \code{dist = "binomial"} is drawn from eqn{Bin(XB, XB(1-XB))}
       |                                                     ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) create_modelDF.Rd:25-38: Lost braces
    25 | convert_xlsx_to_csv<-function(xlsx_file){
       |                                         ^
checkRd: (-1) create_modelDF.Rd:33-36: Lost braces
    33 |   for (i in Sheetnames) {
       |                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
checkRd: (-1) internal.statistics.one.lm.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) internal.statistics.one.lm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
checkRd: (-1) coxsimSpline.Rd:93: Lost braces; missing escapes or markup?
    93 | {FD(h[i](t)) = (exp(g(x[j]) - g(x[l])) - 1) * 100}
       | ^
checkRd: (-1) simPH.Rd:16-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:20-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:25-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:34-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:50-53: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
checkRd: (-1) SimDataDist-class.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SimDataDist-class.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) createData.Rd:7: Lost braces
     7 |         This function can be used to create data from a set of parameters created from \code{\link{draw}}, called a code{paramSet}. This function is used internally to create data, and is available publicly for accessibility and debugging.
       |                                                                                                                         ^
checkRd: (-1) exportData.Rd:7: Lost braces
     7 |         This function can be used to export data created from a set of parameters created from \code{\link{draw}}, called a code{paramSet}. This function can export data to be analyzed with either Mplus or LISREL.
       |                                                                                                                                 ^
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    Version (Date)
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    67 |  \code{within.SD} to be extremely small (e.g., $1 * 10^{-7}$) and all corresponding correlations in matrix
       |                                                        ^
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    15 | For example, in latex it would take "2" and output "{\\bf 2}"; in html
       |                                                     ^
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Auto-generated content requiring editing in Rd file 'SI.SSM.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
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    27 | individual curves, adjusted for {abcd} to lie on top of (i.e. be
       |                                 ^
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   110 | \code{\link{nlme}}) (default {nlmeControl(returnObject = TRUE)}).}
       |                              ^
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    20 |   \item{distr.type}{school district type (constructed for illustration purposes; (values={"A", "B", "C", "D"})).}
       |                                                                                          ^
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    61 | \item{replacementUnitsFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "replacementUnits.csv"}
       |                                                                    ^
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    63 | \item{subUnitTableFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "subUnitTable.csv"}
       |                                                                ^
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    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                  ^
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    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                                                                                  ^
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    26 | \item{alpha}{The eqn{\\alpha} error used to compute the \eqn{100*(1-\\alpha)\%} confidence interval}
       |                     ^
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    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |     ^
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    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |                 ^
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    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                            ^
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    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                                        ^
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    44 |   \item I.cov.rob - The matrix (V'GnV)^{-1} used to compute the statistics to detect the idiosyncratic outliers.
       |                                        ^
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    22 | https://i.cdn.turner.com/nba/nba/.element/img/4.0/global/logos/512x512/bg.white/svg/{team_short_name}.svg
       |                                                                                     ^
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    24 | sum(x' V^{-1} (y - x beta)) = 0 as the covariance V tends from V[, , 1] +
       |          ^
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     6 | A subset of world.cities{maps}. Extracted in order to shink number of dependencies. 
       |                         ^
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    17 |     \item{\code{resp}}{a factor indicating the transport mode choice, and \code{B} denotes taking the bus, code{D} denotes driving one's own vehicle, \code{F} denotes getting a ride with a friend, \code{O} denotes other, and \code{W} denotes walking}
       |                                                                                                                ^
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    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                  ^
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    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                            ^
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    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                          ^
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    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                                    ^
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    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                              ^
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    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                        ^
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    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                      ^
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    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                                ^
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   115 |  is the empirical explained variance from \cite{Meinshausen and B{u}hlmann, 2015}.  See \cite{Lund et al., 2020} for more details and references.
       |                                                                  ^
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   170 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
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    44 | estimMk returns the transition probability matrix of size (S^{k})xS (with S = length(E)) 
       |                                                              ^
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    10 | or code{smoof_multi_objective_function}. Both single- and multi-objective functions share the following attributes.
       |        ^
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    63 | Kaspar Ru{f}{i}bach (maintainer), \email{kaspar.rufibach@gmail.com} , \cr \url{http://www.kasparrufibach.ch}
       |          ^
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    63 | Kaspar Ru{f}{i}bach (maintainer), \email{kaspar.rufibach@gmail.com} , \cr \url{http://www.kasparrufibach.ch}
       |             ^
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  almost never needs to use ::: for its own objects:
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    25 | {Hector Haffenden} {haffendenh@cardiff.ac.uk}
       |                    ^
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    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                  ^
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    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                           ^
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    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                                      ^
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    40 | Operations with V^{-1} are computed using the factorization \code{fac} (see \code{sk_var}), or
       |                   ^
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    37 | \code{quad_form} is z^T V^{-1} z, for the observed response vector z, which is constructed
       |                           ^
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    41 | returns the quadratic form X^T V^{-1} X.
       |                                  ^
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    33 | either matrix \code{V}, or X^T V^{-1} X, or a factorization ('chol' or 'eigen')
       |                                  ^
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    32 | This function efficiently constructs group-knockoffs of {0,1,2} variables distributed
       |                                                         ^
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    11 | \item{X}{a {0,1,2} matrix of size n-by-p containing the original variables.}
       |            ^
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    29 | A {0,1,2} matrix of size n-by-p containing the knockoff variables.
