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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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    14 | \item{case}{string. One of {"a", "b", "c"}, corresponding to three models.}
       |                            ^
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    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.}
       |                                                                                                                                                                                             ^
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    98 | Supplementary Material S1 from \doi{10.1186/1472-6947-12-147}{Obadia et al., 2012}.
       |                                                              ^
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    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from one estimation method.
       |                                                      ^
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    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from an
       |                                                      ^
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Error(s) in re-building vignettes:
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--- re-building ‘R2admb.Rnw’ using knitr
Error: processing vignette 'R2admb.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'R2admb.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.121 \hldef
            {fitted.model} \hlkwb{<-} \hlkwd{do_admb}\hldef{(fn,data,params,}
? 
! Emergency stop.
! Emergency stop.
l.121 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘R2admb.Rnw’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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    64 |   compute a smooth surface from \code{x} and {y}. If users already have
       |                                              ^
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     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).
       |                                                                                                                                                                                                                                                                                                                                                                                                ^
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    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}
       |                                                                       ^
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    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).
       |                                               ^
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    25 | Example: {fromField:"val1", toField:"value"}.}
       |          ^
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    16 | is randomized to a certain treatment {j}, the entry of \code{(i,j)} of the
       |                                      ^
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    18 |   \item{scale}{either "prob" where probabilities are returned, the default, or "raw" where the probabilities are returned on the logit or probit scale, depending on which scale was selected in the texttt{randomLCA} function}
       |                                                                                                                                                                                                            ^
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    18 | where the vector dimension is 2^{response.number}.}
       |                                 ^
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    48 | \\env{$XDG_CACHE_HOME} if defined
       |      ^
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    17 | Returns the maximum of all values in a vector by passing \{code{\link{max}} as \code{fn} argument to \code{\link{univar}} function.
       |                                                                ^
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    17 | Returns the minimum of all values in a vector by passing \{code{\link{min}} as \code{fn} argument to \code{\link{univar}} function.
       |                                                                ^
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    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.
       |                                                                                         ^
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    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
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   6.7Mb
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installed size is 95.0Mb
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     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.
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    10 | \item{m_bar}{the sample vector of moments for a specified vector $(h_{a,r},y)$}
       |                                                                      ^
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    16 | \item{N_k}{index of the $ h_{a,r}$ function considered}
       |                             ^
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
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installed size is 21.7Mb
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installed size is 10.6Mb
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    data   5.6Mb
    etc    1.9Mb
    po     1.2Mb
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checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
installed size is 21.5Mb
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    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.}
       |                                                                                           ^
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installed size is 25.2Mb
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installed size is  7.2Mb
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installed size is 13.4Mb
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installed size is  5.4Mb
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GNU make is a SystemRequirements.
installed size is 68.4Mb
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GNU make is a SystemRequirements.
checkRd: (-1) rbeta.Rd:31-32: Lost braces in \itemize; meant \describe ?
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installed size is 68.1Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 12.2Mb
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    blp    5.9Mb
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installed size is 55.4Mb
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    libs  54.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
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    28 | \item pre-working age: {a1, alpha1}
       |                        ^
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    29 | \item working age: {a2, alpha2, mu2, lambda2}
       |                    ^
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    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’
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    29 | if(resolution == "300m"){
       |                         ^
checkRd: (-1) nc_open_CGLS.Rd:33-36: Lost braces
    33 | if(resolution == "1km"){
       |                        ^
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   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}. 
       |                                                                                                                                                                                                                                                 ^
installed size is 13.6Mb
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    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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘GuideBiclustGUI.Rnw’ using knitr
Error: processing vignette 'GuideBiclustGUI.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'GuideBiclustGUI.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.2365 \hldef
             {newmethod_WINDOW} \hlkwb{<-} \hlkwa{function}\hldef{()\{}
? 
! Emergency stop.
! Emergency stop.
l.2365 
       
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘GuideBiclustGUI.Rnw’

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

Error: Vignette re-building failed.
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    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.
installed size is  8.6Mb
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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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    16 | \item{info.type}{character. \code{AD}: allele depth value, {AD-tot}:total
       |                                                            ^
Package suggested but not available for checking: ‘conics’
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installed size is  7.6Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/Rcplex.Rcheck/00install.out’ for details.
installed size is 20.9Mb
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installed size is  6.5Mb
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    include   6.5Mb
    libs      2.2Mb
Specified C++11: please drop specification unless essential
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    libs   8.4Mb
installed size is 40.3Mb
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    include  37.8Mb
    libs      2.3Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  7.9Mb
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    libs   7.7Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 48.7Mb
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    include  48.6Mb
Specified C++11: please drop specification unless essential
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
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
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    include   9.5Mb
    libs     24.7Mb
Specified C++11: please drop specification unless essential
installed size is  8.6Mb
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/RcppMeCab.Rcheck/00install.out’ for details.
Specified C++11: please drop specification unless essential
installed size is  9.5Mb
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installed size is  9.6Mb
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    include   6.7Mb
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installed size is  6.6Mb
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GNU make is a SystemRequirements.
installed size is  8.3Mb
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installed size is 14.3Mb
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installed size is 23.9Mb
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    jsonexamples   3.8Mb
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installed size is  7.3Mb
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    libs      5.7Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘Rcssplot.Rnw’ using knitr
Error: processing vignette 'Rcssplot.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'Rcssplot.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.100 \hldef
            {a} \hlkwb{<-} \hlkwd{setNames}\hldef{(}\hlkwd{c}\hldef{(}\hlnum...

? 
! Emergency stop.
l.100 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘Rcssplot.Rnw’

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

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
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    38 | {Yao Liu} \email{liuyao@stu.xmu.edu.cn}
       | ^
checkRd: (-1) rdacca.hp.Rd:86: Lost braces; missing escapes or markup?
    86 | {Pedro Peres-Neto} \email{pedro.peres-neto@concordia.ca}
       | ^
checkRd: (-1) rdacca.hp.Rd:88: Lost braces; missing escapes or markup?
    88 | {Kim Nimon} \email{kim.nimon@gmail.com}
       | ^
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
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    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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installed size is  9.1Mb
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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)}.}
       |                                                                      ^
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    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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   112 | and another argument named {zCoef} for covariate coefficient vector.
       |                            ^
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checkRd: (-1) refdb_import_BOLD.Rd:63: Lost braces
    63 | link[bold]{bold_stats} and \link[bold]{bold_seqspec}
       |           ^
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    13 | not that quotes need to be escaped (code{\"}).}
       |                                         ^
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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}.)
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
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    10 | \item{input, output, session}{Internal parameters for {shiny}.
       |                                                       ^
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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--- re-building ‘relevance-descr.Rnw’ using knitr
Error: processing vignette 'relevance-descr.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'relevance-descr.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.280 \hlkwd{getOption}\hldef
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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{
       |            ^
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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.
       |                                          ^
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    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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! Undefined control sequence.
l.281 \hlkwd{library}\hldef
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SUMMARY: processing the following file failed:
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No news entries found.
checkRd: (-1) repo_build.Rd:44-47: Lost braces
    44 | ## chunk "item 1" {
       |                   ^
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Packages suggested but not available for checking: 'PADOG', 'safe'
Packages unavailable to check Rd xrefs: ‘PADOG’, ‘safe’
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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}
       |      ^
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Error: processing vignette 'resde-vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'resde-vignette.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.200 \hlkwd{sdemodel}\hldef
                            {(}\hlkwc{phi}\hldef{=}\hlopt{~}\hldef{x,} \hlkw...

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Error: Vignette re-building failed.
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GNU make is a SystemRequirements.
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    52 |     \item B. Bollob\'{a}s, 1998.  \emph{Modern Graph Theory}.  Springer.
       |                      ^
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checkRd: (-1) harmonize_values.Rd:44: Lost braces; missing escapes or markup?
    44 | \item{perl}{Use perl-like regex? Defaults to {FALSE}.}
       |                                              ^
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   114 |      code{reutils.test.remote} to \code{TRUE} to run the full suite of tests.
       |          ^
installed size is  5.2Mb
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Running ‘testthat.R’ [22m/28m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(revdbayes)
  > 
  > test_check("revdbayes")
  
  Execution halted
checkRd: (-1) cpUpper.Rd:39: Lost braces
    39 | \code{"fastfloyd"}{ (default) uses an iterative variant of the Floyd-Warshall algorithm, in which the check of consistency of the current observation with a given cluster is done in a single step of the Floyd-Warshall algorithm. Much faster than \code{"floyd"}.}
       |                   ^
checkRd: (-1) cpUpper.Rd:41: Lost braces
    41 | \code{"floyd"}{ uses the algorithm described in Crawford and Pendakur (2013): at each step the complete Floyd-Warshall algorithm is run to check whether each cluster can accomodate the current observation.}
       |               ^
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg38’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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checkRd: (-1) saveRev.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{use_wd}{logical - If TRUE, the history will be prepended by setwd({'users current working directory'}). This function will set the script's working directory to
       |                                                                         ^
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installed size is 46.1Mb
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checkRd: (-1) fs_search.Rd:76: Lost braces
    76 | \\code{\link{fs_auth}} \code{\link{fs_browse}}
       |       ^
Problems with news in ‘NEWS.md’:
No news entries found.
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Running ‘testthat.R’ [68s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       ▆
    1. ├─testthat::expect_error(...) at test-forestry.R:48:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─Rforestry::forestry(x = iris[, -1], y = iris[, 1], seed = seed_i)
    7.   └─base::tryCatch(...)
    8.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10.         └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1422 ]
  Error: Test failures
  Execution halted
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checkRd: (-1) tk.browse.Rd:29: Lost braces
    29 |     Single logical value, whether to wait for the interface window to be closed before unfreezing the R console. The \code{FALSE} default let you use R and the interface in parallel (see the 'Typing R commands while browsing' section below), the code{TRUE} value is used essentially in the stand alone version.
       |                                                                                                                                                                                                                                                           ^
checkRd: (-1) tk.convert.Rd:17: Lost braces
    17 |     Single logical value, whether to wait for the interface window to be closed before unfreezing the R console. The \code{FALSE} default let you use R and the interface in parallel, the code{TRUE} is used essentially in the stand alone version.
       |                                                                                                                                                                                                ^
checkRd: (-1) tk.tracks.Rd:8: Lost braces
     8 |   This function allows to load and edit the \code{\linkS4class{drawable.list}} object that is to be passed to \code{\link{tk.browse}} and code{\link{browsePlot}}, using a Tcl-tk interface
       |                                                                                                                                               ^
installed size is  5.5Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  8.4Mb
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checkRd: (-1) GenDataPopulation.Rd:21: Lost braces
    21 | {data}{Population of data}
       |       ^
checkRd: (-1) GenDataSample.Rd:23: Lost braces
    23 | {data}{Sample of data}
       |       ^
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
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checkRd: (-1) RiemannianMetric.Rd:450-453: Lost braces
   450 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
checkRd: (-1) RiemannianMetric.Rd:484-487: Lost braces
   484 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
checkRd: (-1) RiemannianMetric.Rd:588-591: Lost braces
   588 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
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checkRd: (-1) Ghana_2021_school_attendance_geometry.Rd:75: Lost braces in \itemize; meant \describe ?
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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.
       |                      ^
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    17 | A list including information related to the noise filtering process contained in the object \code{object} of class {rfdata} with the following elements:
       |                                                                                                                    ^
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    53 | /url{http://www.sawtoothsoftware.com/help/lighthouse-studio/manual/index.html?hid_web_cbc_exporting.html}
       |     ^
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     8 | R interface for creating tables using Handsontable, url{https://handsontable.com/}
       |                                                        ^
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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:31-32: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:33-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:35-36: Lost braces
    35 |    \item{pam_cluster_64_7_5715},{N=64, seven clusters with 5715 vectors per
       |                                 ^
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:37-38: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:39-40: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:21-22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:23-24: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Specified C++11: please drop specification unless essential
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  15.9Mb
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
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
checkRd: (-1) iex.chart.Rd:23: Lost braces; missing escapes or markup?
    23 | r takes only of of the values accepted IN API request. {"5y", "2y", "1y", "ytd", "6m", "3m", "1m", "1d"}
       |                                                        ^
checkRd: (-1) descrip.Rd:122: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:123: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:124-125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:126-128: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:129-133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:134-135: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:136-138: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:139-140: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:141-144: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:145-146: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:147: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:148: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:149: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) correct_sign.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct_sign.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
'LazyData' is specified without a 'data' directory
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  23.8Mb
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.}
       |                              ^
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   8.7Mb
'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}}
       |                                                                                                                                                                                                                                                   ^
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 ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
License stub is invalid DCF.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 55.9Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs     51.7Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    exe  23.8Mb
'LazyData' is specified without a 'data' directory
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    libs  27.9Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
installed size is 44.9Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
'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: \$
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   16.1Mb
'LazyData' is specified without a 'data' directory
installed size is 165.9Mb
  sub-directories of 1Mb or more:
    libs  164.9Mb
GNU make is a SystemRequirements.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/rlibkriging.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'DoubletFinder', 'RcppPlanc'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
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.
       |             ^
Running examples in ‘rllama-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_defillama_chain_hist_tvl
> ### Title: Chain History Data
> ### Aliases: get_defillama_chain_hist_tvl
> 
> ### ** Examples
> 
> # total tvl by date
> chain_tvl = get_defillama_chain_hist_tvl( "Ethereum" )
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [api.llama.fi] Resolving timed out after 10003 milliseconds
Calls: get_defillama_chain_hist_tvl ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
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
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    rmd   6.0Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/RMark.Rcheck/00install.out’ for details.
Warning: Software mark not found in path.
         If you have mark executable, you will need to set MarkPath object to its location (e.g. MarkPath="C:/Users/Jeff Laake/Desktop"

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
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.
       |               ^
installed size is 146.6Mb
  sub-directories of 1Mb or more:
    libs  146.2Mb
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
checkRd: (-1) plot.mcfs.Rd:24: Lost braces; missing escapes or markup?
    24 |     \item\code{ri} {plots top features set with their RIs as well as max RI obtained from permutation experiments. Red color denotes important features.}
       |                    ^
'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
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/RmecabKo.Rcheck/00install.out’ for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   6.0Mb
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfft-class.Rd:65: Lost braces
    65 | code{dfft(object, index=0)} on an object created from a forecast with 
       |     ^
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) mgraph.Rd:62: Lost braces
    62 |   \item{TC}{target class (for multi-class classification class) within {1,...,\emph{Nc}}, where \emph{Nc} is the number of classes. If multi-class and TC==-1 then TC is set to 
       |                                                                        ^
checkRd: (-1) mmetric.Rd:112: Lost braces
   112 |   \item{TC}{target class index or vector of indexes (for multi-class classification class) within {1,...,\emph{Nc}}, where \emph{Nc} is the number of classes:<cr>
       |                                                                                                   ^
checkRd: (-1) mparheuristic.Rd:27: Lost braces
    27 | except for SVM several \code{rbfdot} kernel based models (\code{"ksvm"},\code{"rsvm"},\code{"lssvm"}, which can assume \code{2^}{search-range}; please check the result of this function to confirm if the search is linear or \code{2^}{search-range}). 
       |                                                                                                                                 ^
checkRd: (-1) mparheuristic.Rd:27: Lost braces
    27 | except for SVM several \code{rbfdot} kernel based models (\code{"ksvm"},\code{"rsvm"},\code{"lssvm"}, which can assume \code{2^}{search-range}; please check the result of this function to confirm if the search is linear or \code{2^}{search-range}). 
       |                                                                                                                                                                                                                                         ^
Specified C++11: please drop specification unless essential
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R          1.0Mb
    libs       1.1Mb
    minizinc   3.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 44.9Mb
  sub-directories of 1Mb or more:
    libs  43.9Mb
installed size is 30.8Mb
  sub-directories of 1Mb or more:
    libs  30.6Mb
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 ?
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/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’
installed size is 85.0Mb
  sub-directories of 1Mb or more:
    libs  84.4Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
GNU make is a SystemRequirements.
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    libs  30.8Mb
checkRd: (-1) myTarGetClientList.Rd:33: Lost braces
    33 | {MyTarget API Documenation}{https://target.my.com/doc/api/detailed/#resource_agency_clients}
       |                            ^
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    doc    2.3Mb
Package suggested but not available for checking: ‘rnaturalearthhires’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
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.
       |                                                                                                                                                                                                                                                                       ^
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
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
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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
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checkRd: (-1) rncl.Rd:121-124: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
Packages which this enhances but not available for checking:
  'pbdMPI', 'Rmpi'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Packages unavailable to check Rd xrefs: ‘pbdMPI’, ‘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
installed size is 120.8Mb
  sub-directories of 1Mb or more:
    extdata    2.0Mb
    libs     118.6Mb
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    1.7Mb
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
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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 ?
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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 ?
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checkRd: (-1) outliergram.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R  11.3Mb
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  18.6Mb
Error(s) in re-building vignettes:
--- re-building ‘imputation.Rnw’ using knitr
Error: processing vignette 'imputation.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'imputation.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.435 \hlkwd{library}\hldef
                           {(}\hlsng{"robCompositions"}\hldef{)}
? 
! Emergency stop.
! Emergency stop.
l.435 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘imputation.Rnw’

--- re-building ‘robCompositions-overview.Rnw’ using Sweave
--- finished re-building ‘robCompositions-overview.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 40.7Mb
  sub-directories of 1Mb or more:
    libs  40.6Mb
Package suggested but not available for checking: ‘illuminaHumanv3.db’
installed size is  7.1Mb
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    libs   7.0Mb
'LazyData' is specified without a 'data' directory
installed size is 97.1Mb
  sub-directories of 1Mb or more:
    libs  96.3Mb
GNU make is a SystemRequirements.
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 ?
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘robustfa-knitr.Rnw’ using knitr
Error: processing vignette 'robustfa-knitr.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'robustfa-knitr.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.1481   \hldef
               {faCovPcaRegMcd} \hlkwb{=} \hlkwd{FaCov}\hldef{(}\hlkwc{x} \h...

? 
! Emergency stop.
l.1481 
       
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘robustfa-knitr.Rnw’

SUMMARY: processing the following file failed:
  ‘robustfa-knitr.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 39.5Mb
  sub-directories of 1Mb or more:
    libs  38.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              5.1Mb
    simulationStudy   1.5Mb
'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
Error(s) in re-building vignettes:
  ...
--- re-building ‘rococo.Rnw’ using knitr
Error: processing vignette 'rococo.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'rococo.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.197 \hlkwd{install.packages}\hldef
                                    {(}\hlsng{"rococo"}\hldef{)}
? 
! Emergency stop.
! Emergency stop.
l.197 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘rococo.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         3.7Mb
    extdata   2.7Mb
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
sh: cmake: command not found
------------------ CMAKE NOT FOUND --------------------

CMake was not found on the PATH. Please install CMake:

 - installr::install.cmake()  (Windows; inside the R console)
 - yum install cmake          (Fedora/CentOS; inside a terminal)
 - apt install cmake          (Debian/Ubuntu; inside a terminal)
 - brew install cmake         (MacOS; inside a terminal with Homebrew)
 - port install cmake         (MacOS; inside a terminal with MacPorts)

Alternatively install CMake from: <https://cmake.org/>

-------------------------------------------------------


It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
sh: cmake: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not 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
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
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/ROracle.Rcheck/00install.out’ for details.
'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
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   2.7Mb
    libs   5.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rotations-intro.Rnw’ using knitr
Error: processing vignette 'rotations-intro.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'rotations-intro.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.152 \hldef
            {r} \hlkwb{<-} \hldef{pi}\hlopt{/}\hlnum{2}
? 
! Emergency stop.
! Emergency stop.
l.152 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘rotations-intro.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    libs   7.8Mb
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 ?
installed size is 90.7Mb
  sub-directories of 1Mb or more:
    libs  89.5Mb
GNU make is a SystemRequirements.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'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).}
       |                                                                                                                                 ^
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.9Mb
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
installed size is 53.1Mb
  sub-directories of 1Mb or more:
    libs  53.0Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
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
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) check_node.Rd:11: Lost braces
    11 | \item{x}{\\code{list}, the node to check}
       |                ^
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
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
installed size is 100.2Mb
  sub-directories of 1Mb or more:
    libs  99.6Mb
checkRd: (-1) ex.Rd:20: Lost braces
    20 | Execute a ops-dag using `code{wrap()}` data as values.
       |                              ^
checkRd: (-1) sql_node.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{expand_braces}{logical if TRUE use {col} notation to ensure {col} is a column name.}
       |                                          ^
checkRd: (-1) sql_node.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{expand_braces}{logical if TRUE use {col} notation to ensure {col} is a column name.}
       |                                                                   ^
checkRd: (-1) R2_lik.Rd:37: Lost braces; missing escapes or markup?
    37 | \code{R2_lik()} is also computed for LMMs and GLMMs in the {MuMIn} package.
       |                                                            ^
checkRd: (-1) R2_pred.Rd:32: Lost braces; missing escapes or markup?
    32 | Note that the version of \code{binaryPGLMM()} in the package ape is replaced by a version contained within {rr2} that outputs all of the required information for the calculation of R2_resid.
       |                                                                                                            ^
checkRd: (-1) R2_resid.Rd:69: Lost braces; missing escapes or markup?
    69 | Note that the version of \code{binaryPGLMM()} in the package ape is replaced by a version contained within {rr2} that outputs all of the required information for the calculation of \code{R2_resid()}
       |                                                                                                            ^
checkRd: (-1) Boost.Rd:40: Lost braces; missing escapes or markup?
    40 | \item{niter}{number of boosting iterations (for RRBoost: T_{1,max} + T_{2,max}) (numeric)}
       |                                                            ^
checkRd: (-1) Boost.Rd:40: Lost braces; missing escapes or markup?
    40 | \item{niter}{number of boosting iterations (for RRBoost: T_{1,max} + T_{2,max}) (numeric)}
       |                                                                        ^
checkRd: (-1) Boost.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{niter}{number of iterations for the boosting algorithm (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                                             ^
checkRd: (-1) Boost.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{niter}{number of iterations for the boosting algorithm (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                                                         ^
checkRd: (-1) Boost.control.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{n_init}{number of iterations for the SBoost step of RRBoost ($T_{1,max}$) (int)}
       |                                                                       ^
checkRd: (-1) Boost.validation.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{niter}{number of iterations (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                  ^
checkRd: (-1) Boost.validation.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{niter}{number of iterations (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                              ^
checkRd: (-1) rrecsys.Rd:72: Lost braces; missing escapes or markup?
    72 |  The average deviation rating $dev_{ij}$ between co-rated items is defined by:
       |                                    ^
checkRd: (-1) rrecsys.Rd:76: Lost braces; missing escapes or markup?
    76 |  Where $c_{ij}$ is the number of co-ratings between items $i$ and $j$ and $r_{ui}$ is an existing rating for user $u$ on item $i$. The Weighted Slope One takes into account both, information from users who rated the same item and the number of observed ratings.
       |           ^
checkRd: (-1) rrecsys.Rd:76: Lost braces; missing escapes or markup?
    76 |  Where $c_{ij}$ is the number of co-ratings between items $i$ and $j$ and $r_{ui}$ is an existing rating for user $u$ on item $i$. The Weighted Slope One takes into account both, information from users who rated the same item and the number of observed ratings.
       |                                                                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) lateformeeting.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:12: Lost braces in \itemize; meant \describe ?
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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 ?
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
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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.
       |                                                                                                                                                          ^
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
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
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 25.2Mb
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    libs  24.9Mb
installed size is 27.5Mb
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    libs  24.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is  7.3Mb
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    libs   6.3Mb
Error(s) in re-building vignettes:
--- re-building ‘intro.Rnw’ using knitr
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.xnio.nio.NioXnio$2 (file:/Users/urbanek/Library/Application%20Support/org.R-project.R/R/rsolr/solr-undertow-1.6.0-with-solr-5.5.0/lib/xnio-nio-3.3.4.Final.jar) to constructor sun.nio.ch.KQueueSelectorProvider()
WARNING: Please consider reporting this to the maintainers of org.xnio.nio.NioXnio$2
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Error: processing vignette 'intro.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'intro.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.123 \hlkwd{library}\hldef
                           {(nycflights13)}
? 
! Emergency stop.
! Emergency stop.
l.123 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘intro.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    libs  47.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.2Mb
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    libs  11.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 313.7Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.7Mb
    libs  306.2Mb
GNU make is a SystemRequirements.
installed size is 96.4Mb
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    libs  96.1Mb
GNU make is a SystemRequirements.
installed size is 46.0Mb
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    libs  45.4Mb
GNU make is a SystemRequirements.
installed size is 49.8Mb
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    exec   1.7Mb
    lib   34.7Mb
    libs  11.5Mb
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
       |                                                     ^
installed size is  6.0Mb
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    external   1.6Mb
    libs       3.9Mb
installed size is 37.8Mb
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    libs  21.8Mb
Specified C++11: please drop specification unless essential
installed size is 28.0Mb
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    libs  27.5Mb
installed size is 23.4Mb
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    swipl  23.1Mb
GNU make is a SystemRequirements.
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installed size is  6.1Mb
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    R      2.0Mb
    doc    1.5Mb
    help   2.4Mb
checkRd: (-1) RTDE.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RTDE.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                              ^
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
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    rmarkdown  11.1Mb
GNU make is a SystemRequirements.
checkRd: (-1) tw_options.Rd:22: Lost braces in \itemize; meant \describe ?
installed size is  5.7Mb
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    libs       2.0Mb
    projects   2.9Mb
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
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    libs   7.1Mb
installed size is 115.4Mb
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installed size is  8.4Mb
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    libs   7.5Mb
'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
installed size is  6.2Mb
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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
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  19.9Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 222.7Mb
  sub-directories of 1Mb or more:
    data    1.5Mb
    libs  220.2Mb
GNU make is a SystemRequirements.
Running examples in ‘RtsEva-Ex.R’ failed
The error most likely occurred in:

