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   172 |     the height of the area containing the panels and a margin of size code{100 * 0.1} 
       |                                                                           ^
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    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                              ^
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    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                                            ^
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    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       | ^
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    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       |                                 ^
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    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       |                                                ^
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    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |   ^
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    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                  ^
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    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                                             ^
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    28 | code{NA} means the performance value is not available, possibly because the algorithm run was aborted.
       |     ^
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    40 |   code{NA} means the cost is not available, possibly because the feature computation was aborted.
       |       ^
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    47 |   code{NA} means the cost is not available, possibly because the feature computation was aborted.
       |       ^
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    55 |   code{NA} means the feature is not available, possibly because the feature computation was aborted.
       |       ^
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    62 |   code{NA} means the feature is not available, possibly because the feature computation was aborted.
       |       ^
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   199 |   yakka. (Note that \code{flap} stands for dQuote{function list
       |                                                  ^
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    34 |   always, the identifier has the format YYYY-NNNP{PP}, where YYYY is the year
       |                                                  ^
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    36 |   during year YYYY and P{PP} is a part specifier comprising 1 to 3 capital letters
       |                         ^
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    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.
       |                                                                       ^
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    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.
       |                                                                                                ^
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    14 | \item{x_discrete}{TRUE if the distribution of the covariate is uniform on {-3.0, -2.9, ..., 3.0} and
       |                                                                           ^
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    23 | \item{att_oracle}{the sample analog of E[D{Y(1) - Y(0)}|D=1]}
       |                                           ^
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    50 | \item \code{covars_data}   {The \code{data.frame} that is filtered out of \code{df} with only the selected \code{covars}}. The values of the
       |                            ^
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    53 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
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    40 | \item \code{multiplicative_bias}{The absolute log of the multiplicative bias term for each of the auto-selected prioritised covariates}
       |                                 ^
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    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}}
       |                           ^
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    27 | code{\link{help}}
       |     ^
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    25 | code{\link{help}}
       |     ^
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    22 | code{\link{help}}
       |     ^
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    29 | code{\link{help}}
       |     ^
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    32 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    20 | \item{fit}{See glm {stats}.}
       |                    ^
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    21 | \item{fit}{See glm {stats}.}
       |                    ^
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    21 | \item{host}{For \code{cosmos_mongo_endpoint}, the URL of the Cosmos DB MongoDB endpoint. Usually of the form "https://{account-name}.mongo.cosmos.azure.com:443/".}
       |                                                                                                                       ^
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Depends: includes the non-default packages:
  'dplyr', 'glue', 'janitor', 'lubridate', 'readr', 'snakecase',
  'stringr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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    27 | read.dna() from package {ape} was used to obtain DNAbin object for unaligned non-coding barcodes.
       |                         ^
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    30 | the {dplyr}'s verbs and thus use it in local memory completely.
       |     ^
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    52 | Writes a remote table to disk that was called via {bdplyr}.
       |                                                   ^
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     5 | \title{Compatibility with {dplyr} verbs without using SQL language}
       |                           ^
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    14 |   \item{\code{algo.id} [\code{character(1)}]:}{algo.id}{Algorithm ID.}
       |                                                        ^
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    13 | \item{ids}{[code{integer}]\cr
       |                 ^
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    13 | \item{ids}{[code{integer}]\cr
       |                 ^
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    28 | Default is dQuote{<name of registry>_files} in current working directory.}
       |                  ^
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    41 |  \item{namespaces}{code{character} with required packages to load via \code{\link[base]{requireNamespace}}.}
       |                        ^
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    31 | Algorithms are functions which get the code{data} part as well as the problem instance (the return value of the
       |                                            ^
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installed size is 103.3Mb
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GNU make is a SystemRequirements.
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    32 | plot{...} functions are generated programmatically so the function calls in
       |     ^
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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}.}
       |                                                                    ^
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GNU make is a SystemRequirements.
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    53 | online trajectories related to the state parameter, the simulated BOLD responses, \mjseqn{\hat{Y}}{ascii}.
       |                                                                                                   ^
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    18 |   \item{optim.method}{optimization method in \code{optim()}{stats}.}
       |                                                            ^
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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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installed size is 244.0Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  8.5Mb
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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.