       |   ^
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    26 | \item{call.rate}{\code{numeric}. Threshold for removing marker by missing genotype rate. SNP with \code{call rate} below threshold are removed from dataset. Must be between {0, 1}}
       |                                                                                                                                                                              ^
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    28 | \item{maf}{Threshold for removing SNP by minor allele frequency. Must be between {0, 1}}
       |                                                                                  ^
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   101 | data. Default value for code{which} is \code{2:4} if \code{p>1}, otherwise
       |                             ^
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File ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
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    82 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
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    99 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
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    35 | \link{soc.csa}, \link{map.csa.all}, link{map.csa.mca.array}
       |                                         ^
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    85 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
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    80 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
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    82 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
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    82 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
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     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                          ^
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     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                                                        ^
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     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                                                                     ^
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     8 | S-SODA assumes within each slice the X vector follow multivariate normal distribution. This function predicts the response y by reverting the P(X | slice(y)) to P(slice(y) | X), and estimates the E(y|X) as sum_{h} E(y | slice(y)=h, X) P (slice(y)=h | X)
       |                                                                                                                                                                                                                   ^
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    41 | database structure will be set to true. See GET /{db}. You can also obtain a list of
       |                                                  ^
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    70 | TermVector DEFAULT_FIELD_NAMES = new String[] {"contents"}
       |                                               ^
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checkRd: (-1) solve_pH_from_AT.Rd:93: Lost braces in \itemize; meant \describe ?
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   101 | code{spe} command; (4) \code{alpha} stores significance level as in
       |     ^
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Auto-generated content requiring editing in Rd file 'niche.overlap.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
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    20 | \code{a1, a2, a3}, then code{sdf_explode(df, a)} will produce output with each record replicated
       |                             ^
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    54 | \item{triangle=TRUE}{Input \code{rows} and {cols} represent lower
       |                                            ^
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    59 | \item{triangle=FALSE}{Input \code{rows} and {cols} represent a full
       |                                             ^
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     5 | \title{Solve the equation X = AQ^{-1}t(A) under permutations}
       |                                  ^
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    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |    ^
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    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |             ^
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    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                      ^
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    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                   ^
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    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                            ^
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    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                                     ^
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    22 | \env{main1, main2, main3}{
       |                          ^
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    25 | \env{xlabel}{
       |             ^
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    29 | \env{plot.one}{
       |               ^
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    27 | \env{interval}{
       |               ^
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    31 | \env{ci}{
       |         ^
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    35 | \env{order}{
       |            ^
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    39 | \env{normal}{
       |             ^
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    43 | \env{select}{
       |             ^
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    47 | \env{printit}{
       |              ^
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    50 | \env{stage}{
       |            ^
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/sparsevb.Rcheck/00install.out’ for details.
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    40 |   matrix and weight matrix (plus a matrix with {eID} identifiers
       |                                                ^
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GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', 'spatstat', 'rpanel', 'tcltk'
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  'spatstat.data', 'spatstat.sparse', 'spatstat.univar',
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  'spatstat.model', 'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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  'spatstat.random', 'spatstat.explore', 'spatstat.model'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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  'spatstat.data', 'spatstat.univar', 'spatstat.sparse',
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
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    39 | Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemi\`{e}re F, Verschoren A, Goethals B, Laukens K. (2011) An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics. 2011 Oct 20;12:405.
       |                                                              ^
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    70 | Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemi\`{e}re F, Verschoren A, Goethals B, Laukens K. (2011) An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics. 2011 Oct 20;12:405.
       |                                                              ^
Problems with news in ‘NEWS.md’:
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    Roadmap of specklestar package
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    23 |       p(y|ens) = 1 / K * sum {dnorm(y, z.i, s)} \cr
       |                              ^
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    25 | The default compilation is that of \ code {speech_build (., compiler = TRUE}).
       |                                           ^
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    61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc}, 
       |                                                   ^
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    14 | code{adaptIntegrateBallPolar()} will likely miss these abrupt changes and give
       |     ^
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  ‘AlphaGA_3.txt’ ‘AlphaML_3.txt’ ‘BetaGA_3.txt’ ‘BetaML_3.txt’
  ‘Performance_GA_ML_ 3 .pdf’ ‘SPIGA_3Pmon.Pm_St1.pdf’
  ‘SPIGA_3Pmon.Pm_St2.pdf’ ‘SPI_AG_3.txt’ ‘SPI_ML_3.txt’
  ‘SPI_ML_3Pm_St1.pdf’ ‘SPI_ML_3Pm_St2.pdf’ ‘SPI_ML_3Pm_St3.pdf’
  ‘SPI_ML_3Pm_St4.pdf’ ‘SPI_PARAM_3.txt’ ‘SPI_PARAM_3Pm_St1.pdf’
  ‘SPI_PARAM_3Pm_St2.pdf’ ‘SPI_PARAM_3Pm_St3.pdf’
  ‘SPI_PARAM_3Pm_St4.pdf’
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    16 | \doi{10.1111/add.14071}{Boffo et al., 2018}. Participants were presented stimuli from a "test"
       |                        ^
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    16 | described in detail in \doi{10.1016/j.tate.2019.102887}{Hedge, Powell, and Sumner (2018)}. 