> ### Name: tsEstimateAverageSeasonality
> ### Title: Estimate Average Seasonality
> ### Aliases: tsEstimateAverageSeasonality
> 
> ### ** Examples
> 
> timeAndSeries <- ArdecheStMartin
> timeStamps <- ArdecheStMartin[,1]
> series  <- ArdecheStMartin[,2]
> timeWindow <- 30*365  # 30 years
> rs <- tsEvaDetrendTimeSeries(timeStamps, series, timeWindow)
> nRunMn <- rs@nRunMn
> cat("computing trend seasonality ...\n")
computing trend seasonality ...
> seasonalitySeries <- rs@detrendSeries
> result <- tsEstimateAverageSeasonality(timeStamps, seasonalitySeries, timeWindow=rs@nRunMn)
Warning in pracma::interp1(avgTmStamp, monthAvgVec, timeStampsN, method = "spline") :
  Points in argument in 'x' unsorted; will be sorted.
Warning in pracma::interp1(avgTmStamp, monthAvgVex, timeStampsN, method = "spline") :
  Points in argument in 'x' unsorted; will be sorted.
> plot(result$regime, type = "l", xlab = "Day", ylab = "Regime", main = "Estimated Regime")
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'ylim' values
Calls: plot -> plot.default -> localWindow -> plot.window
Execution halted
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.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.5Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) rules.Rd:24: Lost braces; missing escapes or markup?
    24 | \item Absent names are replaced with the 'rule__\\{ind\\}' where \\{ind\\} is the
       |                                                   ^
checkRd: (-1) rules.Rd:24: Lost braces; missing escapes or markup?
    24 | \item Absent names are replaced with the 'rule__\\{ind\\}' where \\{ind\\} is the
       |                                                                    ^
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  ‘nimble’ ‘nimbleAPT’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.2Mb
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    doc   4.7Mb
'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) }
       |                                                                                   ^
installed size is 48.3Mb
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    libs  47.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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    include   5.1Mb
installed size is 60.8Mb
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    include   5.0Mb
    libs     55.3Mb
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}).
       |                               ^
checkRd: (-1) dGenWish.Rd:48: Lost braces
    48 |   -df/2*log|L(2*Sigma)L'| -1/2*tr{ (L(2*Sigma)L')^-1 L(-D)L' }
       |                                  ^
checkRd: (-1) get.Q.Rd:9: Lost braces
     9 |   equal to exp{b1*x_1ij + ... + bp*x_pij}, where beta=(b1,b2,...,bp) is
       |               ^
checkRd: (-1) get.Q.Rd:10: Lost braces; missing escapes or markup?
    10 |   a vector of log-conductance values of the covariates {x_kij}.  Each
       |                                                        ^
checkRd: (-1) mcmc.wish.icar.Rd:73: Lost braces; missing escapes or markup?
    73 |   a vector of log-conductance values of the covariates {x_kij}.  Each
       |                                                        ^
Package suggested but not available for checking: ‘rWCVPdata’
installed size is  5.9Mb
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    data      3.2Mb
    extdata   2.4Mb
Specified C++11: please drop specification unless essential
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is  6.4Mb
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    data   2.1Mb
    doc    3.9Mb
installed size is  5.1Mb
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    data   5.0Mb
Malformed Title field: should not end in a period.
checkRd: (-1) wtss_to_ts.Rd:31: Lost braces; missing escapes or markup?
    31 | This period can be either {"month", "week", "day"}, 
       |                           ^
checkRd: (-1) wtss_to_ts.Rd:32: Lost braces; missing escapes or markup?
    32 | {"months", "weeks", "days"} or
       | ^
checkRd: (-1) wtss_to_ts.Rd:33: Lost braces; missing escapes or markup?
    33 | {12, 52, 365}. This function creates a new time series with the required 
       | ^
'LazyData' is specified without a 'data' directory
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installed size is 15.1Mb
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installed size is 30.0Mb
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installed size is  7.0Mb
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installed size is  5.8Mb
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checkRd: (-1) plot.eff.ridge.Rd:6: Lost braces
     6 |  emph{Single Interior Knot} at the MSE Optimal m-Extent of Shrinkage. The
       |      ^
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Specified C++11: please drop specification unless essential
installed size is  9.5Mb
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    libs    7.7Mb
    yacas   1.3Mb
Specified C++14: please drop specification unless essential
installed size is 10.3Mb
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    libs    8.4Mb
    yacas   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is 15.8Mb
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checkRd: (-1) ZigZagLogistic.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                   ^
checkRd: (-1) ZigZagLogistic.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                                 ^
checkRd: (-1) ZigZagLogistic.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{dataY}{Vector of length n containing {0, 1}-valued observations of the dependent variable y.}
       |                                            ^
installed size is 12.3Mb
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checkRd: (-1) ciReg.Rd:10: Lost braces
    10 | \item{fit}{an object of class{lm}, i.e. the output from \code{\link{lm}}.}
       |                              ^
Specified C++14: please drop specification unless essential
installed size is 37.9Mb
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checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘sadists.Rnw’ using knitr
Error: processing vignette 'sadists.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'sadists.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.352 \hlkwd{require}\hldef
                           {(ggplot2)}
? 
! Emergency stop.
! Emergency stop.
l.352 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘sadists.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
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    libs   6.5Mb
checkRd: (-1) sim_setup_preconfigured.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:31: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) sf_get_all_jobs_bulk.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_jobs_bulk.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_query_jobs_bulk.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_query_jobs_bulk.Rd:45-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_query_jobs_bulk.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) valid_metadata_list.Rd:10: Lost braces
    10 | code{list}; contains name and valid inputs for data types
       |     ^
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
Running ‘testthat.R’ [15s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [11] "( 0.949, 1.248)" | "( 0.949, 1.248)" [11]
  [12] "0.785"           | "0.785"           [12]
  
       actual             | expected               
  [13] "1"                | "1"                [13]
  [14] "1795"             | "1795"             [14]
  [15] "-0.342"           | "-0.342"           [15]
  [16] "(-0.577, -0.106)" - "(-0.576, -0.108)" [16]
  [17] "-1.704"           | "-1.704"           [17]
  [18] "(-1.908, -1.500)" | "(-1.908, -1.500)" [18]
  [19] "1.229"            | "1.229"            [19]
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 38 ]
  Error: Test failures
  Execution halted
checkRd: (-1) binaryChoice.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:111: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:113: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:114: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rnw’ using knitr
Error: processing vignette 'my-vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'my-vignette.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.873 \hlkwd{library}\hldef
                           {(samplingDataCRT)}
? 
! Emergency stop.
! Emergency stop.
l.873 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘my-vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
Specified C++11: please drop specification unless essential
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
installed size is 54.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  51.6Mb
Specified C++11: please drop specification unless essential
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.9Mb
checkRd: (-1) ModelHMMR-class.Rd:37: Lost braces; missing escapes or markup?
    37 |         class {StatHMMR}).
       |               ^
Packages suggested but not available for checking:
  'networkTomography', 'org.Sc.sgd.db'
‘sandwich-CL.Rnw’... [10s/12s] NOTE
differences from ‘sandwich-CL.Rout.save’
82c82
< Classes and Methods for R originally developed in the
---
> Classes and Methods for R developed in the
85,87c85,87
< Stanford University (2002-2015),
< by and under the direction of Simon Jackman.
< hurdle and zeroinfl functions by Achim Zeileis.
---
> Stanford University
> Simon Jackman
> hurdle and zeroinfl functions by Achim Zeileis
  ‘sandwich-OOP.Rnw’... [2s/2s] OK
  ‘sandwich.Rnw’... [1s/1s] OK
'LazyData' is specified without a 'data' directory
installed size is 54.8Mb
  sub-directories of 1Mb or more:
    libs  54.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    bin   4.5Mb
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.1Mb
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       5.1Mb
    extdata   1.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   3.1Mb
checkRd: (-1) gen.ds.Rd:43-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gen.ds.Rd:50-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gen.ds.Rd:64-65: Lost braces
    64 |    \item{the dependence parameter \code{dep} or the vector of dependence parameters \code{dep}. When missing, these coefficients are obtained from independent standard uniform sampling.
       |         ^
checkRd: (-1) gen.ds.Rd:66: Lost braces
    66 |    \item{the list \code{asy} of asymmetric weights \eqn{\beta_{i,b}} for \eqn{b \in B}  and \eqn{i \in b}. When missing, these coefficients are obtained from independent standard uniform sampling followed by renormalization in order to satisfy the sum-to-one constraints.}
       |         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   3.9Mb
checkRd: (-1) OTC.Rd:42: Lost braces; missing escapes or markup?
    42 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
checkRd: (-1) OTC.Rd:83: Lost braces; missing escapes or markup?
    83 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
checkRd: (-1) OTHist.Rd:29: Lost braces; missing escapes or markup?
    29 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
checkRd: (-1) dOTC.Rd:72: Lost braces; missing escapes or markup?
    72 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) setData.ReducedRankRegressions.Rd:14-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setData.ReducedRankRegressions.Rd:17-18: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
License stub is invalid DCF.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) getSigmaR.Rd:13-14: Lost braces
    13 |   \item{digits}{digits}{number of decimal places to use when rounding,
       |                        ^
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
checkRd: (-1) get.events.Rd:51: Lost braces
    51 |   code{\link[deSolve]{events}}
       |       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) scatterD3.Rd:209: Lost braces; missing escapes or markup?
   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       | ^
checkRd: (-1) scatterD3.Rd:209: Lost braces
   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       |                                              ^
checkRd: (-1) PermBiclust.beta.ks.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.beta.ks.Rd:30: Lost braces
    30 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
checkRd: (-1) PermBiclust.sigclust.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.sigclust.Rd:33: Lost braces
    33 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
checkRd: (-1) PermBiclust.sigclust_stop.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.sigclust_stop.Rd:36: Lost braces
    36 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package suggested but not available for checking: ‘Linnorm’
checkRd: (-1) scdensity.Rd:119-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:121-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:124-126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:127-130: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:131-135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:136-138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:139-142: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:143-144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:145-147: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
checkRd: (-1) get_profile.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) schoRsch.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:45: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/scorematchingad.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) reduce_dimensionality.Rd:19: Lost braces
    19 | \item{ndim}{the maximum dimension of the space which the data are to be represented in; must be in {1, 2, \ldots, n-1}.}
       |                                                                                                    ^
checkRd: (-1) ti_scorpius.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{distance_method}{A character string indicating which correlationcoefficient (or covariance) is to be computed. One of "pearson", "spearman" (default), or "cosine". Domain: {spearman, pearson, cosine}. Default: spearman. Format: character.}
       |                                                                                                                                                                                   ^
checkRd: (-1) ti_scorpius.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{smoother}{\code{principal_curve} parameter; choice of smoother. Domain: {smooth_spline, lowess, periodic_lowess}. Default: smooth_spline. Format: character.}
       |                                                                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
checkRd: (-1) scriptloc.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Get location of script in a fashion analagous to ${BASH_SOURCE[0]}}
       |                                                          ^
'LazyData' is specified without a 'data' directory
'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
'LazyData' is specified without a 'data' directory
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                  ^
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                                         ^
checkRd: (-1) geom_flat_violin.Rd:7: Lost braces
     7 | url{https://gist.github.com/dgrtwo/eb7750e74997891d7c20}
       |    ^
checkRd: (-1) sda.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:24: Lost braces in \itemize; meant \describe ?
installed size is  6.8Mb
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    libs   4.0Mb
checkRd: (-1) sdc_extabs.Rd:59: Lost braces
    59 | (including ]code{forcelist} variables) that can be used to form tables.}
       |                 ^
installed size is  7.9Mb
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    R      2.1Mb
    libs   5.5Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 89.4Mb
  sub-directories of 1Mb or more:
    libs  87.4Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) msdpd.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:91: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) msdpdth.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hyperpar.Rd:17: Lost braces
    17 | \item{c}{denotes the expected range of eqn{f} .}
       |                                           ^
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
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    R   8.6Mb
checkRd: (-1) seas.check.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:58: Lost braces in \itemize; meant \describe ?
installed size is 19.3Mb
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    extdata  18.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘secrlinear-vignette.Rmd’ using rmarkdown

Quitting from lines 585-611 [secrdesign] (secrlinear-vignette.Rmd)
Error: processing vignette 'secrlinear-vignette.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘secrlinear-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  14.4Mb
GNU make is a SystemRequirements.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) seedCCA.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{u}{numeric, maximum number of projections. The default is 10. This is used for \code{type="seed1"}, \code{type="seed2"} and {tyepe="pls"}.}
       |                                                                                                                                   ^
installed size is 10.7Mb
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    data   2.9Mb
    libs   7.6Mb
Package suggested but not available for checking: ‘rsbml’
Error(s) in re-building vignettes:
  ...
--- re-building ‘SEI_vignette.Rnw’ using knitr
Error: processing vignette 'SEI_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'SEI_vignette.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.269 \hldef
            {x} \hlkwb{<-} \hlkwd{rgamma}\hldef{(}\hlnum{1000}\hldef{,} \hlk...

? 
! Emergency stop.
l.269 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SEI_vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    www  34.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) convert2snafu.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:36: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) convert2snafu.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) correct.changes.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) textcleaner.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) textcleaner.Rd:100-101: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) textcleaner.Rd:116: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:119: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:130: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) append.dictionary.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:44-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:89-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:95-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NRW.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NRW.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.compareShiny.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.compareShiny.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.compareShiny.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) information.criteria.Rd:33: Lost braces
    33 |         \emph{Psychometrika}  bold{52}, 345--370.
       |                                   ^
checkRd: (-1) specifyModel.Rd:49: Lost braces
    49 |     to specifying the ]code{file} argument or reading the model specification from
       |                            ^
checkRd: (-1) 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
Package suggested but not available for checking: ‘ctsemOMX’
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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   2.5Mb
Specified C++11: please drop specification unless essential
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs    21.1Mb
    models   1.6Mb
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.1Mb
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.3Mb
Error(s) in re-building vignettes:
--- re-building ‘seqDesignInstructions.Rnw’ using knitr
Error: processing vignette 'seqDesignInstructions.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'seqDesignInstructions.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.85 \hldef
           {N.pla} \hlkwb{<-} \hlnum{1900}
? 
! Emergency stop.
! Emergency stop.
l.85 
     
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘seqDesignInstructions.Rnw’

--- re-building ‘seqDesignReportTemplate.pdf.asis’ using asis
--- finished re-building ‘seqDesignReportTemplate.pdf.asis’

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

Error: Vignette re-building failed.
Execution halted
Specified C++14: please drop specification unless essential
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
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}]
       |                                                                     ^
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs  10.3Mb
Error(s) in re-building vignettes:
--- re-building ‘seqHMM.Rnw’ using knitr
Error: processing vignette 'seqHMM.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'seqHMM.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.555 \hlkwd{library}\hldef
                           {(}\hlsng{"seqHMM"}\hldef{)}
? 
! Emergency stop.
! Emergency stop.
l.555 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘seqHMM.Rnw’

--- re-building ‘seqHMM_algorithms.Rnw’ using knitr
--- finished re-building ‘seqHMM_algorithms.Rnw’

--- re-building ‘seqHMM_estimation.Rnw’ using knitr
--- finished re-building ‘seqHMM_estimation.Rnw’

--- re-building ‘seqHMM_visualization.Rnw’ using knitr
Error: processing vignette 'seqHMM_visualization.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'seqHMM_visualization.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.172 \hlkwd{library}\hldef
                           {(}\hlsng{"seqHMM"}\hldef{)}
? 
! Emergency stop.
! Emergency stop.
l.172 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘seqHMM_visualization.Rnw’

SUMMARY: processing the following files failed:
  ‘seqHMM.Rnw’ ‘seqHMM_visualization.Rnw’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Found the following significant warnings:
  SingleChromosomeVCFIndex.cpp:109:51: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat]
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/seqminer.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.sdk’
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
GNU make is a SystemRequirements.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pwalign’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
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', 'monocle', 'presto'
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   8.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 268.6Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    libs    262.2Mb
    sqlite    1.5Mb
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rmarkdown’
checkRd: (-1) st_as_sftime.Rd:71: Lost braces
    71 | remove these columns from code{data.frame}?}
       |                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rnw’ using knitr
Error: processing vignette 'vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.326 \hlkwd{library}\hldef
                           {(SGB)}
? 
! Emergency stop.
! Emergency stop.
l.326 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.8Mb
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
Error(s) in re-building vignettes:
--- re-building ‘AsymptoticMarkowitz.Rnw’ using knitr
--- finished re-building ‘AsymptoticMarkowitz.Rnw’

--- re-building ‘SharpeR.Rnw’ using knitr
Error: processing vignette 'SharpeR.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'SharpeR.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.205 \hlkwd{library}\hldef
                           {(SharpeR)}
? 
! Emergency stop.
! Emergency stop.
l.205 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SharpeR.Rnw’

--- re-building ‘SharpeRatio.Rnw’ using knitr
Warning in as.character.POSIXt(as.POSIXlt(x), ...) :
  as.character(td, ..) no longer obeys a 'format' argument; use format(td, ..) ?
Warning in as.character.POSIXt(as.POSIXlt(x), ...) :
  as.character(td, ..) no longer obeys a 'format' argument; use format(td, ..) ?
Error: processing vignette 'SharpeRatio.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'SharpeRatio.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.1695 \hlkwd{require}\hldef
                            {(MASS)}
? 
! Emergency stop.
! Emergency stop.
l.1695 
       
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SharpeRatio.Rnw’

SUMMARY: processing the following files failed:
  ‘SharpeR.Rnw’ ‘SharpeRatio.Rnw’

Error: Vignette re-building failed.
Execution halted
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})}
       |                              ^
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) shiftrPrepare.Rd:37: Lost braces
    37 |     See code{\link{shiftrPermBinary}} function and the respective example.
       |             ^
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
'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’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    shinymgr    1.4Mb
    tutorials   3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘uchardet’
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
'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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'LazyData' is specified without a 'data' directory
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installed size is 14.1Mb
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    R     2.0Mb
    www  10.3Mb
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    13 | A string `"{tagId}-shinyreforms-validation"`.
       |            ^
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    18 | Custom function for adding a CSS class used in {shinysurveys}.
       |                                                ^
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    16 | Custom function for disabling an HTML element in {shinysurveys}.
       |                                                  ^
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    16 | Custom function for disabling an HTML element in {shinysurveys}.
       |                                                  ^
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    12 | \item{extension}{A shiny input type not natively supported by {shinysurveys}. See the examples section for more information.}
       |                                                               ^
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    15 | default, and the built-in {shinysurveys} userID will be used.}
       |                           ^
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    18 | \item{...}{Additional arguments specific to {shinysurveys} required questions.}
       |                                             ^
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    18 | Custom function for removing a CSS class used in {shinysurveys}.
       |                                                  ^
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    18 | Custom function for toggling enable/disable state of HTML element in {shinysurveys}.
       |                                                                      ^
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    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
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  ...
--- re-building ‘shotGroups.Rnw’ using knitr
Error: processing vignette 'shotGroups.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'shotGroups.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.183 \hlkwd{library}\hldef
                           {(shotGroups,} \hlkwc{verbose}\hldef{=}\hlnum{FAL...

? 
! Emergency stop.
l.183 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘shotGroups.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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installed size is 12.4Mb
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Specified C++11: please drop specification unless essential
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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.'
       |                       ^
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    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}. 
       |                                                                                                                                                                                                                         ^
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    36 |   \code{drr} {is Rosin - Rammler probability density function}\cr
       |              ^
checkRd: (-1) drr.Rd:37: Lost braces; missing escapes or markup?
    37 |   \code{urr} {is Rosin - Rammler cumulative distribution function (CDF) representing undersize mass fraction}\cr
       |              ^
checkRd: (-1) drr.Rd:38: Lost braces
    38 |   \code{orr} {is Rosin - Rammler complementary CDF representing oversize mass fraction ie. relative remainder on the sieve with the mesh size \code{x}}\cr
       |              ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
installed size is  6.0Mb
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    help      1.7Mb
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checkRd: (-1) add_k_mer_state.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
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'LazyData' is specified without a 'data' directory
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Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) sig.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
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    64 | \item x_{l,i}, local variable l,
       |         ^
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    70 | \item d_{r,i} the distance between the center of pixel r and the observation at site i.
       |         ^
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    51 |     \item \code{dist = "binomial"} is drawn from eqn{Bin(XB, XB(1-XB))}
       |                                                     ^
Specified C++11: please drop specification unless essential
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--- re-building ‘simcausal_vignette.Rnw’ using knitr
Error: processing vignette 'simcausal_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'simcausal_vignette.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.736 \hlkwd{library}\hldef
                           {(}\hlsng{"simcausal"}\hldef{)}
? 
! Emergency stop.
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!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘simcausal_vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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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) {
       |                         ^
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'LazyData' is specified without a 'data' directory
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installed size is  6.1Mb
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GNU make is a SystemRequirements.
installed size is 14.6Mb
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    doc    1.5Mb
    libs  12.5Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
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}
       | ^
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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
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checkRd: (-1) cross.Rd:11: Lost braces
    11 | \item{x}{\code{\link{Pop-class}} or code{\link{Colony-class}} or \code{\link{MultiColony-class}},
       |                                         ^
installed size is  5.5Mb
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Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘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.
       |                                                                                                                                 ^
Package suggested but not available for checking: ‘INLA’
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    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
       |                                                     ^
checkRd: (-1) NAP.Rd:109: Lost braces
   109 | bounds for P{X<Y}, based on two independent samples. \emph{The Annals of
       |             ^
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checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ?
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Error(s) in re-building vignettes:
--- re-building ‘cindex.Rnw’ using knitr
Error: processing vignette 'cindex.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cindex.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.125 \hlkwd{library}\hldef
                           {(siplab)}
? 
! Emergency stop.
! Emergency stop.
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!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘cindex.Rnw’

--- re-building ‘gentle.Rnw’ using knitr
Error: processing vignette 'gentle.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'gentle.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.142 \hlkwd{curve}\hldef
                         {(}\hlkwd{abs}\hldef{(x} \hlopt{-} \hlnum{2}\hldef{...

? 
! Emergency stop.
l.142 
      
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!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘gentle.Rnw’

SUMMARY: processing the following files failed:
  ‘cindex.Rnw’ ‘gentle.Rnw’

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   6.8Mb
Specified C++11: please drop specification unless essential
installed size is  7.4Mb
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checkRd: (-1) sitar-package.Rd:27: Lost braces; missing escapes or markup?
    27 | individual curves, adjusted for {abcd} to lie on top of (i.e. be
       |                                 ^
checkRd: (-1) sitar.Rd:110: Lost braces; missing escapes or markup?
   110 | \code{\link{nlme}}) (default {nlmeControl(returnObject = TRUE)}).}
       |                              ^
checkRd: (-1) rawCCD.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{distr.type}{school district type (constructed for illustration purposes; (values={"A", "B", "C", "D"})).}
       |                                                                                          ^
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    61 | \item{replacementUnitsFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "replacementUnits.csv"}
       |                                                                    ^
checkRd: (-1) selectMatch.Rd:63: Lost braces; missing escapes or markup?
    63 | \item{subUnitTableFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "subUnitTable.csv"}
       |                                                                ^
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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.
       |                                  ^
checkRd: (-1) selectMatch.Rd:66: Lost braces; missing escapes or markup?
    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                                                                                  ^
'LazyData' is specified without a 'data' directory
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
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
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checkRd: (-1) ss.cc.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ss.ci.Rd:26: Lost braces
    26 | \item{alpha}{The eqn{\\alpha} error used to compute the \eqn{100*(1-\\alpha)\%} confidence interval}
       |                     ^
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    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |     ^
checkRd: (-1) ss.rr.Rd:84: Lost braces; missing escapes or markup?
    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |                 ^
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    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                            ^
checkRd: (-1) ss.rr.Rd:87: Lost braces; missing escapes or markup?
    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                                        ^
Error(s) in re-building vignettes:
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--- re-building ‘skellam.rnw’ using knitr
Error: processing vignette 'skellam.rnw' failed with diagnostics:
Running 'texi2dvi' on 'skellam.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.98 \hlkwd{library}\hldef
                          {(}\hlsng{'skellam'}\hldef{)}
? 
! Emergency stop.
! Emergency stop.
l.98 
     
End of file on the terminal!