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Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 14.0Mb
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    22 | A data frame where new rows have been inserted to regularize the \code{date} column. This results in values provided for \code{id}, \code{date}, and {dt} while inserting NAs for all other columns. Additionally, observations with duplicate date-times are removed.
       |                                                                                                                                                      ^
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installed size is 13.3Mb
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installed size is  8.8Mb
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Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
installed size is 97.2Mb
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GNU make is a SystemRequirements.
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installed size is  7.1Mb
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checkRd: (-1) BayesTreePrior.Rd:38: Lost braces in \itemize; meant \describe ?
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installed size is  7.1Mb
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installed size is 10.8Mb
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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Specified C++11: please drop specification unless essential
checkRd: (-1) runUI.Rd:11: Lost braces
    11 | Runs a \bold{Shiny} application. This function normally does not return; interrupt bold{R} to stop the application (usually by pressing Ctrl+C or Esc).
       |                                                                                        ^
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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Error(s) in re-building vignettes:
--- re-building ‘article.Rnw’ using Sweave
Setting levels: control = No, case = Yes
Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 4.1-8
Setting levels: control = No, case = Yes
Setting levels: control = No, case = Yes
Loading required package: Biostrings
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm,
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    do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rownames, sapply, setdiff, table, tapply, union, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

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Error: processing vignette 'article.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
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--- failed re-building 'article.Rnw'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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installed size is 43.7Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) goftype1.Rd:4: Lost braces
     4 | \description{The goodness-of-fit (GOF) measures consist of Anderson-Darling (\code{AD}) and Cram\'{e}er-von Misses (\code{CVM}) statistics for progressive type-I interval censoring scheme are given, respectively, by
       |                                                                                                   ^
installed size is  7.5Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) WindowSweep.Rd:32: Lost braces
    32 | `code{\link{GetVT}}`.   Otherwise, any column (e.g. \code{"Depth"}) in the 
       |      ^
checkRd: (-1) WindowSweep.Rd:36: Lost braces
    36 | \code{T.mid}  from the output of the `code{\link{GetVT}}`.}
       |                                           ^
Package suggested but not available for checking: ‘BRugs’
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checkRd: (-1) gene_s.Rd:17: Lost braces; missing escapes or markup?
    17 | giving the virus access to the cell and thus facilitating the COVID-19 disease. The gene sequence is mapped to the alphabet {0,1,2,3} via the obvious map A->0, C->1, G->2, T->3.
       |                                                                                                                             ^
checkRd: (-1) sars_cov_2.Rd:16: Lost braces; missing escapes or markup?
    16 | It consists of n = 29903 base pairs. The gene sequence is mapped to the alphabet {0,1,2,3} via the obvious map A->0, C->1, G->2, T->3.
       |                                                                                  ^
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installed size is 118.5Mb
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GNU make is a SystemRequirements.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
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installed size is 50.5Mb
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GNU make is a SystemRequirements.
installed size is 65.0Mb
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GNU make is a SystemRequirements.
installed size is 14.5Mb
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'LazyData' is specified without a 'data' directory
installed size is 54.9Mb
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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
installed size is 43.5Mb
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GNU make is a SystemRequirements.
checkRd: (-1) sockeye.Rd:13-14: Lost braces in \itemize; meant \describe ?
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installed size is 62.9Mb
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GNU make is a SystemRequirements.
installed size is 31.1Mb
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Specified C++11: please drop specification unless essential
installed size is 63.9Mb
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    libs  60.7Mb
checkRd: (-1) gen.data.Rd:42: Lost braces
    42 | code{cortype = 2} denotes the constant structure, where the \eqn{(i,j)} entry of covariance
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) BETSsearch.Rd:56: Lost braces
    56 |        \item{To exclude whole expressions from the search, surround them with code{' '} and insert a \code{~} before each of them.
       |                                                                                   ^
checkRd: (-1) dummy.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{date}{a \code{list}. The periods for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                               ^
checkRd: (-1) dummy.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{from}{An \code{integer vector} The starting period of a sequence of perids for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                                                                         ^
checkRd: (-1) dummy.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{to}{The ending period of a sequence of perids for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                                            ^
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checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
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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 10.8Mb
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GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Depends: includes the non-default packages:
  'coda', 'ggplot2', 'gridExtra', 'lpl', 'MASS', 'survival'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is 166.1Mb
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installed size is  5.2Mb
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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}.
       |                                                                                                                                                                                                                                                                                  ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  9.6Mb
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Package suggested but not available for checking: ‘ffbase’
Package suggested but not available for checking: ‘INLA’
installed size is  5.6Mb
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installed size is  8.5Mb
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Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.3Mb
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Specified C++14: please drop specification unless essential
installed size is  6.2Mb
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checkRd: (-1) bdm.ptsne.Rd:47: Lost braces; missing escapes or markup?