       |                                                        ^
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    19 | \doi{10.1016/j.tate.2019.102887}{Abacioglu and colleagues (2019)}. 
       |                                 ^
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    15 | problems within the last year (\doi{https://doi.org/10.15288/jsa.1989.50.30}{White & Labouvie, 1989}).
       |                                                                             ^
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    17 | described in detail in \doi{10.1016/j.tate.2019.102887}{Hedge, Powell, and Sumner (2018)}. 
       |                                                        ^
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    22 | \doi{10.1111/acer.12853}{(Pronk, Deursen, Beraha, Larsen, & Wiers, 2015)}.
       |                         ^
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    15 |   \item \code{vignette("rapi_sum")} Sum-score for data of the 23-item version of the Rutgers Alcohol Problem Index (\doi{https://doi.org/10.15288/jsa.1989.50.30}{White & Labouvie, 1989})
       |                                                                                                                                                                  ^
Specified C++11: please drop specification unless essential
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    Feature Changes
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   118 | rfcv{randomForest} and gbm
       |     ^
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   108 | variable and anisotropy parameters. see notes vgm{gstat} for details.
       |                                                  ^
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    updates of 10th May 2021
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     7 | \format{An object of class /code{"list"}.}
       |                                 ^
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    27 | The function is Eq. Table 1-C1 in insertRef{Streck.2020}{spsh} using eq 21 which can be used
       |                                            ^
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    27 | The function is Eq. Table 1-C1 in insertRef{Streck.2020}{spsh} using eq 21 which can be used
       |                                                         ^
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    27 | The function is Eq. Table 1-B in insertRef{Streck.2020}{spsh}
       |                                           ^
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    27 | The function is Eq. Table 1-B in insertRef{Streck.2020}{spsh}
       |                                                        ^
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    27 | The function is Eq. Table 1-A  in insertRef{Streck.2020}{spsh}
       |                                            ^
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    27 | The function is Eq. Table 1-A  in insertRef{Streck.2020}{spsh}
       |                                                         ^
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    42 | and a matching \code{Qres} list attribute if {Q} was given.
       |                                              ^
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   158 |   the matrix of regressors, of order \emph{(Nxp_{g})}. Moreover, 
       |                                                 ^
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    67 | \item{het}{default {FALSE}: if {TRUE} uses the methods 
       |                    ^
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    67 | \item{het}{default {FALSE}: if {TRUE} uses the methods 
       |                                ^
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    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                   ^
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    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                              ^
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    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                                             ^
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   248 | and code{port} arguments of sqldf.
       |         ^
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    55 |     \code{tol}{ - a small, positive scalar that determines when iterations 
       |               ^
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    60 |     \code{maxiter}{ - an integer denoting the maximum limit on the number of 
       |                   ^
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    63 |     \code{trace}{ - a logical variable denoting whether some of the intermediate 
       |                 ^
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    67 |     \code{intermed}}{ - a logical variable denoting whether the intermediate 
       |                     ^
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   134 |       along with the corresponding log-likelihood value.  When the code{objfn} is not specified it will return the fixed-point residual instead of the objective function values. 
       |                                                                        ^
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    83 |   \item \code{X1_sto_shared} (default \code{TRUE}): {logical}; if \code{TRUE}, the stochastic environmental effect included in the environmental effect x1 will be shared between individuals. If \code{FALSE}, each individual will experience a different stochastic environmental effect x1 (i.e. a new stochastic environmental effect is generated for each individual).
       |                                                     ^
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    33 | Otherwise, if {pdim=TRUE}, the pxp SSCM is computed, and then from the SSCM an estimator of the correlation matrix, which is done by the function \code{\link{SSCM2Shape}}, see there for details.
       |               ^
'LazyData' is specified without a 'data' directory
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
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No news entries found.