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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
installed size is  7.1Mb
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    doc    1.1Mb
    libs   4.9Mb
GNU make is a SystemRequirements.
installed size is 39.2Mb
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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] +
       |          ^
Problems with news in ‘NEWS.md’:
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    14 | \item{d}{A list d{[[j]]} whose elements are vectors of variable names from A defining marginal tables/cubes 
       |                  ^
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    24 | D = {D[[j]]} of marginal tables/cubes of A spesified by the list d = d{[[j]]} generated 
       |     ^
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    24 | D = {D[[j]]} of marginal tables/cubes of A spesified by the list d = d{[[j]]} generated 
       |                                                                       ^
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    31 | \item{d}{A list d{[[j]]} whose elements are vectors of variable names from A defining marginal tables/cubes D
       |                  ^
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    15 | \item{d}{A list d{[[j]]} whose elements are vectors of variable names from A defining marginal tables/cubes D
       |                  ^
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GNU make is a SystemRequirements.
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     6 | A subset of world.cities{maps}. Extracted in order to shink number of dependencies. 
       |                         ^
Problems with news in ‘NEWS.md’:
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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}
       |             ^
Problems with news in ‘NEWS.md’:
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There are ::: calls to the package's namespace in its code. A package
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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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Error: processing vignette 'snplist.Rnw' failed with diagnostics:
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! Undefined control sequence.
l.8 \hldef
          {genes} \hlkwb{<-} \hlkwd{c}\hldef{(}\hlsng{"BRCA1"}\hldef{,}\hlsn...

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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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    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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     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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   101 | code{spe} command; (4) \code{alpha} stores significance level as in
       |     ^
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--- finished re-building ‘adaptation.Rmd’

--- re-building ‘isotherms.rnw’ using knitr
Error: processing vignette 'isotherms.rnw' failed with diagnostics:
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LaTeX errors:
! Undefined control sequence.
l.182 \hlkwd{library}\hldef
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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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    47 | We want the counterfactual Yhat_{g' <- G} |X=x,G=g (or alternatively
       |                                 ^
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    48 | Yhat_{g' <- G} |G=g).
       |      ^
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    58 | To estimate Y'=Yhat_{g' <- G} | G=g, we need to
       |                     ^
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    65 | To estimate Y'=Yhat_{g' <- G} |X=x, G=g, we need to
       |                     ^
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    27 | indices representing sample(s) from counterfactual  Yhat_{g' <- G} |X=x,G=g
       |                                                          ^
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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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       |                      ^
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       |                                   ^
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       |                                            ^
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    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                                     ^
S3 methods shown with full name in Rd file 'SparseM.ontology.Rd':
  ‘as.matrix.csr’ ‘is.matrix.csr’ ‘is.matrix.csc’ ‘is.matrix.ssr’
  ‘is.matrix.ssc’ ‘is.matrix.coo’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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    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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    47 | \env{printit}{
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    50 | \env{stage}{
       |            ^
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/spaths.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.
installed size is  6.1Mb
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GNU make is a SystemRequirements.
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Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', 'spatstat', 'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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  'spatstat.data', 'spatstat.sparse', 'spatstat.univar',
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model'
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.sparse',
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.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
selectively is preferable.
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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’:
  Cannot extract version info from the following section titles:
    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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Undocumented S4 methods:
  generic '[' and siglist 'SpectraInTime,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTime,missing,ANY,ANY'
  generic '[' and siglist 'SpectraInTime,missing,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,ANY,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,missing,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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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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    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})
       |                                                                                                                                                                  ^
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Problems with news in ‘NEWS.md’:
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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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    15 | href{https://developer.spotify.com/documentation/general/guides/track-relinking-guide/}{Track Relinking}}
       |     ^
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    15 | href{https://developer.spotify.com/documentation/general/guides/track-relinking-guide/}{Track Relinking}}
       |                                                                                        ^
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       |                                 ^
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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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       |                                                         ^
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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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       |                                                         ^
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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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       |                    ^
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    67 | \item{het}{default {FALSE}: if {TRUE} uses the methods 
       |                                ^
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       |                   ^
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       |                              ^
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    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                                             ^
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    36 | \item{...}{Other values "obsData", "fittedData" and "residuals" are provided only for temporal prediction. This is to analyse the code{spTimer} forecast output using package \code{forecast} through function \code{\link{as.forecast.object}}.}
       |                                                                                                                                       ^
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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
'LazyData' is specified without a 'data' directory
installed size is 43.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  40.6Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘ssizeRNA.Rnw’ using knitr
Error: processing vignette 'ssizeRNA.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'ssizeRNA.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.140 \hlkwd{library}\hldef
                           {(ssizeRNA)}
? 
! Emergency stop.
! Emergency stop.
l.140 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘ssizeRNA.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 127.2Mb
  sub-directories of 1Mb or more:
    libs  126.7Mb
GNU make is a SystemRequirements.
checkRd: (-1) new.distance.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:33-34: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) sensitivity.plot.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:38-40: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                   ^
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                              ^
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                                      ^
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) SRanalysis.Rd:100: Lost braces
   100 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
checkRd: (-1) StabilizedRegression.Rd:109: Lost braces
   109 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) stabsel_parameters.Rd:42: Lost braces
    42 |     always use code{"none"}.}
       |                    ^
checkRd: (-1) stabsel_stabsel.Rd:25: Lost braces
    25 |     always use code{"none"}.}
       |                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) stackExample.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stackExample.Rd:11: Lost braces in \itemize; meant \describe ?
installed size is 36.4Mb
  sub-directories of 1Mb or more:
    libs  35.8Mb
checkRd: (-1) stamppFst.Rd:20: Lost braces
    20 | \code{Fsts}{a matrix of pairwise Fst values between populations}
       |            ^
checkRd: (-1) stamppFst.Rd:21: Lost braces
    21 | \code{Pvalues}{a matrix of p-values for each of the pairwise Fst values containined in the 'Fsts' matrix}
       |               ^
checkRd: (-1) stamppFst.Rd:22: Lost braces
    22 | \code{Bootstraps}{a dataframe of each Fst value generated during Bootstrapping and the associated confidence intervals}
       |                  ^
installed size is 51.2Mb
  sub-directories of 1Mb or more:
    libs  50.8Mb
checkRd: (-1) standardize.Rd:94: Lost braces; missing escapes or markup?
    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                ^
checkRd: (-1) standardize.Rd:94: Lost braces; missing escapes or markup?
    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                                           ^
checkRd: (-1) alertify.Rd:69: Lost braces
    69 | \item{closable}{Logical; if \code{TRUE} (the default), a |code{Close} button is displayed in the header of the dialog.}
       |                                                               ^
checkRd: (-1) notify.Rd:47: Lost braces
    47 | \item{hide}{Logical; if \code{TRUE} (the default), notice is closed after |code{delay} specified in milliseconds.}
       |                                                                                ^
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    include  11.7Mb
    lib       3.7Mb
GNU make is a SystemRequirements.
installed size is 103.4Mb
  sub-directories of 1Mb or more:
    libs  102.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_fields.Rd:27: Lost braces
    27 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
checkRd: (-1) identify_form_fields.Rd:34: Lost braces
    34 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
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    67 |    \item $S_{275-295}$ slope between 275 and 295 nm calculated with nonlinear regression
       |             ^
checkRd: (-1) abs_parms.Rd:68: Lost braces; missing escapes or markup?
    68 |    \item $S_{350-400}$ slope between 350 and 400 nm calculated with nonlinear regression
       |             ^
checkRd: (-1) abs_parms.Rd:69: Lost braces; missing escapes or markup?
    69 |    \item $S_{300-700}$ slope between 275 and 295 nm calculated with nonlinear regression
       |             ^
checkRd: (-1) abs_parms.Rd:70: Lost braces; missing escapes or markup?
    70 |    \item SR slope ratio, calculated by $S_{275-295}$/$S_{350-400}$
       |                                           ^
checkRd: (-1) abs_parms.Rd:70: Lost braces; missing escapes or markup?
    70 |    \item SR slope ratio, calculated by $S_{275-295}$/$S_{350-400}$
       |                                                         ^
checkRd: (-1) abs_parms.Rd:71: Lost braces; missing escapes or markup?
    71 |    \item E2:E3 ratio $a_{250}$/$a_{365}$
       |                         ^
checkRd: (-1) abs_parms.Rd:71: Lost braces; missing escapes or markup?
    71 |    \item E2:E3 ratio $a_{250}$/$a_{365}$
       |                                   ^
checkRd: (-1) abs_parms.Rd:72: Lost braces; missing escapes or markup?
    72 |    \item E4:E6 ratio $a_{465}$/$a_{665}$
       |                         ^
checkRd: (-1) abs_parms.Rd:72: Lost braces; missing escapes or markup?
    72 |    \item E4:E6 ratio $a_{465}$/$a_{665}$
       |                                   ^
checkRd: (-1) abs_parms.Rd:73: Lost braces; missing escapes or markup?
    73 |    \item $a_{254}$ absorbance at 254 nm
       |             ^
checkRd: (-1) abs_parms.Rd:74: Lost braces; missing escapes or markup?
    74 |    \item $a_{300}$ absorbance at 300 nm
       |             ^
checkRd: (-1) stargazer.Rd:229: Lost braces
   229 |   \item{report}{a character string containing only elements of {\code{"v"}, \code{"c"}, \code{"s"},\code{"t"}, \code{"p"}, \code{"*"}} that determines whether, and in which order, variable names (\code{"v"}), coefficients (\code{"c"}), standard errors/confidence intervals (\code{"s"}), test statistics (\code{"t"}) and p-values (\code{"p"}) should be reported in regression tables. If one of the aforementioned letters is followed by an asterisk (\code{"*"}), significance stars will be reported next to the corresponding statistic.}
       |                                                                ^
checkRd: (-1) stargazer.Rd:246: Lost braces
   246 |   \item{table.placement}{a character string containing only elements of {\code{"h"}, \code{"t"},\code{"b"}, \code{"p"}, \code{"!"}, \code{"H"}} that determines the table placement in its LaTeX floating environment.}
       |                                                                         ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘starsdata’
installed size is  6.4Mb
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    doc   2.4Mb
    nc    1.7Mb
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) AutoPollution.Rd:16: Lost braces
    16 |     \code{Side} \tab {Side of vehicle: code{1}=right or \code{2}=left}\cr
       |                                            ^
'LazyData' is specified without a 'data' directory
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    22 | \code{statcan_data()} function has 2 arguments to fulfill to get data: {tableNumber} & {lang}.
       |                                                                        ^
checkRd: (-1) statcan_data.Rd:22: Lost braces; missing escapes or markup?
    22 | \code{statcan_data()} function has 2 arguments to fulfill to get data: {tableNumber} & {lang}.
       |                                                                                        ^
checkRd: (-1) statcan_search.Rd:18: Lost braces; missing escapes or markup?
    18 | The \code{statcan_search()} function has 2 arguments to fulfill to find a database: {keywords} and {lang}.
       |                                                                                     ^
checkRd: (-1) statcan_search.Rd:18: Lost braces; missing escapes or markup?
    18 | The \code{statcan_search()} function has 2 arguments to fulfill to find a database: {keywords} and {lang}.
       |                                                                                                    ^
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Specified C++11: please drop specification unless essential
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   5.2Mb
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
installed size is  5.0Mb
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installed size is  7.3Mb
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checkRd: (-1) plot.QTLMPP.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.QTLMPP.Rd:35: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) plot.QTLMPP.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.gDataMPP.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.gDataMPP.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.gDataMPP.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.gDataMPP.Rd:45-46: Lost braces in \itemize; meant \describe ?
installed size is  7.5Mb
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Package suggested but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: ‘networksis’
unable to reach CRAN

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sample2indp.pow.Rd:48: Lost braces
    48 | Pooled standard deviation= \code{sp} = sqrt{((n1 - 1) sigma1^2 +(n2 - 1) sigma2^2) / (n1 + n2 - 2)}
       |                                            ^
Package suggested but not available for checking: ‘imputeMissings’
installed size is  6.2Mb
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    shiny-apps   6.2Mb
checkRd: (-1) rankSTB.Rd:31: Lost braces; missing escapes or markup?
    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                        ^
checkRd: (-1) rankSTB.Rd:31: Lost braces; missing escapes or markup?
    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                                                                  ^
checkRd: (-1) rankSTB.Rd:31: Lost braces; missing escapes or markup?
    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                                                                      ^
checkRd: (-1) stb.default.Rd:43: Lost braces
    43 | sampling from the standard normal distribution. Another example is defining func=function(n){rchisq(n=n, df=3, ncp=2)}
       |                                                                                             ^
installed size is  7.0Mb
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installed size is 25.0Mb
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checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
installed size is 94.9Mb
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checkRd: (-1) keypoints.Rd:35-36: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:37-39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:40-44: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:45-48: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:49-50: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:63-65: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:66-67: Lost braces in \enumerate; meant \describe ?
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) STEPCAM_ABC.Rd:19: Lost braces
    19 |   \code{rows}{ every row corresponds to a different plot or community} \cr
       |              ^
checkRd: (-1) STEPCAM_ABC.Rd:20: Lost braces
    20 |   \code{columns}{ every column corresponds to a different species.} \cr
       |                 ^
checkRd: (-1) STEPCAM_ABC.Rd:25: Lost braces
    25 |   \code{rows}{ every row corresponds to a different species} \cr
       |              ^
checkRd: (-1) STEPCAM_ABC.Rd:26: Lost braces
    26 |   \code{columns}{ the first column contains the name of the species, every consecutive column corresponds to a different trait} \cr
       |                 ^
checkRd: (-1) plotSTEPCAM.Rd:16: Lost braces
    16 |             - \code{DA}{ a vector containing the posterior distribution for the parameter dispersal assembly} \cr
       |                        ^
checkRd: (-1) plotSTEPCAM.Rd:17: Lost braces
    17 |             - \code{HF}{ a vector containing the posterior distribution for the parameter habitat filtering} \cr
       |                        ^
checkRd: (-1) plotSTEPCAM.Rd:18: Lost braces
    18 |             - \code{LS}{ a vector containing the posterior distribution for the parameter limiting similarity} \cr
       |                        ^
checkRd: (-1) tuneParam.Rd:28: Lost braces; missing escapes or markup?
    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
checkRd: (-1) tuneParamCL2.Rd:28: Lost braces; missing escapes or markup?
    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
'LazyData' is specified without a 'data' directory
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Error(s) in re-building vignettes:
  ...
--- re-building ‘StepR.Rnw’ using knitr
Error: processing vignette 'StepR.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'StepR.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.224 \hlkwd{set.seed}\hldef
                            {(}\hlnum{1}\hldef{)}
? 
! Emergency stop.
! Emergency stop.
l.224 
      
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!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘StepR.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) landmarkMatrixToList.Rd:10: Lost braces
    10 |   \item{semilandmark.pattern}{a regular expression pattern passed to \code{sub()} for identifying and grouping curve points. The default is landmark names ending in one or more numbers. To disable grouping, set to code{''}.}
       |                                                                                                                                                                                                                           ^
checkRd: (-1) docker_config_collection.Rd:11: Lost braces; missing escapes or markup?
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("config")}
       | ^
checkRd: (-1) docker_container.Rd:13: Lost braces
    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_container")}
       | ^
checkRd: (-1) docker_image_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("image")}
       | ^
checkRd: (-1) docker_plugin_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("plugin")}
       | ^
checkRd: (-1) docker_service_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("service")}
       | ^
checkRd: (-1) docker_task.Rd:13: Lost braces
    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_task")}
       | ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.5Mb
Specified C++11: please drop specification unless essential
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.5Mb
installed size is 46.2Mb
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    libs  44.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘stockR.rnw’ using knitr
Error: processing vignette 'stockR.rnw' failed with diagnostics:
Running 'texi2dvi' on 'stockR.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.103 \hlkwd{install.packages}\hldef
                                    {(} \hlsng{"stockR"}\hldef{)}
? 
! Emergency stop.
! Emergency stop.
l.103 
      
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!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘stockR.rnw’

SUMMARY: processing the following file failed:
  ‘stockR.rnw’

Error: Vignette re-building failed.
Execution halted
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Running examples in ‘stortingscrape-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_topics
> ### Title: Get list of topics and sub-topics for the Norwegian parliament
> ### Aliases: get_topics
> 
> ### ** Examples
> 
> 
> # Request the data
> tops <- get_topics()
Error in `req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached: [data.stortinget.no] Resolving timed out after 10006 milliseconds
Backtrace:
    ▆
 1. └─stortingscrape::get_topics()
 2.   └─httr2::req_perform(req_error(base, is_error = function(resp) FALSE))
 3.     └─base::tryCatch(...)
 4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6.           └─value[[3L]](cond)
Execution halted
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installed size is 10.5Mb
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checkRd: (-1) powderymildew.Rd:14-16: Lost braces
    14 | \code{$demographic.coord}{
       |                          ^
checkRd: (-1) powderymildew.Rd:18-20: Lost braces
    18 | \code{$genetic.coord}{
       |                      ^
checkRd: (-1) powderymildew.Rd:22-24: Lost braces
    22 | \code{$demographic.measures}{
       |                             ^
checkRd: (-1) powderymildew.Rd:26-28: Lost braces
    26 | \code{$genetic.frequencies}{
       |                            ^
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
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Package suggested but not available for checking: ‘StrathE2E2examples’
checkRd: (-1) StrathE2E2-package.Rd:70: Lost braces; missing escapes or markup?
    70 | {Basic model operations:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:79: Lost braces; missing escapes or markup?
    79 | {Parameter estimation:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:88: Lost braces; missing escapes or markup?
    88 | {Sensitivity and Monte Carlo analyses:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:98: Lost braces; missing escapes or markup?
    98 | {Compare model runs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:105: Lost braces; missing escapes or markup?
   105 | {Fishery yield analysis:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:111: Lost braces; missing escapes or markup?
   111 | {Visualize model inputs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:117: Lost braces; missing escapes or markup?
   117 | {Visualize model outputs:} \cr
       | ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) isle.Rd:38: Lost braces
    38 | \code{\link[streamDAG]{stream.order}}, \code{\link[igraph]{delete.vertices}}, code{\link[igraph]{add.vertices}}, code{\link[igraph]{add.edges}}
       |                                                                                   ^
checkRd: (-1) isle.Rd:38: Lost braces
    38 | \code{\link[streamDAG]{stream.order}}, \code{\link[igraph]{delete.vertices}}, code{\link[igraph]{add.vertices}}, code{\link[igraph]{add.edges}}
       |                                                                                                                      ^
installed size is 13.0Mb
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    doc    1.7Mb
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Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘STRaitRazoR’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
installed size is  5.5Mb
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    53 | \emph{Festschrift 50 Jahre \"{O}sterreichische Statistische Gesellschaft}, 133-146,
       |                              ^
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    54 | \"{O}sterreichische Statistische Gesellschaft.
       |   ^
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   223 | Zeileis A., Kleiber C., Kr\"{a}mer W., Hornik K. (2003), Testing and Dating of
       |                             ^
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   109 | Kr\"{a}mer W., Ploberger W., Alt R. (1988), Testing for structural change in
       |     ^
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   119 | Ploberger W., Kr\"{a}mer W. (1992), The CUSUM test with OLS residuals,
       |                   ^
Specified C++11: please drop specification unless essential
installed size is 11.4Mb
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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
Error: processing vignette 'suppdata-intro.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'suppdata-intro.tex' failed.
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! Undefined control sequence.
l.89 \hlkwd{require}\hldef
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     6 | getFittedValues <- function(object) {
       |                                     ^
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    14 | getFittedValues <- function(object) {
       |                                     ^
surfaceSimulate : phytransform: no visible global function definition
  for ‘rescale’
Undefined global functions or variables:
  rescale
installed size is  6.7Mb
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installed size is  8.1Mb
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installed size is  8.5Mb
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installed size is 64.9Mb
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GNU make is a SystemRequirements.
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installed size is 10.4Mb
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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)}
       |                                                                     ^
installed size is 10.1Mb
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    66 | A {data.table} which is stored as an attribute of
       |   ^
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Error: processing vignette 'plots.Rnw' failed with diagnostics:
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! Undefined control sequence.
l.93 \hlkwd{data}\hldef
                       {(}\hlsng{"kidney"}\hldef{,} \hlkwc{package}\hldef{=}...