    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                         ^
checkRd: (-1) bdm.ptsne.Rd:47: Lost braces; missing escapes or markup?
    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                                                                                   ^
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
installed size is  7.3Mb
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installed size is  9.0Mb
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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 28.2Mb
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installed size is  9.7Mb
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installed size is 13.6Mb
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installed size is  5.6Mb
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installed size is 19.4Mb
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installed size is 96.6Mb
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GNU make is a SystemRequirements.
installed size is  6.7Mb
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Specified C++11: please drop specification unless essential
installed size is  5.9Mb
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'LazyData' is specified without a 'data' directory
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installed size is 19.6Mb
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GNU make is a SystemRequirements.
checkRd: (-1) calc_ed.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_pi.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
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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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installed size is  5.3Mb
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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}.
       |                                                                                                                                                                              ^
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
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Specified C++11: please drop specification unless essential
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installed size is 54.9Mb
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GNU make is a SystemRequirements.
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installed size is  6.6Mb
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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}.
       |                                                                                    ^
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    15 | format A vector that contains the code{id}
       |                                       ^
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GNU make is a SystemRequirements.
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installed size is  7.0Mb
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checkRd: (-1) durban.Rd:16: Lost braces; missing escapes or markup?
    16 | This data set was obtained from the durban.rowcol {agridat} example in package 'agridat' 
       |                                                   ^
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    25 | evenly spaced points between \code{min} and {max}.
       |                                             ^
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checkRd: (-1) bluebike.Rd:17: Lost braces
    17 | \item{\code{import_month_data}}\cr {Takes in numeric year/month values and imports data from \href{https://www.bluebikes.com/system-data}{Blue Bikes System Data} for the specified time}
       |                                    ^
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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 189.6Mb
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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 125.3Mb
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
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GNU make is a SystemRequirements.
installed size is  6.8Mb
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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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Packages suggested but not available for checking:
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Depends: includes the non-default packages:
  'tseries', 'fGarch', 'timeSeries', 'timeDate', 'fBasics', 'geoR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/boodist.Rcheck/00install.out’ for details.
installed size is 396.6Mb
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GNU make is a SystemRequirements.
installed size is 93.4Mb
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GNU make is a SystemRequirements.
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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 | $$SD = sqrt(sum(x_{i+1} - xbar)^2/n-1)$$
       |                   ^
installed size is 52.7Mb
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GNU make is a SystemRequirements.
installed size is  9.8Mb
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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installed size is 45.3Mb
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘cmdstanr’
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checkRd: (-1) bscontrol.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{opt.solver}{a character string in the set {'enum', 'enum_c', 'gurobi', 'cplex', 'lpSolve', 'greedy'} indicating the optimization solver to be used in the program. The choice of 'cplex' requires the package \code{cplexAPI}, 'gurobi' requires the package \code{gurobi}, and 'lpSolve' requires the package \code{lpSolve}. These solver options are only available in the full version at \url{https://github.com/profyliu/bsnsing/}. The default (and the best) is 'enum_c'.}
       |                                                 ^
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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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GNU make is a SystemRequirements.
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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
       |                                                               ^
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘org.Mm.eg.db’
installed size is  6.2Mb
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    extdata   3.4Mb
Running examples in ‘bulkAnalyseR-Ex.R’ failed
The error most likely occurred in:

> ### Name: DEanalysis
> ### Title: Perform differential expression (DE) analysis on an expression
> ###   matrix
> ### Aliases: DEanalysis DEanalysis_edger DEanalysis_deseq2
> 
> ### ** Examples
> 
> expression.matrix.preproc <- as.matrix(read.csv(
+   system.file("extdata", "expression_matrix_preprocessed.csv", package = "bulkAnalyseR"), 
+   row.names = 1
+ ))[1:100, 1:4]
> 
> anno <- AnnotationDbi::select(
+   getExportedValue('org.Mm.eg.db', 'org.Mm.eg.db'),
+   keys = rownames(expression.matrix.preproc),
+   keytype = 'ENSEMBL',
+   columns = 'SYMBOL'
+ ) %>%
+   dplyr::distinct(ENSEMBL, .keep_all = TRUE) %>%
+   dplyr::mutate(NAME = ifelse(is.na(SYMBOL), ENSEMBL, SYMBOL))
Error in (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 'select': there is no package called ‘org.Mm.eg.db’
Calls: %>% ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘bunching_examples.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'bunching_examples.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.4/bunching.Rcheck/vign_test/bunching/vignettes/bunching_examples.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See bunching_examples.log for more info.