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    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                   ^
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    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                              ^
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    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                                      ^
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    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                                                ^
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   100 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
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   109 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
Problems with news in ‘NEWS.md’:
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    42 |     always use code{"none"}.}
       |                    ^
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    25 |     always use code{"none"}.}
       |                    ^
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    20 | \code{Fsts}{a matrix of pairwise Fst values between populations}
       |            ^
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    21 | \code{Pvalues}{a matrix of p-values for each of the pairwise Fst values containined in the 'Fsts' matrix}
       |               ^
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    22 | \code{Bootstraps}{a dataframe of each Fst value generated during Bootstrapping and the associated confidence intervals}
       |                  ^
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    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                ^
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    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                                           ^
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
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    27 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
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    34 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
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    67 |    \item $S_{275-295}$ slope between 275 and 295 nm calculated with nonlinear regression
       |             ^
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    68 |    \item $S_{350-400}$ slope between 350 and 400 nm calculated with nonlinear regression
       |             ^
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    69 |    \item $S_{300-700}$ slope between 275 and 295 nm calculated with nonlinear regression
       |             ^
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    70 |    \item SR slope ratio, calculated by $S_{275-295}$/$S_{350-400}$
       |                                           ^
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    70 |    \item SR slope ratio, calculated by $S_{275-295}$/$S_{350-400}$
       |                                                         ^
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    71 |    \item E2:E3 ratio $a_{250}$/$a_{365}$
       |                         ^
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    71 |    \item E2:E3 ratio $a_{250}$/$a_{365}$
       |                                   ^
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    72 |    \item E4:E6 ratio $a_{465}$/$a_{665}$
       |                         ^
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    72 |    \item E4:E6 ratio $a_{465}$/$a_{665}$
       |                                   ^
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    73 |    \item $a_{254}$ absorbance at 254 nm
       |             ^
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    74 |    \item $a_{300}$ absorbance at 300 nm
       |             ^
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   229 |   \item{report}{a character string containing only elements of {\code{"v"}, \code{"c"}, \code{"s"},\code{"t"}, \code{"p"}, \code{"*"}} that determines whether, and in which order, variable names (\code{"v"}), coefficients (\code{"c"}), standard errors/confidence intervals (\code{"s"}), test statistics (\code{"t"}) and p-values (\code{"p"}) should be reported in regression tables. If one of the aforementioned letters is followed by an asterisk (\code{"*"}), significance stars will be reported next to the corresponding statistic.}
       |                                                                ^
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   246 |   \item{table.placement}{a character string containing only elements of {\code{"h"}, \code{"t"},\code{"b"}, \code{"p"}, \code{"!"}, \code{"H"}} that determines the table placement in its LaTeX floating environment.}
       |                                                                         ^
Package suggested but not available for checking: ‘starsdata’
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    16 |     \code{Side} \tab {Side of vehicle: code{1}=right or \code{2}=left}\cr
       |                                            ^
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    22 | \code{statcan_data()} function has 2 arguments to fulfill to get data: {tableNumber} & {lang}.
       |                                                                        ^
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    22 | \code{statcan_data()} function has 2 arguments to fulfill to get data: {tableNumber} & {lang}.
       |                                                                                        ^
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    18 | The \code{statcan_search()} function has 2 arguments to fulfill to find a database: {keywords} and {lang}.
       |                                                                                     ^
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    18 | The \code{statcan_search()} function has 2 arguments to fulfill to find a database: {keywords} and {lang}.
       |                                                                                                    ^
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Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: ‘networksis’
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    48 | Pooled standard deviation= \code{sp} = sqrt{((n1 - 1) sigma1^2 +(n2 - 1) sigma2^2) / (n1 + n2 - 2)}
       |                                            ^
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    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                        ^
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    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                                                                  ^
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    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                                                                      ^
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    43 | sampling from the standard normal distribution. Another example is defining func=function(n){rchisq(n=n, df=3, ncp=2)}
       |                                                                                             ^
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Problems with news in ‘NEWS.md’:
No news entries found.
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    19 |   \code{rows}{ every row corresponds to a different plot or community} \cr
       |              ^
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    20 |   \code{columns}{ every column corresponds to a different species.} \cr
       |                 ^
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    25 |   \code{rows}{ every row corresponds to a different species} \cr
       |              ^
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    26 |   \code{columns}{ the first column contains the name of the species, every consecutive column corresponds to a different trait} \cr
       |                 ^
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    16 |             - \code{DA}{ a vector containing the posterior distribution for the parameter dispersal assembly} \cr
       |                        ^
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    17 |             - \code{HF}{ a vector containing the posterior distribution for the parameter habitat filtering} \cr
       |                        ^
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    18 |             - \code{LS}{ a vector containing the posterior distribution for the parameter limiting similarity} \cr
       |                        ^
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    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
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    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
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    10 |   \item{semilandmark.pattern}{a regular expression pattern passed to \code{sub()} for identifying and grouping curve points. The default is landmark names ending in one or more numbers. To disable grouping, set to code{''}.}
       |                                                                                                                                                                                                                           ^
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    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("config")}
       | ^
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    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_container")}
       | ^
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    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("image")}
       | ^
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    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("plugin")}
       | ^
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    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("service")}
       | ^
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    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_task")}
       | ^
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  ‘corrviz.html’
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GNU make is a SystemRequirements.
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Malformed Title field: should not end in a period.
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    14 | \code{$demographic.coord}{
       |                          ^
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    18 | \code{$genetic.coord}{
       |                      ^
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    22 | \code{$demographic.measures}{
       |                             ^
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    26 | \code{$genetic.frequencies}{
       |                            ^
'LazyData' is specified without a 'data' directory
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  ‘myNewStrat.R’
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    70 | {Basic model operations:} \cr
       | ^
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    79 | {Parameter estimation:} \cr
       | ^
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    88 | {Sensitivity and Monte Carlo analyses:} \cr
       | ^
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    98 | {Compare model runs:} \cr
       | ^
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   105 | {Fishery yield analysis:} \cr
       | ^
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   111 | {Visualize model inputs:} \cr
       | ^
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   117 | {Visualize model outputs:} \cr
       | ^
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    38 | \code{\link[streamDAG]{stream.order}}, \code{\link[igraph]{delete.vertices}}, code{\link[igraph]{add.vertices}}, code{\link[igraph]{add.edges}}
       |                                                                                   ^
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    38 | \code{\link[streamDAG]{stream.order}}, \code{\link[igraph]{delete.vertices}}, code{\link[igraph]{add.vertices}}, code{\link[igraph]{add.edges}}
       |                                                                                                                      ^
Malformed Title field: should not end in a period.