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--- re-building ‘survSNP.Rnw’ using knitr
Error: processing vignette 'survSNP.Rnw' failed with diagnostics:
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l.76 \hlkwd{library}\hldef
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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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Problems with news in ‘NEWS.md’:
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    pre-release switchboard (2020 - 2021)
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    18 |   \item{epsilon}{positive convergence tolerance \emph{e}; the iterations converge when |fit - fit_{old}|/|fit| < \emph{e}. Default is \emph{e=1e-04}.}
       |                                                                                                   ^
'LazyData' is specified without a 'data' directory
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installed size is 44.8Mb
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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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--- re-building ‘systemfit.Rnw’ using knitr
Error: processing vignette 'systemfit.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'systemfit.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.1496 \hldef
             {sigmaInv} \hlkwb{<-} \hlkwd{solve}\hldef{( residCov )}
? 
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!  ==> Fatal error occurred, no output PDF file produced!
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    32 | inside of curly brackets, i.e., { } . For instance, if estimate = 1.23
       |                                 ^
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    33 | and error = 0.45, then \code{form} = "{estimate} ({error})" will return
       |                                       ^
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    33 | and error = 0.45, then \code{form} = "{estimate} ({error})" will return
       |                                                   ^
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    68 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
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    67 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
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    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |   ^
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    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |                      ^
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Problems with news in ‘NEWS.md’:
No news entries found.
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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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       |                          ^
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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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    32 | link{squaredError}
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   427 |       \item  Changes to \code{simulate.stergm} parameters: addition of \code{duration.dependent} parameter: {Logical: Whether the model terms in formula or model are duration dependent. E.g., if a duration-dependent term  is used in estimation/simulation model, the probability of forming or dissolving a tie may dependent on the age the dyad status. If TRUE, the matrix of tie ages will be allocated.}
       |                                                                                                             ^
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    18 | code{\link[ergm:blocks-ergmConstraint]{blocks}} constraints and
       |     ^
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     9 | code{discordance_fraction} of proposed toggles being made on the set of discordant dyads,
       |     ^
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    19 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
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    23 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
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    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
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       |                                                                                ^
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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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    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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    14 | microbial genes like AbcD, default [A-Za-z][a-z]{2}[A-Z0-9]+}
       |                                                 ^
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checkRd: (-1) setup_sql_functions.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} System Functions}
       |                ^
checkRd: (-1) setup_sql_functions.Rd:17: Lost braces; missing escapes or markup?
    17 | Installs functions needed to operated {timeseriesdb} in
       |                                       ^
checkRd: (-1) setup_sql_grant_rights.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Grant execute on {timeseriesdb} functions}
       |                         ^
checkRd: (-1) setup_sql_grant_rights.Rd:17: Lost braces; missing escapes or markup?
    17 | Grant execute on {timeseriesdb} functions
       |                  ^
checkRd: (-1) setup_sql_tables.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} System Tables}
       |                ^
checkRd: (-1) setup_sql_tables.Rd:17: Lost braces; missing escapes or markup?
    17 | Installs tables needed to operated {timeseriesdb} in
       |                                    ^
checkRd: (-1) setup_sql_triggers.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} Triggers}
       |                ^
checkRd: (-1) POSIXst-class.Rd:247: Lost braces
   247 |   do any conversion on the POSIX{l,c}t objects).
       |                                 ^
checkRd: (-1) alcohol.Rd:16-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:22-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) add_md.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{body}{an XML object generated via {tinkr}}
       |                                         ^
checkRd: (-1) md_ns.Rd:13: Lost braces; missing escapes or markup?
    13 | The {commonmark} package is used to translate markdown to XML, but it does
       |     ^
checkRd: (-1) md_ns.Rd:14: Lost braces; missing escapes or markup?
    14 | not assign a namespace prefix, which means that {xml2} will auto-assign a
       |                                                 ^
checkRd: (-1) stylesheet.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{The {tinkr} stylesheet}
       |            ^
checkRd: (-1) stylesheet.Rd:14: Lost braces; missing escapes or markup?
    14 | This function returns the path to the {tinkr} stylesheet
       |                                       ^
checkRd: (-1) stylesheet.Rd:11: Lost braces; missing escapes or markup?
    11 | stylesheet used by {tinkr}.
       |                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) partition_undirected_graph.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{cutoff}{Numeric. The value max(0, g_{i,j} - cutoff) so that there are <\code{.num_components}> components in the graph.}
       |                                           ^
installed size is 98.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  94.9Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.5Mb
checkRd: (-1) tierChart.Rd:332: Lost braces
   332 |   If the input argument code{boxes} is \code{F}, the \code{lBox},
       |                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   4.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘tlm.Rnw’ using knitr
Error: processing vignette 'tlm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tlm.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.157 \hlkwd{library}\hldef
                           {(tlm)}
? 
! Emergency stop.
! Emergency stop.
l.157 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘tlm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Specified C++14: please drop specification unless essential
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
checkRd: (-1) pmvn.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvn.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvn.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:25: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    examples  12.6Mb
    include    3.6Mb
installed size is 47.9Mb
  sub-directories of 1Mb or more:
    libs  47.6Mb
GNU make is a SystemRequirements.
checkRd: (-1) tv_episode_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the episode_id value found in the change entries.
       |                                                 ^
checkRd: (-1) tv_season_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the season_id value found in the change entries.
       |                                                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) pvalEffectPlot.Rd:90: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) pvalEffectPlot.Rd:93: Lost braces in \itemize; meant \describe ?
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data-tables   1.4Mb
    doc           1.9Mb
    help          1.2Mb
checkRd: (-1) jsonStr.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Format data as a JSON object (like this: {"x": "120"}).}
       |                                                 ^
checkRd: (-1) jsonStr.Rd:18: Lost braces; missing escapes or markup?
    18 | Format data as a JSON object (like this: {"x": "120"}).
       |                                          ^
checkRd: (-1) fixed_width_no_modeling.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.Rd:10: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) Data.Rd:13: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) Data.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:17: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^
checkRd: (-1) getSegsExtra.Rd:14: Lost braces
    14 | \item{data}{data.table returned from function /code{tdtr}}
       |                                                    ^
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'
Error(s) in re-building vignettes:
  ...
--- re-building ‘TopKLists.Rnw’ using knitr
Error: processing vignette 'TopKLists.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'TopKLists.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.137 \hlkwd{library}\hldef
                           {(TopKLists)}
? 
! Emergency stop.
! Emergency stop.
l.137 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘TopKLists.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘gurobi’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
installed size is 199.5Mb
  sub-directories of 1Mb or more:
    R          6.1Mb
    help       1.7Mb
    include    1.8Mb
    libs     189.4Mb
Package suggested but not available for checking: ‘toscaData’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    data  13.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘TPmsm.Rnw’ using knitr
Error: processing vignette 'TPmsm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'TPmsm.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.748 \hlkwd{library}\hldef
                           {(}\hlsng{"TPmsm"}\hldef{);}
? 
! Emergency stop.
! Emergency stop.
l.748 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘TPmsm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) parse_beast_output_files.Rd:23: Lost braces
    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
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.8Mb
checkRd: (-1) Sim-Functions.Rd:99: Lost braces in \itemize; meant \describe ?
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 ?
checkRd: (-1) Sim-Functions.Rd:109-110: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) Sim-Functions.Rd:114-116: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) trait_missing.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) trait_missing.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘taxidata’
installed size is 68.7Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  66.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘tramvs.Rnw’ using knitr
Error: processing vignette 'tramvs.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tramvs.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.257 \hlkwd{args}\hldef
                        {(abess_tram)}
? 
! Emergency stop.
! Emergency stop.
l.257 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘tramvs.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) Blavet.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:19: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) Blavet.Rd:28: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) Blavet.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) trans.Rd:46: Lost braces; missing escapes or markup?
    46 | "Found {trans("file", .n = n_files)} in {trans("directory", .n = n_dirs)}".
       |        ^
checkRd: (-1) trans.Rd:46: Lost braces; missing escapes or markup?
    46 | "Found {trans("file", .n = n_files)} in {trans("directory", .n = n_dirs)}".
       |                                         ^
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Specified C++11: please drop specification unless essential
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Package which this enhances but not available for checking: ‘fwelnet’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'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:
  'CohortGenerator', 'Capr'
checkRd: (-1) trtsel.Rd:69: Lost braces; missing escapes or markup?
    69 | numeric with two values {0,1} and gaussian(link = "identity") otherwise.
       |                         ^
Package suggested but not available for checking: ‘TreeDistData’
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   3.1Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.4Mb
Package suggested but not available for checking: ‘treesitter’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   4.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   3.5Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    doc       1.3Mb
    extdata  14.8Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 136.9Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    libs  131.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 53.3Mb
  sub-directories of 1Mb or more:
    libs  52.8Mb
checkRd: (-1) coef.tridim_transformation.Rd:31: Lost braces
    31 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
checkRd: (-1) coef.tridim_transformation.Rd:32: Lost braces
    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
checkRd: (-1) coef.tridim_transformation.Rd:32: Lost braces; missing escapes or markup?
    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
checkRd: (-1) predict.tridim_transformation.Rd:24: Lost braces
    24 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
checkRd: (-1) predict.tridim_transformation.Rd:25: Lost braces
    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
checkRd: (-1) predict.tridim_transformation.Rd:25: Lost braces; missing escapes or markup?
    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
checkRd: (-1) variable_summary.Rd:18: Lost braces; missing escapes or markup?
    18 | data.frame with "{var_name}" column for the mean and
       |                  ^
checkRd: (-1) variable_summary.Rd:19: Lost braces; missing escapes or markup?
    19 | "{var_name}_{prob}" columns for each probability.
       |  ^
checkRd: (-1) variable_summary.Rd:19: Lost braces; missing escapes or markup?
    19 | "{var_name}_{prob}" columns for each probability.
       |             ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/triptych.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is 41.6Mb
  sub-directories of 1Mb or more:
    libs  41.3Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
checkRd: (-1) summary.armasubsets.Rd:16: Lost braces
    16 | \item{matrix.logical}{With matrix=TRUE, the matrix is logical TRUE/FALSE or string "*"/code{" "}}
       |                                                                                            ^
checkRd: (-1) tsBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diss.AR.LPC.CEPS.Rd:39: Lost braces; missing escapes or markup?
    39 | If \code{order.x} or {order.y} are \code{NULL}, their respective series will be fitted automatically using a AR model.
       |                      ^
checkRd: (-1) diss.AR.PIC.Rd:31: Lost braces; missing escapes or markup?
    31 | If \code{order.x} or {order.y} are \code{NULL}, their respective series will be fitted automatically using a AR model. If \code{permissive} is \code{TRUE} and no AR order is found automatically, an AR order of 1 will be imposed, if this case fails, then no order can be found and the function produces an error.
       |                      ^
'LazyData' is specified without a 'data' directory
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  15.6Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) example.database2.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database2.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database3.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database3.Rd:19: Lost braces in \itemize; meant \describe ?
installed size is 44.1Mb
  sub-directories of 1Mb or more:
    libs  43.5Mb
checkRd: (-1) binary_transform.Rd:16: Lost braces; missing escapes or markup?
    16 | Converts any variable with two possible values to a {0,1} binary
       |                                                     ^
checkRd: (-1) binary_transform.Rd:13: Lost braces; missing escapes or markup?
    13 | A vector with values in {0,1}.
       |                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 128.0Mb
  sub-directories of 1Mb or more:
    libs  126.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 111.6Mb
  sub-directories of 1Mb or more:
    libs  110.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) repr_dwt.Rd:28: Lost braces; missing escapes or markup?
    28 | The final representation has length equal to floor(n / 2^{level}), where n is a length of original time series.
       |                                                          ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Error(s) in re-building vignettes:
  ...
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    74 |         doi{10.1093/biomet/74.2.221}
       |            ^
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    25 | \item{xcov}{Either a \[stats]{formula} with an empty left-hand side specifying external covariates
       |                              ^
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    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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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
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Problems with news in ‘NEWS.md’:
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--- re-building ‘unifDAG-vignette.Rnw’ using knitr
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l.159 \hldef
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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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l.73 \hlkwd{install.packages}\hldef
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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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Quitting from lines 142-143 [tax] (vegdata.Rnw)
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SUMMARY: processing the following file failed:
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    51 | S = dbar/sqrt(2*pi*se_{d}(0)/N),
       |                       ^
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    53 | where d is the loss differential, d = e1 - e2 (e1 = loss(x, xhat1) and e2 = loss(x, xhat2)), dbar is its sample mean, and se_{d}(0) is the standard error for d, which must be estimated, and N is the length of the series investigated.  Let V = 2*pi*se_{d}(0), then V is estimated by
       |                                                                                                                              ^
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    53 | where d is the loss differential, d = e1 - e2 (e1 = loss(x, xhat1) and e2 = loss(x, xhat2)), dbar is its sample mean, and se_{d}(0) is the standard error for d, which must be estimated, and N is the length of the series investigated.  Let V = 2*pi*se_{d}(0), then V is estimated by
       |                                                                                                                                                                                                                                                            ^
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    21 | Do linear regression of form (X^T O X + P)^{-1} X^T y where O is omega, P is
       |                                            ^
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     6 | \title{Indexing to extract subsets of a 'code{\link[via:XArray-class]{VirtualArray}}'-class object}
       |                                              ^
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    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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    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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   350 |   \code{vMod = xMod^(1/lambda)} and {vArg = xArg^(1/lambda)}\cr\cr
       |                                     ^
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GNU make is a SystemRequirements.
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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.}
       |                                   ^
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    38 | Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
       |               ^
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GNU make is a SystemRequirements.
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--- re-building ‘vsgoftest_tutorial.Rnw’ using knitr
Error: processing vignette 'vsgoftest_tutorial.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'vsgoftest_tutorial.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.119 \hlkwd{install.packages}\hldef
                                    {(}\hlsng{'vsgoftest'}\hldef{)}
? 
! Emergency stop.
! Emergency stop.
l.119 
      
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
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     9 | Zeeden et al., (2013) and anchored to the code{\link{astrosignal_example}} \cr
       |                                               ^
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   206 | be off in certain intervals. the link[WaverideR]{retrack_wt_MC} mitigates
       |                                                 ^
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    40 | link[WaverideR]{analyze_wavelet} wavelet function
       |                ^
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    41 | To create a list use the link[base]{list} function}
       |                                    ^
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    44 | To create the matrix use the link[base]{cbind} function and only add the
       |                                        ^
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    24 | Note that coefficients returned by this function are in emph{packet order}. They can be used \emph{as is} but for many applications it might be more useful to deal with the coefficients in packets: see the function \code{\link{getpacket.wst}} for further details. 
       |                                                             ^
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    18 | \code{G}{Codes the value of the linear interpolant matrix for the corresponding entry in \code{gridt}. The value at each point corresponds to the proportion of the original data point pointed to by \code{Gindex} that contributes to the new value at the corresponding \code{gridt} value. See Kovac, (1997), page 81 for further information.}
       |         ^
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    13 | \item{gridn}{The number of grid points in the dyadic grid that the (x,y) gets interpolated to. By default this is the next power of two larger than the length of {x}.}
       |                                                                                                                                                                   ^
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    29 | /bold{12}, 45-56.
       |      ^
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    47 | The wd class of objects has methods for the following generic functions: \code{\link{plot}}, \code{\link{threshold}}, \code{\link{summary}}, \code{\link{print}}, code{\link{draw}}.
       |                                                                                                                                                                       ^
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    23 | \item{crs}{\code{character} or code{integer} object representing a
       |                                    ^
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    58 | <structure search> is assembled as "{\code{substructure} |
       |                                     ^
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    59 | \code{superstructure} | \code{similarity} | \code{identity}} / {\code{smiles}
       |                                                                ^
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    70 | "{\code{fastidentity} | \code{fastsimilarity_2d} | \code{fastsimilarity_3d} |
       |  ^
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    71 | \code{fastsubstructure} | \code{fastsuperstructure}}/{\code{smiles} |
       |                                                      ^
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   146 | sQuote{page load} timeout specifies a time to wait for the page loading
       |       ^
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    15 | /href{https://crawdad.org/coppe-ufrj/RioBuses/20180319/}
       |      ^
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
--- re-building ‘WeightedCluster.Rnw’ using knitr
Error: processing vignette 'WeightedCluster.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'WeightedCluster.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.195 \hldef
            {R> }\hlkwd{install.packages}\hldef{(}\hlsng{"WeightedCluster"}\...

? 
! Emergency stop.
l.195 
      
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!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘WeightedCluster.Rnw’

--- re-building ‘WeightedClusterFR.Rnw’ using knitr
Error: processing vignette 'WeightedClusterFR.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'WeightedClusterFR.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.197 \hldef
            {R> }\hlkwd{install.packages}\hldef{(}\hlsng{"WeightedCluster"}\...

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l.197 
      
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--- failed re-building ‘WeightedClusterFR.Rnw’

--- re-building ‘WeightedClusterPreview.Rnw’ using knitr
Error: processing vignette 'WeightedClusterPreview.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'WeightedClusterPreview.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.155 \hldef
            {R> }\hlkwd{install.packages}\hldef{(}\hlsng{"WeightedCluster"}\...

? 
! Emergency stop.
l.155 
      
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!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘WeightedClusterPreview.Rnw’

SUMMARY: processing the following files failed:
  ‘WeightedCluster.Rnw’ ‘WeightedClusterFR.Rnw’
  ‘WeightedClusterPreview.Rnw’

Error: Vignette re-building failed.
Execution halted
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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}.}
       |                            ^
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   149 | Composite likelihood {E}{M} algorithm with applications to
       |                         ^
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
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    14 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
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    21 | Let x_{i} be the income of the i-th person and \eqn{\overline{x}} be the mean income. Then the Hoover index H is:
       |       ^
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    21 | In the case of an empirical distribution with n elements where y_{i} denotes the wealth of household i and \eqn{\overline{y}} the sample average, the Ricci and Schutz coefficient can be expressed as:
       |                                                                  ^
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘wordnetDicts’
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Malformed Description field: should contain one or more complete sentences.
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Malformed Description field: should contain one or more complete sentences.
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Malformed Description field: should contain one or more complete sentences.
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    35 |         code{TRUE}. If any other value, the axis is not drawn.}
       |             ^
Malformed Title field: should not end in a period.
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    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}}.}
       |                                                                                                                                                                                                     ^
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    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}}.}
       |                                                                                                                                                                                                     ^
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    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}}.}
       |                                                                                                                                                                                                     ^
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    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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    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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    47 | \bold{code{data}} \tab the generated data \cr
       |           ^
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    53 | Refer to \bold{\emph{code{\link{retrieveDataFactory}}}} and to
       |                          ^
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    14 | A emph{\code{list}} with following names
       |       ^
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    26 | \item{code{arguments}}{a \code{pairList} of argument names and values.
       |           ^
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    12 | See \emph{\bold{code{\link{ProcessingContext}}}}. Only
       |                     ^
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    14 | See \emph{\bold{\\code{\link{ProcessingContext}}}}.}
       |                       ^
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GNU make is a SystemRequirements.
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Problems with news in ‘NEWS.md’:
No news entries found.
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   144 | Default {NULL} means the workbook will not be protected with a password}
       |         ^
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    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}
       |                   ^
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    22 |     Output of /code{calc.yhat}
       |                    ^
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     3 | \title{Evaluate bootstrap metrics produced from /code{calc.yhat}}
       |                                                      ^
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     5 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
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    26 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
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    12 |     Output from /code{aps}
       |                      ^
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    12 |     Output from /code{dominance}
       |                      ^
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    12 |     Output from /code{aps}
       |                      ^
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     5 |   This function plots CIs that have been produced from /code{booteval.yhat}.
       |                                                             ^
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    32 |   This function plots CIs that have been produced from /code{booteval.yhat}.   
       |                                                             ^
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    35 | This returns a plot of CIs that have been produced from /code{booteval.yhat}.
       |                                                              ^
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    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.}
       |                                                                                                            ^
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    48 | but if TRUE and installed '{scales}` package, 1.10 will be displayed.}
       |                            ^
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Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(zip)
  
  Attaching package: 'zip'
  
  The following objects are masked from 'package:utils':
  
      unzip, zip
  
  > 
  > test_check("zip")
  Error in loadNamespace(x) : there is no package called 'desc'
  Calls: test_check ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
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   182 |   dQuote{tab-delimited text file} when you have done and close the spreadsheet
       |         ^
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    75 | must be NULL or contain only elements of {"h","t","b","p","!","H"}.}
       |                                          ^
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    78 | must be NULL or contain only elements of {"h","t","b","p","!","H"}.
       |                                          ^
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   133 |     \code{abclass.control()} returns an object of class {abclass.control}
       |                                                         ^
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   109 | to solve the equivalent linear programming problem via the package {Rglpk}.
       |                                                                    ^
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   110 | It is recommended to use a recent version of {GLPK}.
       |                                              ^
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    16 | This parameter is omitted if {sparse.type = "kpc"}.}
       |                              ^
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    22 | This parameter is omitted if {sparse.type = "fpc"}.}
       |                              ^
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    51 | code{cortype = 3} denotes the constant structure,
       |     ^
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installed size is  6.9Mb
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    extdata   2.9Mb
    libs      1.9Mb
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installed size is 12.6Mb
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    include  12.5Mb
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    15 | \item[]{...}
       |        ^
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    htmlwidgets  11.6Mb
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installed size is 13.6Mb
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    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.
       |                                                                                                                                                                                                                                                                                                                                                                                        ^
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    20 | Here, S = {0, 1, \ldots, 2n}. 
       |           ^
Problems with news in 'NEWS.md':
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Problems with news in 'NEWS.md':
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    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
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    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method B}
       |                                                          ^
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    29 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
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    29 |   \item{trt_diff}{Estimate of treatment difference for S_{*+} using Method B}
       |                                                          ^
Specified C++11: please drop specification unless essential
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    25 |   \item{gatype}{Type of GA. \itemize{\item{"gga": generational GA}  \item{"ssga": steady state GA} } {Default value is "gga"}}
       |                                                                                                      ^
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    26 |   \item{objective}{Type of optimization. \itemize{\item{"min": minimization}  \item{"max": maximization} } {Default value is "max"}}
       |                                                                                                            ^
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    34 |                  {Default value is "initbin"}}
       |                  ^
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    56 |                \itemize{\item{"integer"}  \item{"real"} } {Default value is "real"}}
       |                                                           ^
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   185 |     {Default value is "w"}
       |     ^
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    46 | \item{qvals}{a vector of values in [0, 1]U{Inf}. Q-values. See Details}
       |                                           ^
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    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}.
       |                                                                                                                                                                                                          ^
installed size is  7.5Mb
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    doc   7.1Mb
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    23 | and the best result from three values of v = {0.25, 0.5, 0.75}
       |                                              ^
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    R      1.4Mb
    data   2.9Mb
    libs   1.1Mb
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    19 | \item{type}{a character specifying the algorithm which should be used to adjust R-squared (either \code{"simulated"} or \ code{"parametric"}).}
       |                                                                                                                               ^
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    21 |   \code{epsilon}{  the smallest significant distance between two points
       |                 ^
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    25 |   \code{shortprint}{  logical.  Defines whether special \code{show}
       |                    ^
installed size is  5.8Mb
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    adelie   1.2Mb
    libs     4.4Mb
installed size is  9.4Mb
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    data   9.3Mb
installed size is  5.1Mb
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Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
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    20 | medication groups using the construction \emph{"{NAME}"}.
       |                                                 ^
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    26 | Another example is "NotVita" defined as "(!{Vitamines})", which selects all
       |                                            ^
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    15 |   \item{removelist}{a vector of indices into env{X} of the lifted coefficients during the transform (in the order of removal). }
       |                                                 ^
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    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.
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(admiralvaccine)
  > 
  > test_check("admiralvaccine")
  [1] "VAX01DT"
  [1] "VAX02DT"
  [1] "VAX03DT"
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 35 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-derive_vars_merged_vaccine.R:165:3'): derive_vars_merged_vaccine Test 2: Check if supp datasets merged
            properly if they exist ──
  Differences found between the objects!
  
  A summary is given below.
  
  There are columns in BASE that are not in COMPARE !!
  All rows are shown in table below
  