--- failed re-building ‘bunching_examples.Rmd’

--- re-building ‘bunching_theory.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'bunching_theory.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.4/bunching.Rcheck/vign_test/bunching/vignettes/bunching_theory.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See bunching_theory.log for more info.
--- failed re-building ‘bunching_theory.Rmd’

SUMMARY: processing the following files failed:
  ‘bunching_examples.Rmd’ ‘bunching_theory.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
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Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘doMPI’
Specified C++11: please drop specification unless essential
installed size is 20.2Mb
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GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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    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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Package suggested but not available for checking: ‘ReGenesees’
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    19 | \item{y}{response variable (in {0,1}).}
       |                                ^
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   112 | Stop recording images with {camcorder}.
       |                            ^
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Packages required but not available: 'org.Dr.eg.db', 'org.Mm.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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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}
       |      ^
checkRd: (-1) pd.calc.Rd:33: Lost braces
    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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    virtual_patient_simulator   3.1Mb
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
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    13 | The exit status code{R CMD build}, invisibly.
       |                     ^
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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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    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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Problems with news in ‘NEWS.md’:
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Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
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    36 | A code{data.frame} with the requested variables at the requested
       |       ^
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    22 | Centroid value C_{cen}(v) for node v defined as:
       |                  ^
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    23 | where the term f(c_{i}) accounts for the effect of i's local clustering and the term '+1' results from the contribution of \eqn{j}{j} itself. \cr
       |                    ^
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    31 |   {epsi}^{# regression coefficients} times the initial value,
       |   ^
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    31 |   {epsi}^{# regression coefficients} times the initial value,
       |          ^
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    23 | Assuming one-dimensional \code{p1} and \code{p2} for clarity, the algorithm calculates cumulative incidence function for cuase 1 using a recursive formula: \code{ci1[n+1] = ci1[n] + dci1[n]}, where \code{dci1[n] = 0.5*(p2[n] + p2[n+1])*(p1[n] - p1[n+1])}. The increment in cumulative incidence function for cause 2 is similarly calculated, \code{dci2[n] = 0.5*(p1[n] + p1[n+1])*(p2[n] - p2[n+1])}. These equations guarantee that \code{dci1[n] + dci2[n] = p1[n]*p2[n] - p1[n+1]*p2[n+1]}. Event-free probability is simply calculated as code{efp[n] = p1[n]*p2[n]}. Taken together, this numerical integration ensures that \code{efp[n+1] - efp[n] + dci1[n] + dci2[n] = 0}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           ^
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Malformed Title field: should not end in a period.
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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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Running examples in ‘checkmate-Ex.R’ failed
The error most likely occurred in:

> ### Name: checkDataTable
> ### Title: Check if an argument is a data table
> ### Aliases: checkDataTable check_data_table assertDataTable
> ###   assert_data_table testDataTable test_data_table expect_data_table
> 
> ### ** Examples
> 
> library(data.table)
Error in library(data.table) : there is no package called ‘data.table’
Execution halted
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    28 |     40 x {
       |          ^
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    28 |     40 x {
       |          ^
checkRd: (-1) C60.amp.Rd:63-67: Lost braces
    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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  'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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    58 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.
       |                       ^
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    93 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                     ^
checkRd: (-1) data_generator.Rd:93: Lost braces; missing escapes or markup?
    93 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                             ^
checkRd: (-1) data_generator.Rd:95: Lost braces; missing escapes or markup?
    95 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++}, S_{*+}
       |                                                                 ^
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    95 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++}, S_{*+}
       |                                                                         ^
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    96 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                     ^
checkRd: (-1) data_generator_loop.Rd:96: Lost braces; missing escapes or markup?