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
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    22 | \item{quant}{numeric quantile to calculate {0,1}, default 0.95.}
       |                                            ^
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    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                        ^
checkRd: (-1) cmss.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                            ^
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    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                        ^
checkRd: (-1) cmss.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                            ^
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    18 |  used for this will be 1.00*10^{-PoissonThreshold}.}
       |                                ^
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checkRd: (-1) suggests.Rd:14: Lost braces; missing escapes or markup?
    14 | {suggests} aims to make that workflow as minimal and painless as possible,
       | ^
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checkRd: (-1) sunburst.Rd:30: Lost braces; missing escapes or markup?
    30 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{csvdata}
       |                                ^
checkRd: (-1) sunburst.Rd:88: Lost braces; missing escapes or markup?
    88 | \item{jsondata}{\code{deprecated} use data argument instead; data in nested d3 JSON hierarchy with `{name:...,  children:[];}`}
       |                                                                                                     ^
checkRd: (-1) sund2b.Rd:22: Lost braces; missing escapes or markup?
    22 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{list}, \code{character},
       |                                ^
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/sundialr.Rcheck/00install.out’ for details.
checkRd: (-1) BiclustSet-class.Rd:19: Lost braces
    19 |     \item{\code{Number}:}{code{"numeric"}, number of biclusters in the set}
       |                               ^
Package suggested but not available for checking: ‘velocyto.R’
checkRd: (-1) plot.Rd:42: Lost braces; missing escapes or markup?
    42 |  \item{color.off}{color code; specifying the color for set(s) which are "{absent}" for an intersection.}
       |                                                                          ^
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Error(s) in re-building vignettes:
  ...
--- re-building ‘suppdata-intro.Rnw’ using knitr

Quitting from lines 40-42 [unnamed-chunk-2] (suppdata-intro.Rnw)
Error: processing vignette 'suppdata-intro.Rnw' failed with diagnostics:
SI number '2' greater than number of detected SIs (1)
--- failed re-building ‘suppdata-intro.Rnw’

SUMMARY: processing the following file failed:
  ‘suppdata-intro.Rnw’

Error: Vignette re-building failed.
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checkRd: (-1) getFittedProbs.Rd:6-8: Lost braces
     6 | getFittedValues <- function(object) {
       |                                     ^
checkRd: (-1) getFittedProbs.Rd:14-16: Lost braces
    14 | getFittedValues <- function(object) {
       |                                     ^
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Auto-generated content requiring editing in Rd file 'suRtex.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
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GNU make is a SystemRequirements.
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checkRd: (-1) tprob.Rd:138: Lost braces in \itemize; meant \describe ?
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    24 | \item{mpl_h0t}{MPL estimates of the baseline hazard for T, i.e. h_{0T}(x_i)}
       |                                                                   ^
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    25 | \item{mpl_h0c}{MPL estimates of the baseline hazard for C, i.e. h_{0C}(x_i)}
       |                                                                   ^
checkRd: (-1) coxph_mpl_dc.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{mpl_H0t}{MPL estimates of the baseline cumulative hazard for T, i.e. H_{0T}(x_i)}
       |                                                                              ^
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    27 | \item{mpl_H0c}{MPL estimates of the baseline cumulative hazard for C, i.e. H_{0c}(x_i)}
       |                                                                              ^
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    28 | \item{mpl_S0t}{MPL estimates of the baseline survival for T, i.e. S_{0T}(x_i)}
       |                                                                     ^
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    29 | \item{mpl_S0c}{MPL estimates of the baseline survival for C, i.e. S_{0C}(x_i)}
       |                                                                     ^
Specified C++11: please drop specification unless essential
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    66 | A {data.table} which is stored as an attribute of
       |   ^
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GNU make is a SystemRequirements.
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    76 | The estimation procedure here is performed using coxph {survival} and inserting these estimated
       |                                                        ^
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checkRd: (-1) koInstall.Rd:24: Lost braces; missing escapes or markup?
    24 | set, svKomodo loads {svSocket}, starts the socket server listening to the
       |                     ^
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    18 | Komodo and (2) the present {svKomodo} R package that work hand in hand to
       |                            ^
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    28 | Nevertheless, the SciViews-K Komodo addin and the {svKomodo} R package
       |                                                   ^
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    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                          ^
checkRd: (-1) svKomodo-package.Rd:31: Lost braces; missing escapes or markup?
    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                                         ^
checkRd: (-1) svKomodo-package.Rd:37: Lost braces; missing escapes or markup?
    37 | Both SciViews-K and {svKomodo} should be considered archived items. I keep
       |                     ^
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    32 | \code{\link[survey:surveysummary]{survey::svymean()}} and related functions from the {survey}
       |                                                                                      ^
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    28 | numeric (scalar or vector): Relative treatment effect upon crossing over from control. Note that this is not the treatment effect (the treatment effect is specified in the call to other functions such as \code{swPwr} or \code{swSim})!  If \code{tx.effect.frac} is set to a scalar with value of 1, the standard SW CRT treatment effect will be presumed. If code{tx.effect.frac} is set to a scalar with a fractional value between 0 and 1, then only the first time point upon crossing over from control will have fractional relative treatment effect; the remaining exposure times will have a relative treatment effect of 1. If a vector of fractional treatment effect is specified, each element of the vector corresponds to the (fractional) treatment effect upon crossing over from control; if the length of the vector is less than total number of exposure times, the remaining time points will have a relative treatment effect value of 1; if the length of the vector is greater than total number of time points after crossing over, not all elements of \code{tx.effect.frac} will be used. The default value is (scalar) 1.