    ==========
     COLUMNS  
    ----------
     IDVARVAL 
    ----------
  
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 35 ]
  Error: Test failures
  Execution halted
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    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.
       |                                                                                                                                                                                                                                                                                              ^
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    31 | than \code{Y}, then those variables that appear in \code{X} but no in {Y}
       |                                                                       ^
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    36 | \code{Y}, then those variables that appear in \code{X} but no in {Y} should
       |                                                                  ^
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    47 | code{ndims} dimensions. Defaults to all dimensions unless the latter are
       |     ^
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     6 | getCoordinatesFromVertexId2<-function(AFMImage, vId) {
       |                                                      ^
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Package which this enhances but not available for checking: 'asreml'
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    42 | \item{basehaz}{: {baseline hazard structure including baseline
       |                  ^
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    41 | \item{basehaz}{: {baseline hazard structure including baseline
       |                  ^
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    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.
       |                                                                                                      ^
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    39 |  \item \code{Variable} {1st column: The various aims to be completed}
       |                        ^
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    40 |  \item \code{Percentage} {2nd column: The percentage of completeness}
       |                          ^
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    65 | \emph{InputsPert}{[list] object of class \emph{InputsModel} containing the ensembles of perturbed model inputs required to perform data assimilation:}
       |                  ^
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    25 | \item{parameters}{Parameter(s) to return data for. Choices are PM_{2.5}
       |                                                                   ^
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    33 |   \item{las}{ Numeric in {0,1,2,3}; the style of axis labels. 
       |                          ^
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   119 |   If \code{linear} is \\code{TRUE}, linear
       |                             ^
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    61 |                                      names with the format {"Inferred1", "Inferred2", ...}.
       |                                                            ^
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    36 | \item{method}{Method for aggregating across categories: {"none", "max",
       |                                                         ^
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    26 | {"none", "max", "sum"}. Default: "none".}
       | ^
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    32 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
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    33 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
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    39 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
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    39 | here{https://lbs.amap.com/faq/account/key/72}}
       |     ^
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    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}}
       |                  ^
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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(...) {
       |                       ^
Found the following HTML validation problems:
stat_unique.html:110:1 (stat_unique.Rd:65): Warning: trimming empty <li>
stat_unique.html:109:1 (stat_unique.Rd:65): Warning: trimming empty <ul>
'LazyData' is specified without a 'data' directory
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'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
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    R  34.4Mb
checkRd: (-1) PS-methods.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:65-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Sim-Functions.Rd:126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:127-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:138-140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:141-143: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) gof.Rd:32: Lost braces
    32 | Assuming that the data length is \eqn{N} and the number of the parameters in the model is \eqn{p}, eqn{D} and eqn{X^2} are compared to a chi-squared distribution with \eqn{N-p} degrees of freedom.
       |                                                                                                       ^
checkRd: (-1) gof.Rd:32: Lost braces
    32 | Assuming that the data length is \eqn{N} and the number of the parameters in the model is \eqn{p}, eqn{D} and eqn{X^2} are compared to a chi-squared distribution with \eqn{N-p} degrees of freedom.
       |                                                                                                                  ^
checkRd: (-1) iccbin.Rd:23: Lost braces
    23 |   \item{m}{A vector of the numbers of successes (proportions are eqn{y = m / n}).}
       |                                                                     ^
checkRd: (-1) varbin.Rd:22: Lost braces
    22 |   \item{m}{A vector of the numbers of successes (proportions are eqn{y = m / n}).}
       |                                                                     ^
'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}}
       |                                                             ^
Specified C++11: please drop specification unless essential
checkRd: (-1) aphylo-class.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
checkRd: (-1) raphylo.Rd:33: Lost braces; missing escapes or markup?
    33 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
checkRd: (-1) sim_fun_on_tree.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
Found the following HTML validation problems:
mislabel.html:25:1 (mislabel.Rd:20): Warning: trimming empty <p>
raphylo.html:25:1 (raphylo.Rd:57): Warning: trimming empty <p>
sim_fun_on_tree.html:25:1 (sim_fun_on_tree.Rd:50): Warning: trimming empty <p>
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} 
       |                                                                           ^
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    documents     2.4Mb
    libs          1.1Mb
    screenshots   1.6Mb
checkRd: (-1) apple_apps.Rd:22: Lost braces; missing escapes or markup?
    22 | with a corresponding ID that can be used in {appler} functions.
       |                                             ^
checkRd: (-1) get_apple_reviews.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) itunes_artists.Rd:22: Lost braces; missing escapes or markup?
    22 | a corresponding ID that can be used in {appler} functions.
       |                                        ^
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   1.6Mb
    doc    1.8Mb
checkRd: (-1) calcEto.Rd:63-64: Lost braces
    63 | \code{ET.Daily:} {daily estimations of reference crop evapotranspiration
       |                  ^
checkRd: (-1) calcEto.Rd:66-67: Lost braces
    66 | \code{Ra.Daily:} {daily estimations of extraterristrial radiation
       |                  ^
checkRd: (-1) calcEto.Rd:69-70: Lost braces
    69 | \code{Slope.Daily:} {daily estimations of slope of vapour pressure curve
       |                     ^
checkRd: (-1) calcEto.Rd:72: Lost braces; missing escapes or markup?
    72 | \code{ET.type:} {type of the estimation obtained}
       |                 ^
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                              ^
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                                            ^
Package suggested but not available for checking: 'arcgisbinding'
Package suggested but not available for checking: 'ArchaeoData'
'LazyData' is specified without a 'data' directory
'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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.2Mb
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 43.8Mb
  sub-directories of 1Mb or more:
    R      4.3Mb
    libs  38.9Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    bin   11.3Mb
    misc   2.1Mb
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
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
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
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                    ^
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                                                                                                                 ^
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                                                                                                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.AssetPricing.Rd:199-200: Lost braces
   199 |   yakka. (Note that \code{flap} stands for dQuote{function list
       |                                                  ^
Package suggested but not available for checking: 'asteRiskData'
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.0Mb
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
       |                                                                           ^
checkRd: (-1) simulation_dgp.Rd:23: Lost braces
    23 | \item{att_oracle}{the sample analog of E[D{Y(1) - Y(0)}|D=1]}
       |                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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 ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_candidate_covariates.Rd:50: Lost braces
    50 | \item \code{covars_data}   {The \code{data.frame} that is filtered out of \code{df} with only the selected \code{covars}}. The values of the
       |                            ^
checkRd: (-1) get_candidate_covariates.Rd:53: Lost braces
    53 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
checkRd: (-1) get_prioritised_covariates.Rd:40: Lost braces
    40 | \item \code{multiplicative_bias}{The absolute log of the multiplicative bias term for each of the auto-selected prioritised covariates}
       |                                 ^
checkRd: (-1) get_recurrence_covariates.Rd:34: Lost braces
    34 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Autoplotprotein-package.Rd:27: Lost braces
    27 | code{\link{help}}
       |     ^
checkRd: (-1) Autoplotprotein.Rd:25: Lost braces
    25 | code{\link{help}}
       |     ^
checkRd: (-1) data.Rd:22: Lost braces
    22 | code{\link{help}}
       |     ^
checkRd: (-1) domain_data.Rd:29: Lost braces
    29 | code{\link{help}}
       |     ^
checkRd: (-1) length_data.Rd:32: Lost braces
    32 | code{\link{help}}
       |     ^
checkRd: (-1) plotdomain.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotmutagensis.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotsite.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) site_data.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
Specified C++11: please drop specification unless essential
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checkRd: (-1) noauto_scorecard.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{fit}{See glm {stats}.}
       |                    ^
checkRd: (-1) noauto_scorecard2.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{fit}{See glm {stats}.}
       |                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) avar_mo_cpp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_mo_cpp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_mo_cpp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
'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: \$
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checkRd: (-1) cosmos_mongo.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{host}{For \code{cosmos_mongo_endpoint}, the URL of the Cosmos DB MongoDB endpoint. Usually of the form "https://{account-name}.mongo.cosmos.azure.com:443/".}
       |                                                                                                                       ^
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   3.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) contour.angmcmc.Rd:48: Lost braces; missing escapes or markup?
    48 | Ignored if {show.data == FALSE}.}
       |            ^
checkRd: (-1) contour.angmcmc.Rd:51: Lost braces; missing escapes or markup?
    51 | Ignored if {show.data == FALSE}.}
       |            ^
checkRd: (-1) fit_incremental_angmix.Rd:104: Lost braces; missing escapes or markup?
   104 | \item{alpha}{significance level used in the test H_{0K}: expected log predictive density (elpd) for the fitted model with  K components >= elpd for the fitted model
       |                                                    ^
checkRd: (-1) fit_incremental_angmix.Rd:148: Lost braces; missing escapes or markup?
   148 | H_{0K}: expected log predictive density (elpd) for the fitted model with  K components >= elpd for the fitted model
       |   ^
checkRd: (-1) fit_incremental_angmix.Rd:163: Lost braces; missing escapes or markup?
   163 | The incremental fitting stops if  H_{0K} cannot be rejected
       |                                     ^
Found the following HTML validation problems:
rwnorm2.html:111:126 (rwnorm2.Rd:60): Warning: trimming empty <code>
rwnorm2.html:115:73 (rwnorm2.Rd:61): Warning: trimming empty <code>
rwnorm2.html:115:146 (rwnorm2.Rd:61): Warning: trimming empty <code>
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    27 | read.dna() from package {ape} was used to obtain DNAbin object for unaligned non-coding barcodes.
       |                         ^
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.3Mb
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    30 | the {dplyr}'s verbs and thus use it in local memory completely.
       |     ^
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    52 | Writes a remote table to disk that was called via {bdplyr}.
       |                                                   ^
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     5 | \title{Compatibility with {dplyr} verbs without using SQL language}
       |                           ^
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'LazyData' is specified without a 'data' directory
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  Cannot extract version info from the following section titles:
    Earlier versions
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   659 | `function(v, cell) { if(isTRUE(v>0.8)) return("green") }`.\cr
       |                    ^
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   151 | The CSS style rule, e.g. { text-align: center; color: red; }
       |                          ^
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   172 | The CSS style rule, e.g. cell { text-align: center; color: red; }
       |                               ^
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   209 | The CSS style rule, e.g. { text-align: center; color: red; }
       |                          ^
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   232 | The CSS style rule, e.g. cell { text-align: center; color: red; }
       |                               ^
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    23 | code{(4)} the number of
       |     ^
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    14 |   \item{\code{algo.id} [\code{character(1)}]:}{algo.id}{Algorithm ID.}
       |                                                        ^
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    13 | \item{ids}{[code{integer}]\cr
       |                 ^
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    13 | \item{ids}{[code{integer}]\cr
       |                 ^
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    28 | Default is dQuote{<name of registry>_files} in current working directory.}
       |                  ^
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    41 |  \item{namespaces}{code{character} with required packages to load via \code{\link[base]{requireNamespace}}.}
       |                        ^
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    31 | Algorithms are functions which get the code{data} part as well as the problem instance (the return value of the
       |                                            ^
installed size is  8.6Mb
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    doc    1.9Mb
    libs   5.2Mb
GNU make is a SystemRequirements.
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    32 | plot{...} functions are generated programmatically so the function calls in
       |     ^
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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    91 | \item{$H_n1 }{ Bayesian prediction of volatilities and co-volatilities for y_{n+1}.}
       |                                                                              ^
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    92 | \item{$R_n1 }{ Bayesian prediction of coditional correlation for y_{n+1}.}
       |                                                                    ^
installed size is  7.0Mb
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    libs   5.5Mb
GNU make is a SystemRequirements.
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No news entries found.
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    53 | online trajectories related to the state parameter, the simulated BOLD responses, \mjseqn{\hat{Y}}{ascii}.
       |                                                                                                   ^
installed size is  5.4Mb
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    extdata   4.1Mb
    libs      1.2Mb
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Package suggested but not available for checking: 'doMC'
installed size is 13.3Mb
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    doc   10.8Mb
    libs   1.5Mb
installed size is  7.3Mb
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    libs   5.9Mb
GNU make is a SystemRequirements.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
GNU make is a SystemRequirements.
Found the following HTML validation problems:
getSamples.html:74:1 (getSamples.Rd:35): Warning: trimming empty <h3>
installed size is  7.7Mb
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GNU make is a SystemRequirements.
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    18 |   \item{optim.method}{optimization method in \code{optim()}{stats}.}
       |                                                            ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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    69 | the initial values for parameters in models. For example, inits<-function(){list(alpha=0,beta=0,c=0,var1=0.5,r=1,lamda=0.01)}.
       |                                                                            ^
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    help   1.8Mb
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GNU make is a SystemRequirements.
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    18 |   \item{X         }{ If call \code{bayeslm} with matrices input \code{x} and {y} but not formula, pass new matrix to predict here. See example for details.}
       |                                                                              ^
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.2Mb
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    doc    2.7Mb
    libs   1.7Mb
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    71 | the plots are saved into directory {sim.dir}/predictions/migTrajectories.}
       |                                    ^
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    22 | A data frame where new rows have been inserted to regularize the \code{date} column. This results in values provided for \code{id}, \code{date}, and {dt} while inserting NAs for all other columns. Additionally, observations with duplicate date-times are removed.
       |                                                                                                                                                      ^
installed size is  6.6Mb
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    doc    2.8Mb
    libs   2.2Mb
installed size is  6.2Mb
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installed size is  5.3Mb
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    doc    1.0Mb
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installed size is  6.4Mb
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    doc   3.8Mb
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    doc    1.4Mb
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installed size is 12.8Mb
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GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
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    11 | Runs a \bold{Shiny} application. This function normally does not return; interrupt bold{R} to stop the application (usually by pressing Ctrl+C or Esc).
       |                                                                                        ^
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GNU make is a SystemRequirements.
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     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
       |                                                                                                   ^
GNU make is a SystemRequirements.
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    34 | itemize{
       |        ^
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
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    32 | `code{\link{GetVT}}`.   Otherwise, any column (e.g. \code{"Depth"}) in the 
       |      ^
checkRd: (-1) WindowSweep.Rd:36: Lost braces
    36 | \code{T.mid}  from the output of the `code{\link{GetVT}}`.}
       |                                           ^
Package suggested but not available for checking: 'BRugs'
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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.
       |                                                                                  ^
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    extdata   1.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
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GNU make is a SystemRequirements.
installed size is  7.8Mb
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    java   7.7Mb
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installed size is  5.3Mb
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    data   1.7Mb
    libs   3.1Mb
'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.
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    39 | \code{a} in {0, 1, 2} (see details))}
       |             ^
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    42 | code{cortype = 2} denotes the constant structure, where the \eqn{(i,j)} entry of covariance
       |     ^
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Malformed Title field: should not end in a period.
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    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}.}
       |                                                                                                               ^
checkRd: (-1) dummy.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{from}{An \code{integer vector} The starting period of a sequence of perids for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                                                                         ^
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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}.}
       |                                                                                                                            ^
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Running examples in 'bggAnalytics-Ex.R' failed
The error most likely occurred in:

> ### Name: bgg_merge
> ### Title: Merge data from two bggAPI objects
> ### Aliases: bgg_merge
> 
> ### ** Examples
> 
> 
> sr <- bggSearch$new("Terraforming Mars")
> gm <- bggGames$new(sr$ids)
Warning in open.connection(x, "rb") :
  cannot open URL 'https://boardgamegeek.com/xmlapi2/thing?id=420095,167791,380299,401513,328871,371070,358738,358739,358741,358740,381143,376868,344634,376937,322281,265081,395612,339849,241497,311247,312319,332774,419696,255681,370074,400568,375783,296298,346129,377179,218127,408591,265083,265084,364339,401114,406019,358525,352525,406001,230241,247030,387809,381423,230123,202825,226297,416029,390472,422435,365385,296108,380939,273473,279345,359145,365384,231965,254538,379201,326379&stats=1': HTTP status was '400 Bad Request'
Error in open.connection(x, "rb") : 
  cannot open the connection to 'https://boardgamegeek.com/xmlapi2/thing?id=420095,167791,380299,401513,328871,371070,358738,358739,358741,358740,381143,376868,344634,376937,322281,265081,395612,339849,241497,311247,312319,332774,419696,255681,370074,400568,375783,296298,346129,377179,218127,408591,265083,265084,364339,401114,406019,358525,352525,406001,230241,247030,387809,381423,230123,202825,226297,416029,390472,422435,365385,296108,380939,273473,279345,359145,365384,231965,254538,379201,326379&stats=1'
Calls: <Anonymous> ... read_xml.character -> read_xml.connection -> open -> open.connection
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   1.1Mb
    libs   1.5Mb
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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.}
       |                                                                          ^
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
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installed size is 149.2Mb
  sub-directories of 1Mb or more:
    include  148.1Mb
Specified C++11: please drop specification unless essential
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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    19 | expression: input_re = reactive({input})}
       |                                 ^
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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}.
       |                                                                                                                                                                                                                                                                                  ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'ffbase'
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'
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    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. }
       |                                                                                                                                                                                                        ^
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
Found the following HTML validation problems:
snp_ldsc.html:134:1 (snp_ldsc.Rd:74): Warning: trimming empty <dt>
Specified C++11: please drop specification unless essential
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    97 | to be used by package {bigmemory}.
       |                       ^
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    99 | to be used by package {bigmemory}.
       |                       ^
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    57 | Read a file as a Filebacked Big Matrix by using package {bigreadr}.
       |                                                         ^
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'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
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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GNU make is a SystemRequirements.
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     9 |   \item{lv}{{numeric} position, or {character} name, of an
       |                                    ^
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    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
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    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
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    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
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Package which this enhances but not available for checking: 'asreml'
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checkRd: (-1) simulation.Rd:65: Lost braces in \itemize; meant \describe ?
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    help   2.6Mb
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   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}.
       |                                                                                                                                                                              ^
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   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}.
       |                                                                                                                                                                              ^
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      1.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
Depends: includes the non-default packages:
  'colorspace', 'deldir', 'rgl', 'tcltk', 'tcltk2', 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
checkRd: (-1) FighterAircraft.Rd:32: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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    27 |   an integer vector of the same length as code{x} containing positions relativ to code{sort(unique(x), na.last=FALSE)}
       |                                               ^
checkRd: (-1) keypos.rd:27: Lost braces
    27 |   an integer vector of the same length as code{x} containing positions relativ to code{sort(unique(x), na.last=FALSE)}
       |                                                                                       ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
Package suggested but not available for checking: 'cmdstanr'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R          1.2Mb
    libs       5.3Mb
    testdata   1.4Mb
GNU make is a SystemRequirements.
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     8 | A data frame with five variables: \code{fname_c1},\code{lname_c1},  \code{by}, code{bm}, \code{bd}.
       |                                                                                    ^
checkRd: (-1) identity.RLdata500.Rd:15: Lost braces
    15 | format A vector that contains the code{id}
       |                                       ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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    16 | This data set was obtained from the durban.rowcol {agridat} example in package 'agridat' 
       |                                                   ^
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    25 | evenly spaced points between \code{min} and {max}.
       |                                             ^
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    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}
       |                                    ^
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    18 | \item{\code{station_distance}}\cr {Returns stations with distance in ascending order given the user's current location}
       |                                   ^
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    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}
       |                                 ^
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    20 | \item{\code{trip_distance}}\cr {Computes the geographical distance between the start and end stations}
       |                                ^
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    25 | \item{\code{trip_history_sample}} \cr {A sample of 1000 trip data entries from February 2022}
       |                                       ^
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    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
installed size is  9.4Mb
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    libs   8.7Mb
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    20 | Helper function for as.data.frame.{fitted, forecast}. Converts predictive array to data.frame.
       |                                   ^
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
Problems with news in 'NEWS.md':
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installed size is  7.9Mb
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    libs   4.6Mb
GNU make is a SystemRequirements.
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    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.
       |                                                           ^
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    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.
       |                                                                   ^
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    23 | function(eps, u = 0.5, alpha = 1, kappa = 1, gama = 1 / 2, N = 3001) {
       |                                                                      ^
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    19 | function(x, df, mean, sd) {
       |                           ^
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    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |               ^
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    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |                                             ^
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checkRd: (-1) refAnnots.Rd:11-12: Lost braces in \itemize; meant \describe ?
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Found the following HTML validation problems:
bayes.lin.reg.html:27:32 (bayes.lin.reg.Rd:77): Warning: trimming empty <code>
bayes.lin.reg.html:32:32 (bayes.lin.reg.Rd:79): Warning: trimming empty <code>
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Problems with news in 'NEWS.md':
No news entries found.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/BonEV.Rcheck/00install.out' for details.
installed size is  9.4Mb
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    libs   1.1Mb
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    lib      29.5Mb
GNU make is a SystemRequirements.
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    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
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               ^
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    75 | $$SV = sqrt(sum(x_{i+1} - x_i)^2/n-1)$$
       |                   ^
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    80 | $$SD = sqrt(sum(x_{i+1} - xbar)^2/n-1)$$
       |                   ^
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    78 | $$SV = sqrt(sum(x_{i+1} - x_i)^2/n-1)$$
       |                   ^
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    82 | $$SD = sqrt(sum(x_{i+1} - xbar)^2/n-1)$$
       |                   ^
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    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'.}
       |                                                 ^
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    45 | \item{opt.model}{a character string in the set {'gini','error'} indicating the optimization model to solve in the program. The default is 'gini'. The 'error' option is not available in the current version.}
       |                                                ^
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    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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    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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    18 | B{\"o}hning, D.  and Schlattmann, P. and Lindsay, B. (1992). \dQuote{Computer-Assisted Analysis of Mixtures (C.A.MAN): Statistical Algorithms}. \emph{Biometrics}. \bold{48}, 283--303.
       |  ^
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     5 | Hepatitis B data from Schlattmann and B{\"o}hning (1993).
       |                                        ^
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    19 | Schlattmann, P. and B{\"o}hning, D. (1993). \dQuote{Mixture models and disease mapping}. \emph{Statistics in Medicine}. \bold{12}, 1943--1950.
       |                      ^
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   117 | D. B{\"o}hning, P. Schlattmann, B.G. Lindsay: C.A.MAN - Computer Assisted
       |     ^
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    19 | Schelp, F., P. Vivatanasept, P. Sitaputra, S. Sornmani, P. Pongpaew, N. Vudhivai, S. Egormaiphol, and D. B{\"o}hning.  \dQuote{Relationship of the morbidity of under-fives to anthropometric measurements and community health intervention.} \emph{Trop Med Parasitol}, 1990, 41(2), 121--126.
       |                                                                                                           ^
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   112 | Stop recording images with {camcorder}.
       |                            ^
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    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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    14 | This is a dataset from the archived/orphaned {zipcode} package.
       |                                              ^
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    96 |     \item code{train} now removes duplicate models in the tuning grid. Duplicates could occur for models with discrete parameters.
       |               ^
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    46 | formula. This argument is not used for \code{xyplot.calibration}. For {ggplot.calibration}, \code{data}
       |                                                                       ^
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    13 | The exit status code{R CMD build}, invisibly.
       |                     ^
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    30 | \item{pvals}{If code{TRUE} (the default is \code{FALSE}), print two-sided p-values
       |                     ^
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    38 |   axis.  To plot against a factor, you need to specify the full name of one of the indicator variables that define the factor.  For example, for a factor called \code{type} with levels \code{A}, \code{B} and {C}, using the usual drop-first level parameterization of the factor, the regressors for \code{type} would be \code{typeB} or \code{typeC}.  Similarly, to plot against the regressor \code{log(X4)}, you must specify \code{"log((X4)"}, not \code{"X4"}.
       |                                                                                                                                                                                                                 ^
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   137 | For  \code{style="filled"} several subarguments modify the appearance of the region:  code{alpha} is a number between 0 and 1 that specifies opacity with defualt 0.15, \code{border}, \code{TRUE} or \code{FALSE} specifies a border for the envelope, and \code{vertical} either \code{TRUE} or \code{FALSE}, modifies the behavior of the envelope at the edges of the graph.
       |                                                                                           ^
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   130 | \code{x1, x2, x3, \dots}- {input to the model, there must be one column
       |                           ^
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    79 |      Meteorol. Soc. textbf{30} 291-303. 
       |                           ^
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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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    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}
       |            ^
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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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    22 | \item{partialJob}{is /code{TRUE} if it is not required to stop the job
       |                           ^
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    25 | \item{allowIntermediateResults}{is /code{TRUE} if intermediate results
       |                                         ^
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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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     8 |  This dataset gives the daily returns (c_{t+1}/c_t -1) of the UK FTSE 100 index from 2nd April 1984 until the 13th September 2012.
       |                                          ^
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    10 | \item{vec1}{A \code{integer} vector forms a subset of {1, 2, ..., n}.}
       |                                                       ^
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    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
       | ^
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    38 | {Y_label} \code{'<ylab>'}: \tab\tab\tab\tab  Y-axis custom label. Defaults to <y_var>\cr
       | ^
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    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
       | ^
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    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"}.
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    32 | \item \code{type}, the type of the detected entity, either \code{"global"} or {"import"}.
       |                                                                               ^
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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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    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
       |                                                     ^
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    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_{++},
       |                                                                 ^
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    99 |   S_{*+} and PP estimands}
       |     ^
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    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
       |                                                                 ^
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    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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    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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       |                                                                 ^
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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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    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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    36 | kprime is a {p,d,q} set of functions that compute the K-prime distribution. This distribution has many applications,
       |             ^
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    37 | lsecond are {p,d,q} functions that compute the Lambda-second (L") distribution. This
       |             ^
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    39 | pilsecond are {p,d,q} functions that compute the prior-informed Lambda-second (L") distribution. This
       |               ^
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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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installed size is  5.3Mb
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    extdata   2.0Mb
checkRd: (-1) colour_values.Rd:143: Lost braces in \itemize; meant \describe ?
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Unexported object imported by a ':::' call: 'crayon:::mypaste'
  See the note in ?`:::` about the use of this operator.
Problems with news in 'NEWS.md':
No news entries found.
Malformed Description field: should contain one or more complete sentences.
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     6 |              Generates all points on a {p,n} simplex lattice (i.e. a p-part
       |                                        ^
Specified C++11: please drop specification unless essential
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    36 | {0, 1}.
       | ^
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    40 | values in {0, 1}.
       |           ^
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installed size is  7.0Mb
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Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: 'CAM'
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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
       |   ^
'LazyData' is specified without a 'data' directory
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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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Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
run_pipeline_gbq: no visible global function definition for
  'query_exec'
Undefined global functions or variables:
  query_exec
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Specified C++11: please drop specification unless essential
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Packages suggested but not available for checking: 'conosPanel', 'p2data'
installed size is  6.1Mb
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    doc   5.4Mb
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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.  
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ^
installed size is  5.4Mb
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    libs   4.2Mb
GNU make is a SystemRequirements.
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    38 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
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    58 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
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    51 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
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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}.}
       |            ^
checkRd: (-1) copCAR.Rd:40: Lost braces
    40 |        item{\code{maxit}}{the maximum number of iterations to be used by \code{\link{optim}} when optimizing the objective function. Defaults to \code{1000}.}
       |                          ^
checkRd: (-1) condQestCopC.Rd:45: Lost braces; missing escapes or markup?
    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                          ^
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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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    vignette_data   2.6Mb
installed size is  5.2Mb
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    data   3.5Mb
    libs   1.2Mb
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Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
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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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    29 | The function code{gatherFromList} returns a list with components containing elements of the same name.
       |                  ^
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    54 |  individual compound containing 2 carbons and observe a vector of {978,22,0}.
       |                                                                   ^
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    58 |  The equivalent corMID vector would be {1,0,0}, indicating that the non-labeled
       |                                        ^
Error(s) in re-building vignettes:
--- re-building 'CorMID.Rmd' using rmarkdown
checkRd: (-1) carstats.Rd:11: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) titanic.Rd:11: Lost braces in \itemize; meant \describe ?
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    63 | \code{low_estimate}\\code{high_estimate} columns. The \code{SD_estimate} column has the standard deviation of the
       |                          ^
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    21 | \eqn{K+1} categories the arrays will have either \eqn{K+1} or {K} dimensions, depending on whether 
       |                                                               ^
checkRd: (-1) multinom.gen.Rd:46: Lost braces
    46 | For a \emph{K}-variate multinomial, the matrix{m} should have \emph{K-1} columns
       |                                               ^
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installed size is 18.0Mb
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    extdata  17.7Mb
installed size is  7.2Mb
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checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
installed size is  7.0Mb
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    data   4.5Mb
    doc    1.6Mb
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checkRd: (-1) fasttrakg.Rd:18: Lost braces
    18 |     \item{\code{killip}}{Killip level of cardiac event severity (1-4)age75}{1= Age>75; 0=Age<=75}
       |                                                                            ^
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/coursekata.Rcheck/00install.out' for details.
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    extdata   2.6Mb
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    help   4.7Mb
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installed size is  6.8Mb
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    include   6.5Mb
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) sharedat.Rd:23: Lost braces
    23 | \doi{10.7910/DVN/YXMQZM}{Harvard dataverse}
       |                         ^
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installed size is  5.4Mb
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    doc   5.1Mb
checkRd: (-1) crwPredict.Rd:54-68: Lost braces
    54 | \item("predTime"){
       |                  ^
checkRd: (-1) crwPredict.Rd:59: Lost braces
    59 |  no longer the default (see \item{return.type}). If the original data were 
       |                                  ^
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
checkRd: (-1) normFit.Rd:39: Lost braces; missing escapes or markup?
    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}.}
       |                                                                                    ^
checkRd: (-1) confRegCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                                                                                      ^
checkRd: (-1) confRegUCRandUCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
installed size is  5.7Mb
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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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installed size is 13.1Mb
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checkRd: (-1) calculate_cell_volume.Rd:16: Lost braces; missing escapes or markup?
    16 | V A real number. The volume (in angstroms^3 or angstroms^{-3})
       |                                                          ^
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    24 | equals (I-B)^{-1}Gamma. The indirect effect equals the difference between
       |              ^
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installed size is  5.6Mb
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    doc    1.5Mb
installed size is  8.1Mb
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checkRd: (-1) csvy.Rd:58: Lost braces in \itemize; meant \describe ?
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    81 |   beta ~ N( 0 , tau^2 * QQ^{-1} )
       |                            ^
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installed size is 12.1Mb
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    R      1.2Mb
    data   1.7Mb
    libs   7.9Mb
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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installed size is  7.9Mb
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    doc    1.8Mb
    libs   5.8Mb
File 'curl/libs/x64/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Package which this enhances but not available for checking: 'RGtk2'
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    doc    1.2Mb
    libs   1.2Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.7Mb
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    htmlwidgets   1.4Mb
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Found the following HTML validation problems:
saveReportTable.html:80:1 (saveReportTable.Rd:36): Warning: trimming empty <dt>
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{  A small, positive scalar that determines when iterations
       |               ^
checkRd: (-1) fpiter.Rd:60-61: Lost braces
    60 |     \code{maxiter}{  An integer denoting the maximum limit on the number of
       |                   ^
checkRd: (-1) fpiter.Rd:63-65: Lost braces
    63 |     \code{trace}{  A logical variable denoting whether some of the intermediate
       |                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) formatScientificTeX.Rd:33: Lost braces; missing escapes or markup?
    33 | function will return  " 3.0\\\\times 10^{2}"
       |                                         ^
Package which this enhances but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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    data   4.4Mb
checkRd: (-1) gl.filter.maf.Rd:7: Lost braces; missing escapes or markup?
     7 |  {adegenet} object}
       |  ^
checkRd: (-1) gl.pcoa.Rd:68: Lost braces; missing escapes or markup?
    68 | The function is essentially a wrapper for glPca {adegenet} or pcoa \{ape\}
       |                                                 ^
checkRd: (-1) gl.play.history.Rd:17: Lost braces
    17 | code{x2@other$history[c(1,4,5)]}). [optional].}
       |     ^
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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 
       |                                                       ^
installed size is  7.6Mb
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    java   7.5Mb
GNU make is a SystemRequirements.
checkRd: (-1) StartEnd.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) StartEnd.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processFlow.Rd:14: Lost braces
    14 | \item{roundDigits}{Integer. If NA, numerics are not rounded before comparison. If /code{roundDigits} is specified, numerics are 
       |                                                                                        ^
checkRd: (-1) processFlow.Rd:15: Lost braces
    15 | rounded to /code{roundDigits} decimal places using \link[base]{round}.}
       |                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) data_edit.Rd:137: Lost braces
   137 | code{data_edit} is a shiny application built on \code{rhandsontable} that is
       |     ^
checkRd: (-1) number_of_rows.Rd:30-32: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) defaultFactorSummaries.Rd:29: Lost braces
    29 | code{\link{variableType}}, \code{\link{countMissing}}, \code{\link{uniqueValues}},
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) build_date_factor.Rd:15: Lost braces; missing escapes or markup?
    15 | Map a vector of dates to a factor at one of these levels {"yearmonth", "yearquarter", "quarter", "month"}
       |                                                          ^
checkRd: (-1) build_date_factor.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{type}{One of {"year", "yearquarter", "yearmonth", "quarter", "month"}}
       |                    ^
checkRd: (-1) defaultFactorSummaries.Rd:29: Lost braces
    29 | code{\link{variableType}}, \code{\link{countMissing}}, \code{\link{uniqueValues}},
       |     ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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checkRd: (-1) is_datelife_query.Rd:17: Lost braces; missing escapes or markup?
    17 | First, that \code{input} is of class {datelifeQuery}.
       |                                      ^
Found the following HTML validation problems:
get_dated_otol_induced_subtree.html:53:1 (get_dated_otol_induced_subtree.Rd:19): Warning: trimming empty <dt>
get_otol_synthetic_tree.html:67:1 (get_otol_synthetic_tree.Rd:29): Warning: trimming empty <dt>
summary_matrix_to_phylo.html:89:1 (summary_matrix_to_phylo.Rd:42): Warning: trimming empty <dt>
Package suggested but not available for checking: 'SASxport'
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) plot.mleBb.Rd:48: Lost braces
    48 |   \ code{size} is extracted from argument \code{x}.
       |         ^
checkRd: (-1) value_missing_table.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) value_missing_table.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) CI_mc.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{i}{the row index of the interest entry X_{i,j}}
       |                                                ^
checkRd: (-1) CI_mc.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{j}{the row index of the interest entry X_{i,j}}
       |                                                ^
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checkRd: (-1) data.Rd:11: Lost braces
    11 | \doi{10.1007/s40258-021-00647-3}{DOI}
       |                                 ^
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'BRugs'
checkRd: (-1) CalcStatClusterGivenCenter.Rd:36: Lost braces; missing escapes or markup?
    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}),
       |                                                          ^
checkRd: (-1) DetectClustersModel.Rd:60: Lost braces; missing escapes or markup?
    60 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) DetectClustersModel.Rd:61: Lost braces; missing escapes or markup?
    61 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) glmAndZIP.iscluster.Rd:34: Lost braces; missing escapes or markup?
    34 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) glmAndZIP.iscluster.Rd:35: Lost braces; missing escapes or markup?
    35 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) kernel.assign.Rd:27: Lost braces; missing escapes or markup?
    27 |  {q = [0, 1]}. Kernels are of the Müller-Wang type ("MW"), Müller type ("M")
       |  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) detectAgeInterval.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Age}, or code{age}.}
       |                                                                              ^
checkRd: (-1) detectSex.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Sex}, or code{sex}.}
       |                                                                              ^
checkRd: (-1) ggbgetAgesFit.Rd:28: Lost braces
    28 | code{\link{ggbChooseAges}}
       |     ^
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installed size is  5.4Mb
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    data   4.2Mb
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checkRd: (-1) deconv.Rd:85: Lost braces; missing escapes or markup?
    85 |     \code{tg}, std. error of \eqn{g}, \eqn{G} (the cdf of {g}),
       |                                                           ^
'LazyData' is specified without a 'data' directory
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    18 | section{Dependencies}{
       |        ^
checkRd: (-1) deepNN-package.Rd:18-21: Lost braces
    18 | section{Dependencies}{
       |                      ^
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    23 | section{Citation}{
       |        ^
checkRd: (-1) deepNN-package.Rd:23-25: Lost braces
    23 | section{Citation}{
       |                  ^
checkRd: (-1) deepNN-package.Rd:27-38: Lost braces
    27 | references{
       |           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) deltaPlot.Rd:28: Lost braces
    28 |  \item{purify}{logical: should item purification be performed? (Default is code{FALSE}). See \bold{Details}.}
       |                                                                                ^
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
checkRd: (-1) kin.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:53-61: Lost braces
    53 | {\itemize{
       | ^
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checkRd: (-1) kin2sex.Rd:59-67: Lost braces
    59 | {\itemize{
       | ^
checkRd: (-1) kin2sex.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) kin2sex.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
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checkRd: (-1) conifersIP.Rd:9: Lost braces; missing escapes or markup?
     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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    33 | guessed either from\ code{names(formals(f))} (if \code{f} is a function)
       |                          ^
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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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    27 |   \item{s_1}{A function depending on the number of patients included used for adaptive randomization in plateau determination, only used if the estimation method chosen is "MTA-RA". The default function is function(n_cur,n){0.2}.}
       |                                                                                                                                                                                                                                ^
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    30 |   \item{s_1}{A function depending on the number of patients included used for adaptive randomization in plateau determination, only used if the estimation method chosen is "MTA-RA". The default function is function(n_cur){0.2}.}
       |                                                                                                                                                                                                                              ^
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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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    32 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
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    36 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
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    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}}.}
       |                                   ^
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    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
       |   ^
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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)
       |                   ^
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    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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    28 | Elith J., M. Kearney M., and S. Phillips, 2010. The art of modelling range-shifting species. \doi{10.1111/j.2041-210X.2010.00036.x}{Methods in Ecology and Evolution 1:330-342}.
       |                                                                                                                                    ^
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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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    31 | \strong{Support}: {x in [0, \eqn{\infty})}
       |                   ^
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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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    30 | \item{diffbin}{\code{(logical)}: Difference-based duration for discreet time (only applicabble to cases when \code{bin} is provided). If set to \code{TRUE}, single-interval taxa will \code{0} durations. Setting this argument to \code{FALSE} will add code{1} to the durations of all taxa.}
       |                                                                                                                                                                                                                                                               ^
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    27 | Due to stratigraphic constraints, we can only process deep time data, when it is sliced to discrete bins. It is suggested that you do this separately for most of your analyses. This function is also used by the code{\link{divDyn}} function when \code{age} entries are provided.
       |                                                                                                                                                                                                                        ^
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    31 | Setting both \code{bin} If \code{bin=NULL} and code{tax=NULL}, will run \code{FUN} on the entire dataset (no effect). Providing either \code{bin} or \code{tax} and keeping the other \code{NULL} will iterate \code{FUN} for every \code{bin} or \code{tax} entry (whichever is presented).
       |                                                    ^
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Problems with news in 'NEWS.md':
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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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    13 |     \item{\code{x}}{dose (log base 10 CS2mgl^{-1})}
       |                                              ^
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    doc    6.7Mb
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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.}
       |             ^
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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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    New features
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    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
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    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
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    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
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    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
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    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
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    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
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     9 | \item{occupancies}{Either a data frame containing two columns or an object of class \code{"upgrain"} from the \code{\link{upgrain}} function. If using a data frame the first column must be the grain sizes (cell area in squared units e.g. km^{2}). The second column is the proportion of occupancies at each grain size.}
       |                                                                                                                                                                                                                                                  ^
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    13 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
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    13 | \item{new.areas}{vector of grain sizes as cell area (in same units as cell.width but squared e.g. km^{2}) at fine scales for model prediction.}
       |                                                                                                      ^
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    10 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
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    43 |   emph{Generalized Linear Models}, 
       |       ^
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    18 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
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    16 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
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    34 | This function allows values other than {0, 1, -1} for \code{alpha} and \code{delta} but
       |                                        ^
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    35 | This function allows values other than {0, 1, -1} for \code{alpha} and \code{delta} but
       |                                        ^
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    11 | code{\link[DrDimont]{compute_correlation_matrices}}}
       |     ^
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    53 | a dose returns the plot of pr(trt_dose - trt_{reference_dose} | data).}
       |                                              ^
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    70 | a dose returns the plot of pr(trt_dose - trt_{reference_dose} | data).}
       |                                              ^
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installed size is  6.0Mb
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See 'd:/Rcompile/CRANpkg/local/4.4/DRviaSPCN.Rcheck/00install.out' for details.
installed size is  5.2Mb
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    appinformation   4.1Mb
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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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   105 |   argument \code{what}.  For code{"["} the cutted object.
       |                                  ^
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    64 | The empiric model is specified as F(d, beta) = d^{exp(beta)}. The logistic model is
       |                                                  ^
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    29 | {.subgroup} for the subgroup column name and \{.name\} for the subgroup
       | ^
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    29 | {.subgroup} for the subgroup column name and \{.name\} for the subgroup
       | ^
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  Warning: replacing previous import 'Matrix::det' by 'SparseM::det' when loading 'DWDLargeR'
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    27 |      For example, the order {a, b, c} implies that a > b, a  > c, and b > c.
       |                             ^
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   107 |   For \code{coef} a new \R{XXc} field is created so as not to trample
       |                           ^
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    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                          ^
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    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                                                     ^
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    19 | \item{log_style}{is a {crayon::style()} that will colorize
       |                       ^
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    22 | \item{msg_style}{is a {crayon::style()} style that will gray scale the
       |                       ^
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    22 | \item{"sysname"} : {The operating system name.}
       |                    ^
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    23 | \item{"release"} : {The OS release.}
       |                    ^
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    24 | \item{"version"} : {The OS version.}
       |                    ^
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    25 | \item{"nodename"} : {A name by which the machine is known on the network (if any).}
       |                     ^
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    26 | \item{"machine"} : {A concise description of the hardware, often the CPU type.}
       |                    ^
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    27 | \item{"login"} : {The user's login name, or "unknown" if it cannot be ascertained.}
       |                  ^
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    28 | \item{"user"} : {The name of the real user ID, or "unknown" if it cannot be ascertained.}
       |                 ^
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    29 | \item{"r-ver"} : {R Version in (major).(minor) format.}
       |                  ^
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    33 | If \code{side="upward"}{apply control charts that aim to detect upward shifts.} \cr
       |                        ^
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    34 | If \code{side="downward"}{apply control charts that aim to detect downward shifts.} \cr
       |                          ^
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    35 | If \code{side="both"}{apply control charts that aim to detect shifts in both sides}}
       |                      ^
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    38 | If \code{chart="CUSUM"}{apply CUSUM charts.} \cr
       |                        ^
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    39 | If \code{chart="EWMA"}{apply EWMA charts.}}
       |                       ^
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    bin       3.0Mb
    extdata   1.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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    75 | From the initial values, \code{B0} and {S0}, \code{\link{MHLS}} draws \code{beta} and \code{subgrad} samples.
       |                                        ^
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    34 | if (require(incidence)) {
       |                         ^
'LazyData' is specified without a 'data' directory
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    31 | \item{span}{parameter that controls the degree of smoothing (numeric between 0 and 100, Default 25). see more on loess{stats}}
       |                                                                                                                       ^
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    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}}
       |                                                                                                                                  ^
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Package which this enhances but not available for checking: 'gurobi'
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    64 |     \doi{10.18128/D010.V10.0}{IPUMS USA: Version 10.0 [dataset]. Minneapolis, MN: IPUMS}. 
       |                              ^
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    45 |       code{pt-pt-1} on a constant
       |           ^
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    70 |     \code{breach_end}{
       |                      ^
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    75 |     \code{year}{
       |                ^
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    88 |   {replace \code{newDat[, x2]}:  
       |   ^
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   120 |     environment / list to use with code{object},
       |                                        ^
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    48 | `{itemStyle: {color: 'red', fontBold: 'bold'}}`.
       |  ^
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    48 | `{itemStyle: {color: 'red', fontBold: 'bold'}}`.
       |              ^
checkRd: (-1) nesting.Rd:51: Lost braces; missing escapes or markup?
    51 | `{symbolSize: 4}`.
       |  ^
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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.
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    25 | minimization (most others). This function computes a factor from {-1, 1} for
       |                                                                  ^
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    33 | the map. \itemize{ \item{\code{elem} {displays elementary and unified
       |                                      ^
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    34 | districts}} \item{\code{secon} {displays secondary and unified districts}}}
       |                                ^
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    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
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    10 | \item{D}{A matrix in the set D_{n}^{-}.}
       |                                ^