    96 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                             ^
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    98 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++},
       |                                                                 ^
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    99 |   S_{*+} and PP estimands}
       |     ^
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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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Depends: includes the non-default packages:
  'C50', 'car', 'caret', 'corrplot', 'doParallel', 'dplyr', 'e1071',
  'ggplot2', 'gt', 'ipred', 'MachineShop', 'magrittr', 'parallel',
  'pls', 'purrr', 'randomForest', 'ranger', 'reactable',
  'reactablefmtr', 'scales', 'tidyr', 'tree'
Adding so many packages to the search path is excessive and importing
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    clhs_0.7-2
    clhs_0.7-0
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    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
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    clhs_0.2-1
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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},
       |                                                   ^
checkRd: (-1) clinsig.Rd:129: Lost braces
   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                                 ^
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    13 | \item{query}{A phenotype query defined using the code{\link{phenotype}} function and logic operators (see example below)}
       |                                                      ^
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    10 | \item{id}{A single phenotype id. Possible phenotyoes can be explored using the code{\link{cb_search_phenotypes}} function}
       |                                                                                    ^
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    24 | the sense that its Karhunen-Lo\`{e}ve decomposition has qx terms only.}
       |                                 ^
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    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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Packages listed in more than one of Depends, Imports, Suggests, Enhances:
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A package should be listed in only one of these fields.
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    32 | ({FALSE})? If a bin is empty, the center of the bin is returned as the
       |  ^
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    82 | of the bin ({FALSE})? If a bin is empty, the center of the bin is returned
       |             ^
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Unexported object imported by a ':::' call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
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     6 |              Generates all points on a {p,n} simplex lattice (i.e. a p-part
       |                                        ^
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    36 | {0, 1}.
       | ^
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    40 | values in {0, 1}.
       |           ^
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    10 | \item{item}{factor}{200 levels - which item the measurements came from}
       |                    ^
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    11 | \item{fragment}{factor}{4 levels - which of the four fragments from each item the observations were made
       |                        ^
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    13 | \item{logNaO}{numeric}{log of sodium concentration to oxygen concentration}
       |                       ^
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    14 | \item{logMgO}{numeric}{log of magnesium concentration to oxygen concentration}
       |                       ^
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    15 | \item{logAlO}{numeric}{log of aluminium concentration to oxygen concentration}
       |                       ^
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    16 | \item{logSiO}{numeric}{log of silicon concentration to oxygen concentration}
       |                       ^
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    17 | \item{logKO}{numeric}{log of potassium concentration to oxygen concentration}
       |                      ^
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    18 | \item{logCaO}{numeric}{log of calcium concentration to oxygen concentration}
       |                       ^
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    19 | \item{logFeO}{numeric}{log of iron concentration to oxygen concentration}
       |                       ^
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     9 |  \item{"tangle"}: {Dihedral angle defined by atoms A-B-C-D as described below. \code{NA}'s represent the free side chain dihedral angles \emph{chi} for that amino acid.}
       |                   ^
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    10 |  \item{"names"}: {The component atoms of the amino acid side chain.  Represents atom D in the dihedral.}
       |                  ^
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    11 |  \item{"matx"}: {The names of atoms A,B,C in the dihedral, with rows corresponding to the atoms in "names".}
       |                 ^
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    12 |  \item{"bangle"}: {Planar bond angle formed between B-C-D}
       |                   ^
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    13 |  \item{"blength"}: {Bond length between C-D}
       |                    ^
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    82 | a_{ij} = (S_ij + 1) / (S_ij + S_ji + 2). This step should make comparing
       |   ^
GNU make is a SystemRequirements.
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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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Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(connector)
  > 
  > test_check("connector")
  [ FAIL 2 | WARN 1 | SKIP 4 | PASS 186 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test-connect.R:34:3', 'test-connector.R:8:3',
    'test-utils_files.R:3:3'
  • postgres database not available (1): 'test-dbi.R:34:9'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-cnt_logger_integration.R:22:5'): ConnectorLogger integration test with whirl ──
  Expected `whirl::run("_whirl.yml")` to run without any errors.
  i Actually got a <simpleError> with text:
    cannot open the connection
  Backtrace:
      ▆
   1. ├─withr::with_dir(...) at test-cnt_logger_integration.R:21:3
   2. │ └─base::force(code)
   3. └─testthat::expect_no_error(whirl::run("_whirl.yml")) at test-cnt_logger_integration.R:22:5
  ── Failure ('test-cnt_logger_integration.R:26:5'): ConnectorLogger integration test with whirl ──
  length(list.files(".")) (`actual`) not equal to 5 (`expected`).