       |                                                                                                                                                                                                                                                                                                                                                                        ^
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Package suggested but not available for checking: ‘swephRdata’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
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    18 |   \item{epsilon}{positive convergence tolerance \emph{e}; the iterations converge when |fit - fit_{old}|/|fit| < \emph{e}. Default is \emph{e=1e-04}.}
       |                                                                                                   ^
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    14 | \code{n} x 4 matrix of coordinates consisting of {lat or y, lon or x} pairs for each each site
       |                                                  ^
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    28 | before plotting {ex: \code{trans = c(s = "exp", d = "exp")}}/}
       |                 ^
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  ‘test.csv’
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    68 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
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    67 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
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    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |   ^
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    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |                      ^
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   119 | Brownlees, C. T., and Gallo, G. M. (2006). Financial Econometric Analysis at Ultra{--}High Frequency: Data Handling Concerns, \emph{Computational Statistics and Data Analysis} \bold{51}, 2232--2245.
       |                                                                                   ^
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    59 | Brownlees, C. T., and Gallo, G. M. (2006). Financial Econometric Analysis at Ultra{--}High Frequency: Data Handling Concerns, \emph{Computational Statistics and Data Analysis} \bold{51}, 2232--2245.
       |                                                                                   ^
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    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
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    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
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    35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
       |                                                                                                                                                                                                                                                                                                                                                  ^
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See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TDA.Rcheck/00install.out’ for details.
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Package required but not available: ‘TDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Dependence on R version ‘4.2.3’ not with patchlevel 0
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    32 | link{squaredError}
       |     ^
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    19 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
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    23 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
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    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
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    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
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    10 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
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    16 | \item{\code{func}}{prepared for objective functions like SYS_LSF$func <- function(x){return(x[1] + x[2])}}
       |                                                                                     ^
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    37 |  {The 2 in the first row means there are two cycles;}
       |  ^
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    38 |   {The second row means there is a cycle of length 2, with members  (1,3);}
       |   ^
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    39 |  {The third row means  there is a cycle of length 1, with member  (2);}
       |  ^
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    40 |  {The fourth row is redundant for this specific case.}
       |  ^
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    41 |  {One can read from the output of permucycle() to obtain cycle notation (13)(2) of the permutation, and other information.}
       |  ^
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    16 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variatioanl approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
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    26 | It is recommended to use link{sibp_param_search} instead of this function to search over multiple configurations of the most important parameters.  So long as only the training data is used, the analyst can freely experimient with as many parameter configurations as he likes without corrupting his causal inferences.  Once a parameter configuration is chosen, the user can then use \link{sibp_amce} on the test set to estimate the average marginal component effect (AMCE) for each treatment.}
       |                              ^
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    28 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variational approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
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    19 |   \item{sibp.amce}{The table returned by code{sibp_amce}.}
       |                                              ^
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    20 |  \\tabular{rrrrr}{
       |           ^
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    20 |  \\tabular{rrrrr}{
       |                  ^
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    63 | NOTE: Currently only n in {2, 3, 4, 5} are supported. For n=5 some numerical
       |                           ^
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    31 | The teigen family. Stat Comput 22:1021{1029. <doi.org/10.1007/
       |                                       ^
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    Initial Release (v0.1.0)
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    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                    ^
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    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                           ^
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    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                                          ^
Problems with news in ‘NEWS.md’:
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     5 | \title{Install {timeseriesdb} System Functions}
       |                ^
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    17 | Installs functions needed to operated {timeseriesdb} in
       |                                       ^
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     5 | \title{Grant execute on {timeseriesdb} functions}
       |                         ^
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    17 | Grant execute on {timeseriesdb} functions
       |                  ^
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     5 | \title{Install {timeseriesdb} System Tables}
       |                ^
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    17 | Installs tables needed to operated {timeseriesdb} in
       |                                    ^
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     5 | \title{Install {timeseriesdb} Triggers}
       |                ^
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   247 |   do any conversion on the POSIX{l,c}t objects).
       |                                 ^
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    10 | \item{body}{an XML object generated via {tinkr}}
       |                                         ^
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    13 | The {commonmark} package is used to translate markdown to XML, but it does
       |     ^
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    14 | not assign a namespace prefix, which means that {xml2} will auto-assign a
       |                                                 ^
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     5 | \title{The {tinkr} stylesheet}
       |            ^
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    14 | This function returns the path to the {tinkr} stylesheet
       |                                       ^
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    11 | stylesheet used by {tinkr}.
       |                    ^
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Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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    20 | \item{cutoff}{Numeric. The value max(0, g_{i,j} - cutoff) so that there are <\code{.num_components}> components in the graph.}
       |                                           ^
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   332 |   If the input argument code{boxes} is \code{F}, the \code{lBox},
       |                             ^
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Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
Auto-generated content requiring editing in Rd file 'effect.Rd':
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  \keyword: ‘~kwd2’
Auto-generated content requiring editing in Rd file 'effectInfo.Rd':
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    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the episode_id value found in the change entries.
       |                                                 ^
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    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the season_id value found in the change entries.
       |                                                 ^
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     5 | \title{Format data as a JSON object (like this: {"x": "120"}).}
       |                                                 ^
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    18 | Format data as a JSON object (like this: {"x": "120"}).
       |                                          ^
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    21 | Recommended range is in {5, ..., 20}.}
       |                         ^
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    14 | \item{data}{data.table returned from function /code{tdtr}}
       |                                                    ^
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    23 |     item{\code{estimates}: parameter estimates}
       |         ^
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    24 |     item{
       |         ^
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    29 |     item{\code{operators}: the BEAST2 MCMC operator
       |         ^
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    28 |     item{\code{estimates}: parameter estimates}
       |         ^
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       |         ^
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Error(s) in re-building vignettes:
  ...