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    10 | \item{D}{A matrix in the set D_{n}^{-}.}
       |                                    ^
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    23 | \item \code{P4SRS10}: Keep working at something until {he/she} is finished?
       |                                                       ^
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'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Package suggested but not available for checking: 'eggCountsExtra'
installed size is  7.3Mb
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    libs   6.6Mb
GNU make is a SystemRequirements.
checkRd: (-1) Constants.Rd:13: Lost braces in \itemize; meant \describe ?
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    24 | \item{las}{numeric in {0,1,2,3}; the style of axis labels, see ?par}
       |                       ^
checkRd: (-1) boxQTwice.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{las}{numeric in {0,1,2,3}; the style of axis labels, see ?par}
       |                       ^
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    17 | \item{las}{numeric in {0,1,2,3}; the style of axis labels}
       |                       ^
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc       5.1Mb
    extdata   5.1Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
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    54 | \code{t_optims}{optimal parametrizations}
       |                ^
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    55 | \code{G_optims}{optimal rotations}
       |                ^
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    56 | \code{b_optims}{optimal scalings}
       |                ^
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    57 | \code{n_optims}{optimal re-normalization}
       |                ^
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    58 | \code{n_iter}{number of iterations until convergence}
       |              ^
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    47 | as a document at .tasks/task/${taskId}. This is yours to keep or remove
       |                               ^
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    48 | as a document at .tasks/task/${taskId}. This is yours to keep or remove
       |                               ^
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    16 | Variables: \code{id}  = {identification number},
       |                         ^
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    17 | \code{state} = {state}, \code{age} = age in years on a shifted scale (current age minus 70),
       |                ^
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    25 |  TRUE for output on start-state totals e_{r.} (for \code{S}>0)
       |                                          ^
Specified C++11: please drop specification unless essential
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    92 |     J. Kotus and M. Urb\'{a}nski 2003.  \emph{Hausdorff dimension and Hausdorff
       |                          ^
Specified C++11: please drop specification unless essential
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    80 | \code{\link{score}}, \link{elo.run.helpers}{elo.run helpers}, \code{\link{elo.calc}},
       |                                            ^
installed size is  5.5Mb
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GNU make is a SystemRequirements.
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   194 |             \item added {d,r}betabinom
       |                         ^
Specified C++11: please drop specification unless essential
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    86 | execute {EmiStatR} function
       |         ^
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   136 |     \item{EmiStatR}{\code{signature(x = "input")}: execute {EmiStatR} function }
       |                                                            ^
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checkRd: (-1) macacaModels.Rd:10-11: Lost braces in \itemize; meant \describe ?
installed size is  7.0Mb
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    43 | For ordinary least squares estimator, \code{psifun} should be the identity function psifun <- function(t){t}.
       |                                                                                                          ^
Specified C++11: please drop specification unless essential
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    25 |  \code{terms} the code{terms} object used.
       |                       ^
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    65 |  \code{terms} the code{terms} object used.
       |                       ^
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    65 |  \code{terms} the code{terms} object used.
       |                       ^
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    49 |  \code{terms} the code{terms} object used.
       |                       ^
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    50 |  \code{terms} the code{terms} object used.
       |                       ^
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    49 |  \code{terms} the code{terms} object used.
       |                       ^
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     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.
       |                                                                                                                                                                                                            ^
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    41 |   \code{family="binomial"} should be a factor with two levels which is coded as \code{0} and {1}.
       |                                                                                              ^
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    22 | less memory. Genetic data consists of nucleotide data {A,T,C,G} and are usually saved
       |                                                       ^
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    39 |     \item{code{shrinkage}:}{Object of class \code{"numeric"}, defining the shrinkage parameter applied to each tree in expansion.}
       |               ^
installed size is  7.3Mb
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checkRd: (-1) entropy.Dirichlet.Rd:65: Lost braces in \itemize; meant \describe ?
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   124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
       |                                  ^
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    R      2.2Mb
    help   3.6Mb
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   200 |   \code{\link{epois}}, \link[stats]{Poisson}, code{\link{estimate.object}}.
       |                                                   ^
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    77 |   positive integer between \code{1} and code{r} specifying the number of future 
       |                                             ^
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    18 | Compute the empirical MCR, assuming that #{cluster} = #{block},
       |                                           ^
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    18 | Compute the empirical MCR, assuming that #{cluster} = #{block},
       |                                                        ^
installed size is  5.6Mb
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    help   2.5Mb
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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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GNU make is a SystemRequirements.
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Problems with news in 'NEWS.md':
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    16 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then Sigma^{-1} 
       |                                                                         ^
checkRd: (-1) ifa.Rd:17: Lost braces; missing escapes or markup?
    17 | has the corresponding q-factor decomposition Sigma^{-1}=diag(phi)(I-theta theta')diag(phi), where theta is a mxq matrix and phi the vector of 
       |                                                    ^
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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,
       |                                                                                                                       ^
Specified C++11: please drop specification unless essential
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installed size is 14.1Mb
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    doc  13.3Mb
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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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installed size is  5.1Mb
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    extdata   4.0Mb
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    24 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability 0.10 for
       |                    ^
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    24 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability 0.10 for
       |                            ^
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    21 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability given by
       |                    ^
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    21 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability given by
       |                            ^
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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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Running 'spelling.R' [0s]
  Running 'testthat.R' [19s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(exampletestr)
  > 
  > get_os <- function() {
  +   sysinf <- Sys.info()
  +   if (!is.null(sysinf)) {
  +     os <- sysinf["sysname"]
  +     if (os == "Darwin") {
  +       os <- "osx"
  +     }
  +   } else { ## mystery machine
  +     os <- .Platform$OS.type
  +     if (grepl("^darwin", R.version$os)) {
  +       os <- "osx"
  +     }
  +     if (grepl("linux-gnu", R.version$os)) {
  +       os <- "linux"
  +     }
  +   }
  +   if (os == "osx") os <- "mac"
  +   tolower(os)
  + }
  > 
  > if (get_os() != "mac" || Sys.getenv("NOT_CRAN") == "true") {
  +   test_check("exampletestr")
  + }
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-example-extraction.R:15:3'): `extract_examples()` works ──────
  `extract_examples("detect", tempdir(check = TRUE))` threw an error with unexpected message.
  Expected match: "Path .+ does not appear to be inside a project or package."
  Actual message: "✖ Path 'D:/temp/Rtmp25abw9/' does not appear to be inside a project or\n  package.\nℹ Read more in the help for `usethis::proj_get()`."
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test-example-extraction.R:15:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─exampletestr:::extract_examples("detect", tempdir(check = TRUE))
    7.   └─usethis::local_project(path = pkg_dir, quiet = TRUE)
    8.     └─usethis::proj_set(path = path, force = force)
    9.       └─usethis:::ui_abort(...)
   10.         └─cli::cli_abort(...)
   11.           └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
  Error: Test failures
  Execution halted
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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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Malformed Description field: should contain one or more complete sentences.
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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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    32 | code{TRUE}}
       |     ^
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    35 | code{TRUE}}
       |     ^
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Functions and objects (details)
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    80 | \doi{10.1016/s0002-9394(02)01825-1}{Beck et al.}, and
       |                                    ^
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'LazyData' is specified without a 'data' directory
checkRd: (-1) ez-package.Rd:19: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) ez-package.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:33: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fmCov.Rd:37: Lost braces; missing escapes or markup?
    37 | where, \code{alpha(i)} is the intercept, \code{f(t)} is a {K x 1} vector of 
       |                                                           ^
checkRd: (-1) plot.ffm.Rd:82: Lost braces; missing escapes or markup?
    82 | \item{las}{one of {0, 1, 2, 3} to set the direction of axis labels, same as
       |                   ^
checkRd: (-1) summary.ffm.Rd:39: Lost braces; missing escapes or markup?
    39 | Returned object is of class {summary.ffm}.
       |                             ^
checkRd: (-1) fviz_nbclust.Rd:75: Lost braces; missing escapes or markup?
    75 | (2001) proposed: "the smallest k such that gap(k) >= gap(k+1) - s_{k+1}". 
       |                                                                   ^
checkRd: (-1) fviz_nbclust.Rd:77: Lost braces; missing escapes or markup?
    77 | SE.factor*s_{k+1}" where SE.factor is a numeric value which can be 1
       |             ^
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    minor changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) FADPclust.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) FADPclust.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) happy.Rd:14: Lost braces
    14 |                  code{Pretty happy} <  \code{Very happy}}
       |                      ^
checkRd: (-1) fra_sf.Rd:22: Lost braces; missing escapes or markup?
    22 | A map of France as {sf} object. Can be used as dataset or for maps
       |                    ^
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    help   1.2Mb
Specified C++11: please drop specification unless essential
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checkRd: (-1) pi0FAMT.Rd:18: Lost braces
    18 | \code{pi0}{The estimated proportion \code{pi0} of null hypotheses.}}
       |           ^
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is 14.2Mb
  sub-directories of 1Mb or more:
    doc    9.2Mb
    help   1.8Mb
    libs   2.0Mb
Specified C++11: please drop specification unless essential
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installed size is  5.6Mb
  sub-directories of 1Mb or more:
    images   3.1Mb
    libs     1.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    1.1Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ica.c:100:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  ica.c:100:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/fastICA.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'coxKM'
checkRd: (-1) KITdesign.Rd:36: Lost braces; missing escapes or markup?
    36 |  \item{trait}{One of {'c','d','s',NULL} indicating the type
       |                      ^
checkRd: (-1) KITkernel.Rd:51: Lost braces; missing escapes or markup?
    51 |  \item{trait}{One of {'c','d','s',NULL} indicating the type
       |                      ^
checkRd: (-1) geno.Rd:19: Lost braces; missing escapes or markup?
    19 |                 Must be one of {'ibs', 'linear', 'quadratic'}.
       |                                ^
checkRd: (-1) geno.Rd:31: Lost braces; missing escapes or markup?
    31 |                      {'add', 'dom', 'rec'} indicating additive,
       |                      ^
checkRd: (-1) nongeno.Rd:14: Lost braces; missing escapes or markup?
    14 |                 Must be one of {'interactive', 'linear', 'quadratic'}.
       |                                ^
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.2Mb
checkRd: (-1) eigen_compute_single_entry_of_diagonal_matrix.Rd:17: Lost braces; missing escapes or markup?
    17 | The value of m^{-1}_{j,j}
       |                ^
checkRd: (-1) eigen_compute_single_entry_of_diagonal_matrix.Rd:17: Lost braces; missing escapes or markup?
    17 | The value of m^{-1}_{j,j}
       |                     ^
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) update_nhl_db.Rd:51-53: Lost braces in \itemize; meant \describe ?
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installed size is 15.8Mb
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    data  15.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    Rcgi      2.6Mb
    cgi-bin   2.5Mb
.run: no visible binding for global variable 'init'
.run: no visible global function definition for 'init'
.run: no visible binding for global variable 'run'
Undefined global functions or variables:
  init run
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
checkRd: (-1) Error-Classes.Rd:107-119: Lost braces
   107 |   \item \code{do_verbose(response, template)} {
       |                                               ^
checkRd: (-1) Error.Rd:33-45: Lost braces
    33 |   \item \code{do(response, mssg)} {
       |                                   ^
checkRd: (-1) fh_bounds.Rd:14: Lost braces
    14 | \item{params1}{Arguments to pass to the r{dist} function for distribution 1}
       |                                          ^
checkRd: (-1) fh_bounds.Rd:16: Lost braces
    16 | \item{params2}{Arguments to pass to the r{dist} function for distribution 2}
       |                                          ^
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checkRd: (-1) FBNormalization.Rd:40: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) fbad_copy_ad.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_ad.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) fbad_copy_adset.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_adset.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) fbad_copy_campaign.Rd:31: Lost braces; missing escapes or markup?
    31 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_campaign.Rd:33: Lost braces; missing escapes or markup?
    33 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) plot.fbroc.conf.Rd:5: Lost braces
     5 | \title{Plots function for object of class{fbroc.conf}}
       |                                          ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) fcr-package.Rd:15: Lost braces; missing escapes or markup?
    15 | Let $y_{ij}$ denote some outcome measured at
       |        ^
checkRd: (-1) fcr-package.Rd:16: Lost braces; missing escapes or markup?
    16 | $t_{ij}$ on the functional domain (e.g. time) for subject $i$ at observation
       |    ^
checkRd: (-1) fcr-package.Rd:29: Lost braces; missing escapes or markup?
    29 | Initially, a model is fit without $b_i(t_{ij})$. Using the residuals from this initial fit,
       |                                          ^
checkRd: (-1) fcr.Rd:13: Lost braces; missing escapes or markup?
    13 | The formula should only include terms not associated with the random function intercept b_i(t_{ij}). See Examples.}
       |                                                                                               ^
Specified C++11: please drop specification unless essential
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installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    1.5Mb
    help   2.1Mb
    libs   1.5Mb
checkRd: (-1) simulation_model9.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                              ^
checkRd: (-1) simulation_model9.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                                           ^
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
GNU make is a SystemRequirements.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
checkRd: (-1) NASAtemp.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NASAtemp.Rd:15: Lost braces in \itemize; meant \describe ?
Found the following HTML validation problems:
GCCV.S.html:87:32 (GCCV.S.Rd:47): Warning: trimming empty <code>
checkRd: (-1) plot.dma.Rd:46: Lost braces; missing escapes or markup?
    46 | If {x} comes from estimation of Dynamic Model Selection (DMS) or Median Probability Model (MED), after executing \code{plot} the User is asked to choose
       |    ^
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/fdrDiscreteNull.Rcheck/00install.out' for details.
checkRd: (-1) p.fdr.Rd:30: Lost braces
    30 | \item{adjust.method}{A string used to identify the p-value and false discovery rate adjustment method. Defaults to \code{BH}. Options are \code{BH}, \code{BY}, code{Bon},\code{Holm}, \code{Hoch}, and \code{Sidak}.}
       |                                                                                                                                                                     ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mutlicol_terminator.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New Stuff
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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) contemParametros.Rd:19: Lost braces
    19 | \item{exclui3pontos}{verify por ... ? in f<-function(a, ...){ }}
       |                                                             ^
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R         4.7Mb
    doc       2.3Mb
    extdata   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'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) bitspec.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) fun-igraph_financial.Rd:34: Lost braces; missing escapes or markup?
    34 | The same result for both \code{igraph} and {igraph_financial} objects
       |                                            ^
checkRd: (-1) igraph_E_iterators.Rd:31: Lost braces; missing escapes or markup?
    31 | The same result for both \code{igraph} and {igraph_financial} objects
       |                                            ^
checkRd: (-1) igraph_v_iterators.Rd:29: Lost braces; missing escapes or markup?
    29 | The same result for both \code{igraph} and {igraph_financial} objects
       |                                            ^
checkRd: (-1) plot_igraph-methods.Rd:22: Lost braces
    22 | Methods to extend code{igraph}'s plotting functions to \code{igraph_financial} objects
       |                       ^
checkRd: (-1) plot_igraph-methods.Rd:19: Lost braces; missing escapes or markup?
    19 | For both \code{igraph} and {igraph_financial} objects, returns NULL invisibly. It is called to print the graph to any R device. (see method and \href{https://rdrr.io/cran/igraph/man/plot.igraph.html}{igraph::plot.igraph})
       |                            ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
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checkRd: (-1) FiSh-package.Rd:19: Lost braces
    19 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
checkRd: (-1) FiSh-package.Rd:32: Lost braces
    32 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
checkRd: (-1) SEP_FIM.Rd:46: Lost braces
    46 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
installed size is  5.4Mb
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    data      1.3Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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    lib    3.0Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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checkRd: (-1) fitConic.Rd:66-73: Lost braces
    66 | \code{parA }{vector of the six "ABCDEF" coefficients
       |             ^
checkRd: (-1) fitConic.Rd:67: Lost braces
    67 | \code{RSS }{'root sum square' figure of merit describing the relative fit quality}
       |            ^
checkRd: (-1) fitConic.Rd:68: Lost braces
    68 | \code{iters }{number of iterations at convergence}
       |              ^
checkRd: (-1) fitConic.Rd:69-71: Lost braces
    69 | \code{exitCode }{1 means ellipse, 2 means hyperbola, 3 means parabola.
       |                 ^
checkRd: (-1) rotateA.Rd:59: Lost braces; missing escapes or markup?
    59 | For \code{xyrot} {a Nx2 array of the x,y coordinates of the rotated data set. }
       |                  ^
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'gridlayout'
installed size is  5.4Mb
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Packages suggested but not available for checking: 'reliaR', 'STAR'
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Package suggested but not available for checking: 'fivethirtyeightdata'
checkRd: (-1) food_world_cup.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:72: Lost braces in \itemize; meant \describe ?
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Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
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    R      1.4Mb
    doc    3.6Mb
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checkRd: (-1) distribution_vector.Rd:14: Lost braces; missing escapes or markup?
    14 | All standard distributions from {stats} package are covered. For a list
       |                                 ^
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checkRd: (-1) convertInitDesignToGrid.Rd:11: Lost braces; missing escapes or markup?
    11 | The initial design, consisting of \code{d + 1} columns ({d} dimensions and
       |                                                         ^
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    help   2.3Mb
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checkRd: (-1) ModelMixHMM-class.Rd:31: Lost braces; missing escapes or markup?
    31 |         \code{smoothed} of class {StatMixHMM}).
       |                                  ^
checkRd: (-1) ModelMixHMMR-class.Rd:31: Lost braces; missing escapes or markup?
    31 |         \code{smoothed} of class {StatMixHMMR}).
       |                                  ^
checkRd: (-1) summary.flamcv.rd:8: Lost braces
     8 | This function summarizes a call to code{\link{flamCV}} and identifies the tuning parameter chosen by cross-validation.
       |                                        ^
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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)
       |                         ^
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    49 | If k = 2: (xi_1, ..., x_{C_i - 1}, omega, alpha1, tau1, alpha2, tau2)
       |                         ^
installed size is 23.5Mb
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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}
       |                              ^
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   110 | \strong{Behaviour:}{
       |                    ^
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   111 | {
       | ^
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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 
       |                                                                                            ^
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    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
       |                      ^
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    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;}
       |                   ^
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    53 |   \code{tailsFMstable}{  returns a list with the following components
       |                       ^
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    48 |         The metric MdAE is obtained using code{type = "AE"} and  \code{statistic = "Md"}
       |                                               ^
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    Previous versions (not tagged nor released)
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    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}
       |                  ^
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    18 |   \item {z_depth} : {measured focus range depth (z)}}
       |                     ^
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    66 | moderator. By default it is equal to \8code{c(19, 17, 15, 8, 5, 4, 3, 1)}.}
       |                                            ^
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     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |     ^
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     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                        ^
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     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                              ^
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     9 | m_{i+1}), where the indicator function I counts the number of
       |   ^
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    help   2.7Mb
    libs   3.6Mb
Problems with news in 'NEWS.md':
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    32 |                           \code{"GAUSSIAN"}, code{"TRIANGLE"}, \code{"TRAPEZOID"}, \code{"SIGMOID"}, and \code{"BELL"}.
       |                                                  ^
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    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 
       |          ^
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    57 |   \code{freealg} object comprising terms of grade code{n}.
       |                                                       ^
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   197 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
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    18 |         \item{las}{numeric in {0,1,2,3}; the style of axis labels (see \code{\link{par}}).}
       |                               ^
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    18 | This is a code{tbl_df} mapping misspellings of their words, compiled by
       |               ^
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    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                             ^
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    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                                                     ^
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    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.
       |                                                                                                          ^
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FuzzyNumberList.html:76:1 (FuzzyNumberList.Rd:285): Warning: trimming empty <ul>
TrapezoidalFuzzyNumberList.html:118:1 (TrapezoidalFuzzyNumberList.Rd:572): Warning: trimming empty <ul>
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    20 | of the paper on Wilson's warbler, this function computes $tilde{T}^{(mu)}$ (returned as
       |                                                                ^
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    20 | of the paper on Wilson's warbler, this function computes $tilde{T}^{(mu)}$ (returned as
       |                                                                    ^
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    21 | list component \code{mean.raster}) and $R^{(sigma^2)}$ (returned as list component
       |                                           ^
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    44 |     always use code{"none"}.}
       |                    ^
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    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.  
       |                                                                                                                                                                                                                                         ^
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    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()}.
       |                                                                                                                                                                                                                                                                                      ^
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     6 |  \ This is a wrapper to function \code{\link[gamlss]{term.plot}}. code{term.plotZadj} produces term plots for a specified parameter from a    
       |                                                                       ^
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     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
       |                                                                                                                ^
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    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                      ^
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    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                                      ^
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    29 | output array, {row,col}.names are not necessary \code{dimnames[[1]]} and
       |               ^
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    30 | \item{tempt_mean, tempt_std}{Mean and between record standard deviation of parameter $t_{empt}$, typically in minutes.}
       |                                                                                         ^
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    14 | \item{eta0}{inital value in {1,...,r}.}
       |                             ^
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    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.}
       |                                                                                                                                            ^
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    58 | \code{scoreU.cgb2} returns a \eqn{N \times (L-1)} matrix of scores <code{U}.
       |                                                                         ^
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    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}. 
       |                                                                                                                ^
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    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.}
       |                                                                                 ^
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    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.}
       |                                                                                 ^
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   208 | \item Error in if (n.trees > x$n.trees) { : argument is of length zero}. LR or BF probably too low
       |                                         ^
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     5 | \title{List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                           ^
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    17 | List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                    ^
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    17 | value of the shape parameter of the Matern correlation class. The default {alpha = 0.5} corresponds to an exponential correlation model. 
       |                                                                           ^
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    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,
       | ^
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    56 |   U : A matrix which has N-rows and J-columns (J < {N, M}).
       |                                                    ^
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    57 |   V : A matrix which has M-rows and J-columns (J < {N, M}).
       |                                                    ^
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    58 |   J : The number of dimension (J < {N, M}).
       |                                    ^
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    30 | code{infile=}, indicating that the input file should be
       |     ^
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    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
       |                                                                  ^
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     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
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    10 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
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     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
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    10 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
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     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
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     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
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     6 | \title{Compound Extraction experiment of Dopico-Garc{\' i}a et al. (2007)}
       |                                                     ^
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    35 | An analytical experiment conducted by Dopico-Garc{\' i}a et al. (2007) to
       |                                                  ^
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    22 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
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    17 | \item{y}{n-by-1 binary response vector sampled from {0,1}}
       |                                                     ^
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    40 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
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    57 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
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    57 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
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    70 | covariates included in \code{formula_l} or {formula_s} (required).}
       |                                            ^
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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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    help      2.6Mb
Found the following HTML validation problems:
extprod3d.html:24:32 (extprod3d.Rd:24): Warning: trimming empty <code>
extprod3d.html:29:32 (extprod3d.Rd:27): Warning: trimming empty <code>
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GNU make is a SystemRequirements.
Package suggested but not available for checking: 'RandomFields'
Malformed Description field: should contain one or more complete sentences.
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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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    42 | \item{xmin, ymin, xmax, ymax}{Boundaries of the area in pixels. {0,0} is the
       |                                                                 ^
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Unexported object imported by a ':::' call: 'productplots:::bound'
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installed size is  5.9Mb
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installed size is  9.4Mb
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    * Changes all data options to .data to decrease possibility of column naming overlap
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'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:
    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}
       |                                                                           ^
installed size is 11.0Mb
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    doc    9.5Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    Giac  18.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   2.5Mb
checkRd: (-1) gigg.Rd:70-77: Lost braces in \itemize; \value handles \item{}{} directly
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) significantTau.Rd:52-53: Lost braces in \itemize; \value handles \item{}{} directly
Found the following HTML validation problems:
sample_income_data.html:37:1 (sample_income_data.Rd:8): Warning: trimming empty <h4>
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
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    27 |   \item{\code{y}}{n by S matrix updated with censored {values} substituted for
       |                                                       ^
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    32 | Missing times in the data occur where there are gaps in \code{timeCol} column of \code{xdata} and the initial time \code{0} for each sequence.  New versions of the data have \code{NA} (\code{xdata}) or prior values with appropriate weight (\code{ydata}).  Missing times are filled in \code{xdata, ydata, edata}, including a time \code{0} which serves as a prior mean for \code{ydata} for time code{1}.  The group and time indices in columns \code{groupCol} and \code{timeCol} of \code{xdata} reference the time for a given time series.  Missing values in the columns \code{groupVars} of \code{xdata} are filled automatically filled in.  This assumes that values for these variables are fixed for the group.  If \code{FILLMEANS}, the missing  values in \code{ydata} are filled with means for the group and given a low weight specified in \code{missingEffort}.
       |                                                                                                                                                                                                                                                                                                                                                                                                              ^
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: 'doMC'
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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}
       |   ^
installed size is  6.5Mb
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    doc    1.4Mb
    libs   4.2Mb
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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.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
GNU make is a SystemRequirements.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc             1.3Mb
    libs            4.4Mb
    test_data       2.3Mb
    vignette_data   1.1Mb
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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).
       |     ^
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
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    35 |   Returns the current scale factor $r_{ii}$ for row \code{i} of the specified
       |                                       ^
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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.
Package suggested but not available for checking: 'doMC'
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    24 | \item{g}{A formula as \code{y~z}, where code{y} is the response and
       |                                             ^
Package required and available but unsuitable version: 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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    50 | (KKT) system denoted by \eqn{H(z)=0}, for \eqn{z \in \Omega} where eqn{z} is formed by the players strategy 
       |                                                                       ^
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    76 | (KKT) system denoted by \eqn{\Phi(z)=0}{Phi(z)=0}, where eqn{z} is formed by the players strategy 
       |                                                             ^
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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    30 | \item{package_name}{Package name to use. By default, {golem} uses
       |                                                      ^
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    42 | The {desc} object, invisibly.
       |     ^
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    23 | {dockerfiler}.
       | ^
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    80 | \item{config_file}{path to the {golem} config file}
       |                                ^
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     5 | \title{Install {golem} dev dependencies}
       |                ^
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    13 | \item{package_name}{Package name to use. By default, {golem} uses
       |                                                      ^
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    16 | \item{x}{The repository in format {owner}/{repo} e.g. MarkEdmondson1234/googleCloudRunner}
       |                                   ^
checkRd: (-1) GitHubEventsConfig.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{x}{The repository in format {owner}/{repo} e.g. MarkEdmondson1234/googleCloudRunner}
       |                                           ^
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    27 | \item{id}{The id of the buildstep.  In link{cr_buildstep_targets_multi} this is used along with \code{waitFor} to determine the order of execution}
       |                                            ^
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    21 | \item{account_email}{The service account email e.g. \code{accountId@projectid.iam.gserviceaccount.com} or {12345678@cloudbuild.gserviceaccount.com}}
       |                                                                                                           ^
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cr_run.html:115:1 (cr_run.Rd:57): Warning: trimming empty <dt>
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    54 | of `{sf}` objects).}
       |     ^
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    31 | instance from vertex 1.  Internally, it creates the graph Kn-{v1}
       |                                                              ^
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Malformed Description field: should contain one or more complete sentences.
installed size is  6.3Mb
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    R   5.7Mb
installed size is  7.4Mb
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    libs   6.5Mb
checkRd: (-1) solve_game.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
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exponential_anisotropic3D_alt.html:70:1 (exponential_anisotropic3D_alt.Rd:34): Warning: trimming empty <h3>
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    21 |     in code{data} not in this list will be ignored. Use \code{NA} to
       |            ^
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    doc    3.5Mb
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    65 |         least one root larger than one) on bootstrapped \verb{x} and {y}.
       |                                                                      ^
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    68 |         least one root larger than one) on bootstrapped \verb{x} and {z}.
       |                                                                      ^
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    71 |         least one root larger than one) on bootstrapped \verb{x}, \verb{y} and {z}.
       |                                                                                ^
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    doc    1.9Mb
    help   2.0Mb
    libs   1.2Mb
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installed size is  6.8Mb
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    data   3.9Mb
    libs   1.7Mb
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checkRd: (-1) MinimiseEPL.Rd:17: Lost braces in \itemize; meant \describe ?
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summary_greek.html:58:1 (summary_greek.Rd:22): Warning: trimming empty <dt>
GNU make is a SystemRequirements.
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accrualReport: multiple local function definitions for 'gg' with
  different formal arguments
checkRd: (-1) setgreportOption.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) setgreportOption.Rd:20: Lost braces in \itemize; meant \describe ?
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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 ?
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checkRd: (-1) setgreportOption.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) iterate_matrix.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) iterate_matrix.Rd:39-41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iterate_matrix.Rd:42-44: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: 'doMC'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   2.6Mb
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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs                     1.3Mb
    supplementary_material   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
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
checkRd: (-1) Birthwt.Rd:18: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) Lung.Rd:14-16: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) Lung.Rd:31-33: Lost braces in \itemize; meant \describe ?
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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: \&
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
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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
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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
Found the following HTML validation problems:
gsheet2tbl.html:31:5 (gsheet2tbl.Rd:20): Warning: trimming empty <p>
gsheet2tbl.html:31:1 (gsheet2tbl.Rd:20): Warning: trimming empty <li>
checkRd: (-1) besselap.Rd:58: Lost braces
    58 | Thomas Sailer, email{t.sailer@alumni.ethz.ch}.\cr Conversion to R by
       |                     ^
checkRd: (-1) diric.Rd:25: Lost braces; missing escapes or markup?
    25 | evaluated at the elements of the input array {x}.
       |                                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) lisiecki2005.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lisiecki2005.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lisiecki2005.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:29: Lost braces in \itemize; meant \describe ?
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) jura.Rd:29: Lost braces; missing escapes or markup?
    29 |         \item{Cd}{ mg cadmium kg^{-1} topsoil }
       |                                  ^
checkRd: (-1) jura.Rd:30: Lost braces; missing escapes or markup?
    30 |         \item{Co}{ mg cobalt kg^{-1} topsoil }
       |                                 ^
checkRd: (-1) jura.Rd:31: Lost braces; missing escapes or markup?
    31 |         \item{Cr}{ mg chromium kg^{-1} topsoil }
       |                                   ^
checkRd: (-1) jura.Rd:32: Lost braces; missing escapes or markup?
    32 |         \item{Cu}{ mg copper kg^{-1} topsoil }
       |                                 ^
checkRd: (-1) jura.Rd:33: Lost braces; missing escapes or markup?
    33 |         \item{Ni}{ mg nickel kg^{-1} topsoil }
       |                                 ^
checkRd: (-1) jura.Rd:34: Lost braces; missing escapes or markup?
    34 |         \item{Pb}{ mg lead kg^{-1} topsoil }
       |                               ^
checkRd: (-1) jura.Rd:35: Lost braces; missing escapes or markup?
    35 |         \item{Zn}{ mg zinc kg^{-1} topsoil }
       |                               ^
checkRd: (-1) variogramST.Rd:49: Lost braces; missing escapes or markup?
    49 |   time lag $t$, the pseudo cross variogram $(Z_i(s)-Z_{i+t}(s+h))^2$ is averaged over all time 
       |                                                       ^
checkRd: (-1) variogramST.Rd:50: Lost braces; missing escapes or markup?
    50 |   lagged observation sets $Z_i$ and $Z_{i+t}$ available (weighted by the number of pairs involved).
       |                                        ^
Specified C++11: please drop specification unless essential
checkRd: (-1) artset1987.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gte.Rd:98: Lost braces; missing escapes or markup?
    98 | \code{left} and {right} for illustrative purpose), one would need a third variable (\code{status}) taking the value 0 
       |                 ^
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.1Mb
Running 'testthat.R' [38s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > if (requireNamespace("testthat", quietly = TRUE)) {
  + 
  +   library(testthat)
  +   library(gtfstools)
  + 
  +   test_check("gtfstools")
  + 
  + }
  trying URL 'https://github.com/ipeaGIT/gtfstools/raw/master/inst/extdata/spo_gtfs.zip'
  Content type 'application/zip' length 191108 bytes (186 KB)
  ==================================================
  downloaded 186 KB
  
  [ FAIL 2 | WARN 8 | SKIP 2 | PASS 1243 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-download_validator.R:37:1', 'test-validate_gtfs.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-set_trip_speed.R:257:3'): results in identical gtfs if none of the specified trip_ids exist ──
  `same_speeds_gtfs <- set_trip_speed(gtfs, character(0), 1)` produced warnings.
  ── Failure ('test-set_trip_speed.R:263:3'): results in identical gtfs if none of the specified trip_ids exist ──
  `same_speeds_gtfs <- set_trip_speed(gtfs, character(0), numeric(0))` produced warnings.
  
  [ FAIL 2 | WARN 8 | SKIP 2 | PASS 1243 ]
  Error: Test failures
  Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.0Mb
    help   2.0Mb
'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.}
       |                                                          ^
checkRd: (-1) gumbel.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:75: Lost braces in \itemize; meant \describe ?
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) esSim.Rd:81: Lost braces; missing escapes or markup?
    81 | \eqn{83} SNPs are in cluster {-}, \eqn{714} SNPs are in cluster \eqn{0},
       |                              ^
checkRd: (-1) esSimDiffPriors.Rd:91: Lost braces; missing escapes or markup?
    91 | \eqn{64} SNPs are in cluster {-}, \eqn{708} SNPs are in cluster \eqn{0},
       |                              ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following HTML validation problems:
GWASinlps.html:187:1 (GWASinlps.Rd:99): Warning: trimming empty <h4>
Found the following HTML validation problems:
gedit.html:139:6 (gedit.Rd:72): Warning: trimming empty <p>
gedit.html:139:1 (gedit.Rd:72): Warning: trimming empty <li>
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 267.8Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    help    1.0Mb
    java  264.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    shiny   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    HaDeX   4.0Mb
    doc     4.0Mb
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.ga.breed' '.ga.fitness' '.ga.init' '.ga.mutate' '.ga.step'
  '.ga.weight'
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.6Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R         2.6Mb
    extdata   1.3Mb
GNU make is a SystemRequirements.
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 ?
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'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 ?
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'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.}
       |                                                     ^
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
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
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checkRd: (-1) marker_h2_means.Rd:102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:41-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:46-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:49-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:52-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:55-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:61-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:66-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) phermite.Rd:38: Lost braces; missing escapes or markup?
    38 |   {b} and \code{m} to be lower (or greater) than \code{q}.
       |   ^
GNU make is a SystemRequirements.
checkRd: (-1) hero.Rd:67-68: Lost braces
    67 | then \code{\link[pbapply]{pblapply}} is used. If code{package ==
       |                                                      ^
checkRd: (-1) hero.Rd:69: Lost braces
    69 | code{package == "Rmpi"}, then \code{\link[Rmpi]{mpi.applyLB}} is used.}
       |     ^
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) mleHetGP.Rd:57: Lost braces; missing escapes or markup?
    57 | Level \code{2} gives more details. Level {3} additionaly displays all details about initialization of hyperparameters.
       |                                          ^
checkRd: (-1) mleHetTP.Rd:61: Lost braces; missing escapes or markup?
    61 | Level \code{2} gives more details. Level {3} additionaly displays all details about initialization of hyperparameters.
       |                                          ^
checkRd: (-1) mleHomTP.Rd:76: Lost braces; missing escapes or markup?
    76 | \item \code{nit_opt}, \code{msg}: \code{counts} and {msg} returned by \code{\link[stats]{optim}}
       |                                                     ^
checkRd: (-1) predictPair.Rd:20: Lost braces; missing escapes or markup?
    20 | A number in the set {-1, 0, 1}, where 1 means row1 is predicted to
       |                     ^
checkRd: (-1) predictPairInternal.Rd:18: Lost braces; missing escapes or markup?
    18 | A number in the set {-1, 0, 1}, where 1 means row1 is predicted to
       |                     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
get_breaks.html:78:1 (get_breaks.Rd:37): Warning: trimming empty <dt>
'LazyData' is specified without a 'data' directory
checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^
checkRd: (-1) hierNet.Rd:28: Lost braces; missing escapes or markup?
    28 |     terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |               ^
checkRd: (-1) hierNet.logistic.Rd:30: Lost braces; missing escapes or markup?
    30 |     terms, th_{jj}X_j^2, in the model.  Default TRUE.}  
       |               ^
checkRd: (-1) hierNet.logistic.Rd:63: Lost braces
    63 | \seealso{\link{predict.hierNet.logistic},link{hierNet.logistic.path}}
       |                                              ^
checkRd: (-1) hierNet.logistic.path.Rd:39: Lost braces; missing escapes or markup?
    39 |   terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |             ^
checkRd: (-1) hierNet.path.Rd:38: Lost braces; missing escapes or markup?
    38 |   terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |             ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'colorfulVennPlot'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'HadoopStreaming'
Specified C++11: please drop specification unless essential
checkRd: (-1) hlt.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:77-78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hlt.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hlt.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hlt.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hlt.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.3Mb
html_describe_con: multiple local function definitions for 'g' with
  different formal arguments
checkRd: (-1) nafracCalc.Rd:45: Lost braces
    45 |   as if code{y} were not of class \code{"multipleHmmDataSets"}.
       |             ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
checkRd: (-1) sampleMcmc.Rd:93: Lost braces; missing escapes or markup?
    93 |   disable some of them, by adding a \code{$UPDATER_NAME=FALSE} pair to the {updater} argument. Another usage of
       |                                                                            ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
checkRd: (-1) HOasso.Rd:43: Lost braces; missing escapes or markup?
    43 | Arguments \code{x} and {y} are \code{character} objects and can assume values   \code{"sout"}, \code{"dout"}, \code{"lout"}, \code{"sin"}, \code{"din"}, \code{"lin"} representing the out-strength, out-degree, out-log-strength, in-strength, in-degree, and in-log-strength respectively.
       |                        ^
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    app   1.7Mb
    doc   3.3Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) hd.ord.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) HPLB.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
'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) BD_shift.Rd:67-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BD_shift.Rd:74-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BD_shift.Rd:78-82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BD_shift.Rd:83-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) heavy_SIP.Rd:69-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) heavy_SIP.Rd:72-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) heavy_SIP.Rd:76-79: Lost braces in \itemize; meant \describe ?
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.3Mb
    help   1.1Mb
Specified C++14: please drop specification unless essential
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CalcROC.Rd:47: Lost braces
    47 | The accuracy of the classifier is the mean value of dQuote{(optSn, optSp)} for two-class problem and the mean value of \dQuote{(optSn, optSp,optS3)} for three-class problem.
       |                                                           ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
checkRd: (-1) simgl.Rd:50: Lost braces; missing escapes or markup?
    50 | Uses the {updog} R package for simulating read counts and generating
       |          ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ws_download.Rd:31: Lost braces; missing escapes or markup?
    31 | (while using the {hwsdr} package for HWSD v2.0).
       |                  ^
Package suggested but not available for checking: 'microViz'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) extractPeriod.Rd:57: Lost braces
    57 | NOTE: all the dates in the datalist should follow the format in ?as.Date{base}.
       |                                                                         ^
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) IATData.Rd:24: Lost braces; missing escapes or markup?
    24 | Dan Martin {dpmartin42@gmail.com}
       |            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SparkR'
checkRd: (-1) setServerLogLevel.Rd:20: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:23: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) betaS1lr.Rd:28: Lost braces; missing escapes or markup?
    28 |  \item{Rm1U}{matrix R^{-1}U (see reference).}
       |                       ^
checkRd: (-1) lrsmoother.Rd:32: Lost braces; missing escapes or markup?
    32 |   R^{-1}U (see reference) and \link{smoothCon} for the definition of smoothobject}
       |     ^
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'icd'
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) Bpa.Rd:39-40: Lost braces
    39 | stocks. \doi{10.17895/ices.pub.3036}{\emph{ICES Advice
       |                                     ^
checkRd: (-1) Fpa.Rd:42-43: Lost braces
    42 | stocks. \doi{10.17895/ices.pub.3036}{\emph{ICES Advice
       |                                     ^
checkRd: (-1) icesRound.Rd:64-65: Lost braces
    64 | \doi{10.17895/ices.pub.3038}{\emph{ICES Advice Technical
       |                             ^
checkRd: (-1) mohn.Rd:71-72: Lost braces
    71 | \doi{10.17895/ices.pub.5997}{\emph{ICES Scientific Reports
       |                             ^
Specified C++11: please drop specification unless essential
checkRd: (-1) ic.ranks.Rd:46: Lost braces; missing escapes or markup?
    46 | \item{n_adjust}{an integer-valued entry for advanced control over the lower- or upper-bound algorithms. When the "adjustL" parameter is TRUE, the new value of n_adjust is chosen automatically as the best adjustment on the lower affine bound of the chi-square quantiles according to the data. If adjustU is TRUE, then n_adjust contains the point at which the upper affine bound is tangent on the chi-square quantiles. Possible values {1,...,n-1}. If both adjustL and adjustU variables are left FALSE, then the default choice is that the lower affine bound passes between the chi-square quantiles at 1 and n-1 degrees of freedom, and the upper affine bound is tangent on n-1.}
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) data.Rd:7: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data.Rd:9: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rggobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'IFCdata'
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.2Mb
    help   2.0Mb
    libs   5.6Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) simHawkes1a.Rd:35: Lost braces; missing escapes or markup?
    35 | distribution; 'd${dis}' gives the density function \eqn{g(\cdot)}.}
       |                  ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) lab.qcs.Rd:24: Lost braces
    24 | It develops an object of \code{lab.qcs}-code{link{class}} to perform statistical quality control.
       |                                             ^
checkRd: (-1) lab.qcs.Rd:24: Lost braces
    24 | It develops an object of \code{lab.qcs}-code{link{class}} to perform statistical quality control.
       |                                                  ^
checkRd: (-1) define_target_function.Rd:41: Lost braces; missing escapes or markup?
    41 | be done either as a single vector of values (e.g. `function(x) { ... }`), or individual inputs for each parameter
       |                                                                ^
checkRd: (-1) define_target_function.Rd:42: Lost braces; missing escapes or markup?
    42 | (e.g. `function(x1, x2) { ... }`). If a single vector is used, all parameters will be passed to the target function as
       |                         ^
checkRd: (-1) image_contour_detector.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_contour_detector.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_contour_detector.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitSpline.Rd:109: Lost braces
   109 |        \code{response} and it will have the same order of code{x} as \code{data}. 
       |                                                               ^
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         1.4Mb
checkRd: (-1) image_fhog.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
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Specified C++11: please drop specification unless essential
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    doc       3.7Mb
    extdata   1.0Mb
    include   3.3Mb
    libs     11.5Mb
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    23 | \item{grayscale}{logical. Defines color channels of images: 1 if code{TRUE}, 3 if \code{FALSE}.}
       |                                                                      ^
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs   10.5Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
checkRd: (-1) oversample.Rd:23-24: Lost braces
    23 | minority examples and majority ones, that is, the quotient {size of
       |                                                            ^
checkRd: (-1) oversample.Rd:24: Lost braces; missing escapes or markup?
    24 | minority class}/{size of majority class}. There are methods, such as
       |                 ^
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    data   3.2Mb
    doc    1.6Mb
'LazyData' is specified without a 'data' directory
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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.}
       | ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'accdata'
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    27 |   \item{call}{a string containing the matched function call that generates this sQuote{inaparc} object.}
       |                                                                                       ^
Specified C++11: please drop specification unless essential
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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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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Specified C++11: please drop specification unless essential
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Problems with news in 'NEWS.md':
No news entries found.
Package which this enhances but not available for checking: 'gurobi'
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     8 | code{write_workflow} writes a workflow script for inference. Beyond possibly saving some typing, this suggests what may be a reasonably good starting workflow. One should not expect to control all options of the workflow through the \code{write_workflow} arguments.
       |     ^
'LazyData' is specified without a 'data' directory
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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.
       |                                              ^
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    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.
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    32 | A data set to replicate the findings of Escrib\`{a}-Folch,
       |                                                 ^
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    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}
       |         ^
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    40 | \item{dqfunc}{function, density of the results of the quantile function, e.g., function(x){dnorm(qnorm(x))} (used for 'general' scores, 
       |                                                                                           ^
installed size is 10.2Mb
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    doc   9.7Mb
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    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.
       |               ^
Specified C++11: please drop specification unless essential
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   132 | \code{surv_lambda} (or code{cure_lambda}) that produces all-zero
       |                            ^
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    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'
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    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.
       |                                                               ^
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    19 | impact. emph{Journal of Applied Psychology}, 92(5), 1380.
       |             ^
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File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(IPDFileCheck)
  > 
  > test_check("IPDFileCheck")
  The following errors were returned during `::()`, `gtsummary()`, and `modify_header()`:
  x For variable `age` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `marker` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `response` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-IPDFilecheck.R:948:3'): testing getting summary from gtsummary ──
  summary_tempdata$N (`actual`) not equal to 4 (`expected`).
  
  `actual` is NULL
  `expected` is a double vector (4)
  ── Error ('test-IPDFilecheck.R:951:3'): testing getting summary from gtsummary ──
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(dplyr::tibble(variable = names(fns)), summary_type = map_chr(.data$variable, 
      ~x$inputs$type[[.x]]), row_type = map_chr(.data$variable, 
      ~location[[.x]]), label = map2(.data$variable, .data$row_type, 
      ~dplyr::filter(x$table_body, .data$variable == .x, .data$row_type == 
          .y)$label))`: i In argument: `summary_type = map_chr(.data$variable, ~x$inputs$type[[.x]])`.
  Caused by error in `.data$variable`:
  ! Column `variable` not found in `.data`.
  
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  Error: Test failures
  Execution halted
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    47 | \code{conv_plot}: code{ipm} invisibly.
       |                       ^
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    28 |     \code{constraint}{ a character string containing value constraints }
       |                      ^
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    29 |     \code{url}{ optional url of the BSS measurements service }
       |               ^
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    28 |       \code{constraint}{ a character string containing value constraints }
       |                        ^
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    29 |       \code{url}{ optional url of the MUSTANG measurements service} 
       |                 ^
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    28 |      \code{constraint}{ a character string containing value constraints }
       |                       ^
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    29 |      \code{url}{ optional url of the MUSTANG measurements service }
       |                ^
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    30 |      \code{processing}{optional character string with processing commands }
       |                       ^
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   284 | item parameter estimates across the groups in the code{\link{est_mg}} function.
       |                                                       ^
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    22 | function. See \code{\link{est_irt}}, \code{\link{irtfit}}, \\code{\link{info}},
       |                                                                  ^
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    66 |         False positive rate used for detection threshold (not output) to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                                                     ^
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    69 |         False negative rate used to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                ^
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    71 |         False positive rate used for detection threshold (not output) to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                                                     ^
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    74 |         False negative rate used to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                ^
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    30 | item{tau0}{the mean circular Kendall Tau of the initial order with the data.}
       |     ^
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    30 | item{tau0}{the mean circular Kendall Tau of the initial order with the data.}
       |           ^
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    doc    2.3Mb
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installed size is  5.3Mb
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    17 |       {\code{a}: 1st sample};
       |       ^
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    18 |       {\code{b}: 2nd sample}.}
       |       ^
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    20 |       {\code{20+}: 20 minutes or longer since injection};
       |       ^
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    21 |       {\code{pre}: before injection.}}
       |       ^
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    23 |       {\code{20}:  20 minutes since injection};
       |       ^
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    24 |       {\code{30+}: 30 minutes or longer since injection};
       |       ^
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    25 |       {\code{pre}: before injection.  }}
       |       ^
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    17 | \item{pi}{the matrix E[XZ']E[ZZ']^{-1}}
       |                                   ^
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    20 | \item{pi}{matrix, corresponds to E[XZ']E[ZZ']^{-1}, the first stage
       |                                               ^
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    41 | The {bootstrap} method uses resampling with replacement binary vectors to compute a p-value (see optional arguments).
       |     ^
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GNU make is a SystemRequirements.
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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'.
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    extdata   4.0Mb
installed size is  6.2Mb
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GNU make is a SystemRequirements.
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    14 | \item{X5}{categorical covariate taking values from {1, 2, 3, 4, 5}; time-invariant}
       |                                                    ^
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    18 | \item{g}{true latent class identifier {1, 2, 3, 4}, which is determined by 
       |                                       ^
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    15 | \item{X5}{categorical covariate taking values from {1, 2, 3, 4, 5}; time-varying}
       |                                                    ^
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    20 | \item{g}{true latent class identifier {1, 2, 3, 4}, which is determined by 
       |                                       ^
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   298 | following transformation b_1 + b_2*I_1(Y(t)) + ... + b_{n+2}*I_{n+1}(Y(t)),
       |                                                        ^
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   298 | following transformation b_1 + b_2*I_1(Y(t)) + ... + b_{n+2}*I_{n+1}(Y(t)),
       |                                                                ^
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   299 | where I_1,...,I_{n+1} is the basis of quadratic I-splines. To constraint the
       |                 ^
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    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.
       |                                                                                          ^
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    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.
       |                                                                                                                                               ^
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    45 | \item{Difference models (more or less constrained versions of the
       |      ^
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    54 |  \item{Divide-by-total models (more or less constrained versions of the
       |       ^
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    45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr 
       |                                             ^
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    45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr 
       |                                                ^
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    45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr 
       |                                                      ^
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    26 | Default: "({std.error})"}
       |            ^
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Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
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    14 | The {kdist} functions dk, pk, qk and rk, calculates the K-distribution
       |     ^
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    help   8.2Mb
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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.}
       |                                                                                                                                                                                          ^
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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.}
       |                                                                                                                                                                                                                                                                   ^
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    28 |   \item{primal}{Object of class \code{ipop}}{Return the primal of the problem}
       |                                             ^
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    29 |   \item{dual}{Object of class \code{ipop}}{Return the dual of the problem}
       |                                           ^
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    30 |   \item{how}{Object of class \code{ipop}}{Return information on convergence}
       |                                          ^
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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.
       |                                                                                                                                                                                                                                                                                                       ^
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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
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    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}))}
       |                                                                                           ^
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    52 |        plus the OK values. Prediction corresponds to E[X_{t} | Y_{1...t}] 
       |                                                          ^
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    52 |        plus the OK values. Prediction corresponds to E[X_{t} | Y_{1...t}] 
       |                                                                  ^
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    10 | \item{x}{An object of class \code{KinPairData} or {KinPairSimulation}}
       |                                                   ^
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    21 |     list of two functions,flist=list( f1=function( x ) { x } ,f2=function( x ) { x^2 } )  
       |                                                        ^
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    21 |     list of two functions,flist=list( f1=function( x ) { x } ,f2=function( x ) { x^2 } )  
       |                                                                                ^
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    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.}
       |                                                              ^
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  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

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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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    60 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion.
       |                                    ^
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    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. 
       |                                    ^
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    30 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion.
       |                                    ^
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    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.
       |                                    ^
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    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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    14 | are valid. See /code{LcKS} for accepted functions.}
       |                     ^
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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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    26 | refer to as the sQuote{comm} data.frame.  The other data.frame contains all the
       |                       ^
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    10 | \item{model}{a {data model}, such as one returned by \link{read_dm} or
       |                ^
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   300 | Soranno et al. (2017) \doi{10.1093/gigascience/gix101}{Gigascience 6:12}
       |                                                       ^
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    36 | Soranno et al. (2017) \doi{10.1093/gigascience/gix101}{Gigascience 6:12}
       |                                                       ^
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    71 | x \%g\% y \%:=\% {
       |                  ^
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    34 |         Band-specific sensor $G_{rescale}$ (gain). Require either gain and offset or Grescale and Brescale to convert DN to radiance.
       |                                 ^
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    37 |         Band-specific sensor $B_{rescale}$ (bias). Require either gain and offset or Grescale and Brescale to convert DN to radiance.
       |                                 ^
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    43 |     is specified only with the \code{GD}, code{HME}, or \code{NSIS}
       |                                               ^
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   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},
       |         ^
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    25 |  See Section 4 in the {LatticeKrig Vignette} for the use of these data.
       |                       ^
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    19 | \item{interactive}{\code{logical} input, should be code{TRUE} unless
       |                                                        ^
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    29 | \item{interactive}{\code{logical} input, should be code{TRUE} unless
       |                                                        ^
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    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"}.}
       |                                                                                                                                                                                                                     ^
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    35 | Can be an object like {start:"startTime", end:"endTime"} or a string like "created".}
       |                       ^
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    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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annotate_axis.html:91:1 (annotate_axis.Rd:54): Warning: trimming empty <h3>
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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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    12 | \item{i}{A positive integer, which stands for the i^{th} row of \code{X}.}
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    14 | \item{j}{A positive integer, which stands for the j^{th} row of \code{X}. Both \code{i} and \code{j} should be in [1,nrow(X)] and they should not be equal to each other.}
       |                                                     ^
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    12 | \item{j}{A positive integer, which stands for the j^{th} column (or row) of \code{X}, and it should be within [1,ncol(X)] (or [1,nrow(X)]).}
       |                                                     ^
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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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    16 | \item{q}{A number between \code{0} and \code{1}. The quantile of the distribution of $lambda_{QUT}$ to take.}
       |                                                                                              ^
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    25 | the value of $lambda_{QUT}$ to use in LoRI.
       |                      ^
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    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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    38 | code{\link{arima.sim}} 
       |     ^
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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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    23 | \item{x, y}{original two sample raw data, code{x}:"Control", \code{y}: "Case".}
       |                                               ^
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    26 | specified by \code{t}. code{n0}:"Control", \code{n1}: "Case".}
       |                            ^
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    50 | Wrapping all code{mable} fit of regression models in one function.
       |                  ^
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    23 | \item{x, y}{original two sample raw data, code{x}:"Control", \code{y}: "Case".}
       |                                               ^
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    27 | specified by \code{t}. code{n0}:"Control", \code{n1}: "Case".}
       |                            ^
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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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    49 | If {rel} is missing \code{to} refers to the aggregation target dimension name.}
       |    ^
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    18 | and rda (which needs to have the data stored with the object name "data"!). Use code{\link{toolConvertMapping}}
       |                                                                                     ^
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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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    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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    31 | \item{stringchar}{It can be a {n x n} matrix or a character vector or a list}
       |                               ^
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    39 | \item{data}{It can be a character vector or a {n x n} matrix or a {n x n} data frame or a list}
       |                                               ^
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    39 | \item{data}{It can be a character vector or a {n x n} matrix or a {n x n} data frame or a list}
       |                                                                   ^
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    61 | {k x k} where k is the number of states in the chain and the values
       | ^
GNU make is a SystemRequirements.
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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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GNU make is a SystemRequirements.
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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. }
       |                         ^
Found the following HTML validation problems:
compile_sbtests.html:31:1 (compile_sbtests.Rd:29): Warning: trimming empty <li>
dorepart.html:93:1 (dorepart.Rd:47): Warning: trimming empty <li>
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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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  'tkrplot', 'rpanel', 'rgl'
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     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) 
       |                          ^
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     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) 
       |                                                        ^
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     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) 
       |                                                                     ^
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    39 | {
       | ^
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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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    79 | A code{$summary} table giving the results of the variation partitioning.  The following table
       |       ^
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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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    examples  10.3Mb
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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.
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  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   1.2Mb
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BA.est.html:149:32 (BA.est.Rd:121): Warning: trimming empty <code>
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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.
       | ^
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    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.
       |                                                                                                                                                                                                                                      ^
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    47 | vif_corrected = vif_basic^{(1/(2*df))}
       |                           ^
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   143 | we refer to \doi{10.1177/0049124118799376}{Schouten and Vink, 2018}.
       |                                           ^
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   188 | \doi{10.1080/00949655.2018.1491577}{Schouten, Lugtig and Vink, 2018}.
       |                                    ^
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   223 | Schouten, R.M. and Vink, G. (2018){The Dance of the Mechanisms: How Observed Information Influences the Validity of Missingness Assumptions}.
       |                                   ^
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   348 | The \pkg{mice} software was published in the {Journal of Statistical Software} (Van Buuren and Groothuis-Oudshoorn, 2011). \doi{10.18637/jss.v045.i03}
       |                                              ^
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    87 | \item{Construct \eqn{n_0} sets \eqn{Z_j}, each containing \eqn{d} candidate donors, from Y_{obs} such that \eqn{\sum_d\dot\eta(i,j)} is minimum for all \eqn{j=1,\dots,n_0}. Break ties randomly.}
       |                                                                                            ^
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    62 | code{\link{readFasta}}.
       |     ^
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    5.5Mb
    lib    1.2Mb
    libs   1.2Mb
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    29 | item{open}{function to use the current seed}
       |     ^
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    29 | item{open}{function to use the current seed}
       |           ^
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    30 | item{close}{function to make the current seed equal to .Random.seed}
       |     ^
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    30 | item{close}{function to make the current seed equal to .Random.seed}
       |            ^
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    31 | item{resetStream}{function to move back to start of stream}
       |     ^
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    31 | item{resetStream}{function to move back to start of stream}
       |                  ^
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    32 | item{resetSubStream}{function to move back to start of sub-stream}
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    32 | item{resetSubStream}{function to move back to start of sub-stream}
       |                     ^
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    33 | item{nextSubStream}{function to move to next sub-stream}
       |     ^
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    33 | item{nextSubStream}{function to move to next sub-stream}
       |                    ^
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    34 | item{nextStream}{function to move to next stream}
       |     ^
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    34 | item{nextStream}{function to move to next stream}
       |                 ^
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    58 | \item{two vectors containing the cutpoints for each variable : \emph{cutpoints1} corresponds to /emph{myDist1}, /emph{cutpoints2} corresponds to /emph{myDist2}.}
       |                                                                                                      ^
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    58 | \item{two vectors containing the cutpoints for each variable : \emph{cutpoints1} corresponds to /emph{myDist1}, /emph{cutpoints2} corresponds to /emph{myDist2}.}
       |                                                                                                                      ^
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    58 | \item{two vectors containing the cutpoints for each variable : \emph{cutpoints1} corresponds to /emph{myDist1}, /emph{cutpoints2} corresponds to /emph{myDist2}.}
       |                                                                                                                                                       ^
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    62 | \item{if $emph{plot} == TRUE, a plot object (requires ggplot2 and gridExtra).}
       |               ^
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   426 | \link{MIIVsem}{miivs}
       |               ^
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    60 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
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    62 | Kelly Sovacool, {sovacool@umich.edu}
       |                 ^
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    30 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
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    58 | Kelly Sovacool, {sovacool@umich.edu}
       |                 ^
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    16 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
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    14 |   \item{BROADBND}{Cellular data plan for a smartphone or other mobile device}{1 yes 2 no}
       |                                                                              ^
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    21 |   \item{MHP}{Mobile home costs}{$, yearly}
       |                                ^
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installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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    19 |       (only relevant if code{x} has only one element).}
       |                             ^
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    14 | plausible value in turn; with code{rewrite=FALSE} a new data set is
       |                                   ^
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    35 |   \code{t * 1} and \code{B} is of dimension{t * N}. Ideally, \code{fun.sim}()
       |                                            ^
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  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
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    18 | The function \code{print.selectEM} is the print method for the class{selectEM}, which is the output
       |                                                                     ^
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    doc   1.5Mb
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     9 |       (2) All x-coordinates of R1',..,Rn' are distinct, and take values in {1,..,2n}.
       |                                                                            ^
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    10 |       (3) All y-coordinates of R1',..,Rn' are distinct, and take values in {1,..,2n}.
       |                                                                            ^
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    43 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
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    25 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
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    26 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
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    25 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
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    58 |              Note that code{"XGB"} is only available in Mac OS and Linux. moreover,
       |                            ^
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    44 | using reference based imputation as proposed by \doi{10.1080/10543406.2013.834911}{Carpenter et al (2013)}. This approach
       |                                                                                   ^
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    include  10.0Mb
    libs     17.0Mb
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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")}
       |                                                                    ^
installed size is 13.6Mb
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    20 | A function for calcualting the average timing of variables (in this case the M10 and L5).  Find the average timing mu that min{ sum { min[ (tind_i - mu)^2, (1440 + mu - tind_i )^2 ]}}
       |                                                                                                                               ^
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    20 | A function for calcualting the average timing of variables (in this case the M10 and L5).  Find the average timing mu that min{ sum { min[ (tind_i - mu)^2, (1440 + mu - tind_i )^2 ]}}
       |                                                                                                                                     ^
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    62 | \item Probability of attribution of each unknown individual to each source $p_{u,s}$
       |                                                                               ^
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    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)}.
       |                 ^
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    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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    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                               ^
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    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                                                          ^
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    58 | \item{tol}{Convergence is determined when ||U_j - U_{j-1}||_F < tol,
       |                                                     ^
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    59 | \item{tol}{Convergence is determined when ||U_j - U_{j-1}||_F < tol,
       |                                                     ^
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    39 |         \link{brownian.bridge.dyn}, link{dynBGBvariance}
       |                                         ^
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    16 |   Calculates the stimulus level(s) for a probit model of a psychometric function for given levels of performance.  For a more general version, see \link[MASS]{dose.p} in pkg{MASS}.
       |                                                                                                                                                                              ^
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    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
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    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
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    60 | \item{lnconst}{When inequality constraints are present, \code{lnconst} serves as an adjustment of code{lnInt}. It estimates the logarithm of the proportion of parameter space [0,1]^S that satisfies those inequality constraints, and the log integral term is given by \code{lnInt+lnconst}.
       |                                                                                                       ^
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    38 | The labels on the x-axis. Default is \code{Tree 1} to code{Tree n}.
       |                                                           ^
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    51 | if (requireNamespace("rjags", quietly = TRUE)) {
       |                                                ^
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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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    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
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    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
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    17 |   \item{type}{: Argument that controls the type of parameters to be returned. If \code{type="persons"} (default), a vector with the person parameters is returned. When \code{type="items"} then a vector with the item ranks obtained by the MUDFOLD item selection algorithm is returned. If {type="all"} then a list with both person and item coefficients is returned to the user.
       |                                                                                                                                                                                                                                                                                                ^
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    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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    20 | Makowski, D., Jeuffroy, M.-H., Gu\'{e}rif, M., 2004 Bayesian methods for
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    15 |   \item{\dots}{... }{possible fixed parameters of the R-function}
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    60 | in their study, \doi{10.1177/0956797612466416}{\emph{The
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    34 | in their study, \doi{10.1073/pnas.1402786111}{\emph{Female hurricanes are deadlier than male hurricanes}}.
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    33 | \doi{10.1145/2470654.2481359}{Evaluating the Efficiency of Physical Visualizations}
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    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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    47 | \doi{10.1073/pnas.1402786111}{Female hurricanes are
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    55 | \doi{10.1038/s41562-020-0912-z}{Specification curve analysis}
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    67 | {rater1} and {rater2}, and the 5-point scale values were
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    67 | {rater1} and {rater2}, and the 5-point scale values were
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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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    39 | The "nbdev.mxm" (negative binomial deviance) is missing. For more information on these see \code{\link{cv.ses}}. bold{Note} that they come with "".
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    32 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
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    29 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
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    94 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
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    22 | @source {Simulated to serve as an example}
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    15 | for(i in 1:50){
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    50 | for(kk in 1:length(p)){
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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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    Version  (2017-08-22)
    Version
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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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   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. 
       |                                                                                                                                              ^