--- re-building ‘mtram.Rnw’ using knitr
** Processing: figure/mtram-toenail_OR_2-1.png
1800x1200 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 260592 bytes
Input file size = 261042 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 234718
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 234718

Output IDAT size = 234718 bytes (25874 bytes decrease)
Output file size = 234796 bytes (26246 bytes = 10.05% decrease)


Quitting from lines 1329-1334 [mtram-toenail_glmer_RS] (mtram.Rnw)
Error: processing vignette 'mtram.Rnw' failed with diagnostics:
PIRLS loop resulted in NaN value
--- failed re-building ‘mtram.Rnw’

--- re-building ‘tram.Rnw’ using knitr

warning: solve(): system is singular; attempting approx solution

warning: solve(): system is singular (rcond: 1.92626e-18); attempting approx solution
--- finished re-building ‘tram.Rnw’

SUMMARY: processing the following file failed:
  ‘mtram.Rnw’

Error: Vignette re-building failed.
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    69 | numeric with two values {0,1} and gaussian(link = "identity") otherwise.
       |                         ^
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    31 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
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    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
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    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
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    24 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
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    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
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    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
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    18 | data.frame with "{var_name}" column for the mean and
       |                  ^
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    19 | "{var_name}_{prob}" columns for each probability.
       |  ^
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    19 | "{var_name}_{prob}" columns for each probability.
       |             ^
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
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    16 | \item{matrix.logical}{With matrix=TRUE, the matrix is logical TRUE/FALSE or string "*"/code{" "}}
       |                                                                                            ^
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    39 | If \code{order.x} or {order.y} are \code{NULL}, their respective series will be fitted automatically using a AR model.
       |                      ^
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    31 | If \code{order.x} or {order.y} are \code{NULL}, their respective series will be fitted automatically using a AR model. If \code{permissive} is \code{TRUE} and no AR order is found automatically, an AR order of 1 will be imposed, if this case fails, then no order can be found and the function produces an error.
       |                      ^
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    16 | Converts any variable with two possible values to a {0,1} binary
       |                                                     ^
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    13 | A vector with values in {0,1}.
       |                         ^
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    28 | The final representation has length equal to floor(n / 2^{level}), where n is a length of original time series.
       |                                                          ^
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    74 |         doi{10.1093/biomet/74.2.221}
       |            ^
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    25 | \item{xcov}{Either a \[stats]{formula} with an empty left-hand side specifying external covariates
       |                              ^
Auto-generated content requiring editing in Rd file 'retweets.Rd':
  \keyword: ‘~kwd1’
  \keyword: ‘~kwd2’
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    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |     ^
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    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |                                  ^
Package which this enhances but not available for checking: ‘sl3’
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    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |  ^
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    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |               ^
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    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |                                ^
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    47 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
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    33 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
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   111 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
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  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
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    42 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
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    33 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
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    45 | link[dlogitnorm]{dlogitnorm}for the normal density.
       |                 ^
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    59 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}
       |                                  ^
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    60 | \item{\code{sim_CI}}: {vector containing the cluster indices for each generated unimodal reference distribution}
       |                       ^
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    61 | \item{\code{pvalue_emp}}: {the empirical p-value:  the proportion of times the cluster index from the reference
       |                           ^
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    63 | \item{\code{pvalue_norm}}: {the normalized p-value: the simulated p-value based on comparison to a standard normal distribution }
       |                            ^
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    58 | \item{\code{BestK}}: {A matrix with 1 row and 4 columns named: "Max_CI","Max_CI_wi_1SE","Max_scaled_CI" and "Max_logWCSS_wi_1SE".
       |                      ^
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    63 | \item{\code{full_process}}: {A matrix containing the number of clusters, K, evaluated, the CI from the data, the average CI from the null
       |                             ^
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    66 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}}
       |                                  ^
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    21 |    \code{train}{The mldr dataset with train examples, that includes all
       |                ^
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    23 |    \code{test}{The mldr dataset with test examples, defined by the
       |               ^
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    25 |    \code{validation}{Optionally, only if \code{has.validation = TRUE}.
       |                     ^
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    18 | Generate \code{n} random samples from multivariate Gaussian distribution N(0, (L^TL)^{-1})
       |                                                                                      ^
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    97 | \item{ID_level2}{Optional}{variable for unit ID codes. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                           ^
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    99 | \item{dataset}{Optional}{survey data object convertible to \code{data.table}.}
       |                         ^
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   122 | \item{ind_gr}{Optional}{variable by which divided independently X matrix of the auxiliary variables for the calibration. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                        ^
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   124 | \item{use.estVar}{Logical}{value. If value is \code{TRUE}, then \code{R} function \code{estVar} is used for the  estimation of covariance matrix of the residuals. If value is \code{FALSE}, then \code{R} function \code{estVar} is not used for the estimation of covariance matrix of the residuals.}
       |                           ^
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    69 | \item{percentratio}{Positive}{numeric value. All linearized variables are multiplied with \code{percentratio} value, by default - 1.}
       |                              ^
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   121 | \item{month_at_work}{Variable}{for total number of month at work (sum of the number of months spent at full-time work as employee, number of months spent at part-time work as employee, number of months spent at full-time work as self-employed (including family worker), number of months spent at part-time work as self-employed (including family worker)).  One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                               ^
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     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Burr distribution due to Parana\'{i}ba et al. (2011) given by
       |                                                                                                                        ^
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     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Fr\'{e}chet distribution due to Barreto-Souza et al. (2011) given by
       |                                                                                           ^
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     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                      ^
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     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                                                      ^
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     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Kumaraswamy Burr XII distribution due to Parana\'{i}ba et al. (2013) given by
       |                                                                                                                                   ^
'LazyData' is specified without a 'data' directory
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    40 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + exp(2*X22)*e
       |                                ^
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    42 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + 6*X22 + e
       |                                ^
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    15 | \item{file.suffix}{Regex expression for end of file name. For example, `file.suffix = '_S\\d{1,2}_.*_R1_.*'` will match R1 files.1 files.}
       |                                                                                             ^
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    23 | The function returns the K-by-K matrices {A_1, ..., A_p} as a list object.
       |                                          ^
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    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                    ^
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    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |      ^
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    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |          ^
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    15 | and dimension information (\code{dim} or code{length}) of each item,
       |                                              ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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     6 | \title{Indexing to extract subsets of a 'code{\link[via:XArray-class]{VirtualArray}}'-class object}
       |                                              ^
checkRd: (-1) subset.Rd:20: Lost braces
    20 | \item{drop}{\code{logical} in case the result of subsetting is a single element, should the \\code{\link[via:XArray-class]{VirtualArray}} wrapper be dropped?}
       |                                                                                                   ^
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   311 | albedo must be supplied in code{forcing_veg}. Default = 1.}
       |                                ^
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   323 | supplied in code{forcing_veg}. Default = 1.}
       |                 ^
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   341 | be supplied in code{forcing_veg} Default = 0.}
       |                    ^
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'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("vines")
  Loading required package: copula
  > 
  > test_check("vines", reporter = "summary")
  h: 
  h: 1
  hinverse: 
  hinverse: 2
  
  ══ Failed ══════════════════════════════════════════════════════════════════════
  ── 1. Error ('test-h.R:3:1'): (code run outside of `test_that()`) ──────────────
  Error in `testthat:::test_code(new_desc, substitute(code), env = env)`: argument "reporter" is missing, with no default
  Backtrace:
      ▆
   1. └─vines:::test_that_for_each_copula(...) at test-h.R:3:1
   2.   └─testthat:::test_code(new_desc, substitute(code), env = env) at tests/testthat/helper-copulas.R:37:13
  
  ── 2. Error ('test-hinverse.R:3:1'): (code run outside of `test_that()`) ───────
  Error in `testthat:::test_code(new_desc, substitute(code), env = env)`: argument "reporter" is missing, with no default
  Backtrace:
      ▆
   1. └─vines:::test_that_for_each_copula(...) at test-hinverse.R:3:1
   2.   └─testthat:::test_code(new_desc, substitute(code), env = env) at tests/testthat/helper-copulas.R:37:13
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
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    75 |   \item \strong{Pollen productivity}: In each time step the model computes the pollen productivity (in relative values) of the population using the equation \eqn{P_{t} = \sum x_{it} \times max(S_{t}, B)}, where \emph{t} is time (a given simulation time step), \emph{P} is the pollen productivity of the population at a given time, \emph{x_{i}} represents the biomass of every adult individual, \emph{S} is the environmental suitability at the given time, \emph{B} is the contribution of biomass to pollen productivity regardless of environmental suitability (\emph{pollen.control} parameter in the simulation, 0 by default). If \emph{B} equals 1, \emph{P} is equal to the total biomass sum of the adult population, regardless of the environmental suitability. If \emph{B} equals 0, pollen productivity depends entirely on environmental suitability values.
       |                                                                                                                                                                                                                                                                                                                                                    ^
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    16 |   ...{currently not used}
       |      ^
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    32 | A call to {new} returns a newly allocated object from the class identified by the first argument.
       |           ^
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Problems with news in ‘NEWS.md’:
No news entries found.
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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
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    37 | \item{ownVLFreduced}{ownVLFMatrix}{A matrix containing only those specimen that have VLFs as well as the amino acids at the positions that contain VLFs and NAs in all other positions of the sequence.  Only appears if own is not NULL.}
       |                                   ^
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    36 | \item{ownVLFreduced}{ownVLFMatrix}{A matrix containing only those specimen that have VLFs as well as the nucleotides at the positions that contain VLFs and NAs in all other positions of the sequence.  Only appears if own is not NULL.}
       |                                   ^
Specified C++11: please drop specification unless essential
checkRd: (-1) getTurnType.Rd:38: Lost braces; missing escapes or markup?
    38 | Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
       |               ^