  
    `actual`: 3.0
  `expected`: 5.0
  Backtrace:
      ▆
   1. ├─withr::with_dir(...) at test-cnt_logger_integration.R:21:3
   2. │ └─base::force(code)
   3. └─testthat::expect_equal(length(list.files(".")), 5) at test-cnt_logger_integration.R:26:5
  
  [ FAIL 2 | WARN 1 | SKIP 4 | PASS 186 ]
  Error: Test failures
  Execution halted
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installed size is 19.7Mb
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installed size is 101.0Mb
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GNU make is a SystemRequirements.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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    40 |        item{\code{maxit}}{the maximum number of iterations to be used by \code{\link{optim}} when optimizing the objective function. Defaults to \code{1000}.}
       |            ^
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    40 |        item{\code{maxit}}{the maximum number of iterations to be used by \code{\link{optim}} when optimizing the objective function. Defaults to \code{1000}.}
       |                          ^
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    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                          ^
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    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                                      ^
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    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                  ^
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    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                              ^
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     5 | \title{Draws the contour {f=c}.}
       |                          ^
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    20 | Draws the contour {f=c}.
       |                   ^
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checkRd: (-1) cope.Rd:35: Lost braces in \itemize; meant \describe ?
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc             2.0Mb
    vignette_data   2.6Mb
installed size is  6.2Mb
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    data   3.5Mb
    libs   2.1Mb
installed size is  5.7Mb
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    libs   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) getSurface.Rd:22: Lost braces
    22 | value \code{getSurface} shortens the output of \code{conv} to remove artificial surface layers. The output is thus a subset of the input, and identical in structure to the /code{conv} output.
       |                                                                                                                                                                                  ^
installed size is  5.6Mb
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    sample_data   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProData’
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
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    extdata  17.7Mb
installed size is  7.2Mb
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    doc   6.7Mb
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
installed size is  7.4Mb
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    data   4.8Mb
    doc    1.6Mb
'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:
    R      2.4Mb
    data   1.2Mb
    help   2.3Mb
installed size is  8.3Mb
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    libs   5.3Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
'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  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   4.7Mb
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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.7Mb
Specified C++11: please drop specification unless essential
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) gen_data.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gen_data.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gen_data.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) coxph.RT.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) coxph.RT.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) coxph.RT.Rd:59-71: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
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installed size is  5.3Mb
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    libs   5.1Mb
Error(s) in re-building vignettes:
--- re-building ‘cplm.Rnw’ using Sweave
Loading required package: coda
Loading required package: Matrix
Loading required package: splines
Error: processing vignette 'cplm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cplm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘cplm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.6Mb
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    doc       1.8Mb
    include   6.5Mb
installed size is  8.2Mb
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    include   7.7Mb
installed size is 15.9Mb
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    libs  15.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.9Mb
Specified C++11: please drop specification unless essential
installed size is  6.9Mb
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checkRd: (-1) sharedat.Rd:23: Lost braces
    23 | \doi{10.7910/DVN/YXMQZM}{Harvard dataverse}
       |                         ^
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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    help   2.4Mb
installed size is 10.4Mb
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    data   1.2Mb
    doc    2.2Mb
    libs   6.9Mb
installed size is  5.4Mb
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    doc   5.1Mb
installed size is  6.0Mb
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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 
       |                                  ^
installed size is 50.2Mb
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    libs  50.1Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   2.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer3’
installed size is  6.5Mb
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checkRd: (-1) normFit.Rd:39: Lost braces; missing escapes or markup?
    39 | {analytes}}
       | ^
checkRd: (-1) normPred.Rd:27: Lost braces
    27 | ode{standards}, \code{analytes}}
       |    ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘EnsDb.Hsapiens.v86’
checkRd: (-1) confRegCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                                                                                    ^
checkRd: (-1) confRegCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                                                                                      ^
checkRd: (-1) confRegUCRandUCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
installed size is 29.3Mb
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installed size is  6.8Mb
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Package suggested but not available for checking: ‘INLA’
checkRd: (-1) cruts-package.Rd:21: Lost braces
    21 | section{Dependencies}{
       |        ^
checkRd: (-1) cruts-package.Rd:21-24: Lost braces
    21 | section{Dependencies}{
       |                      ^
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    26 | section{Citation}{
       |        ^
checkRd: (-1) cruts-package.Rd:26-28: Lost braces
    26 | section{Citation}{
       |                  ^
checkRd: (-1) cruts-package.Rd:30-32: Lost braces
    30 | references{
       |           ^
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
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    help   1.2Mb
checkRd: (-1) calculate_cell_volume.Rd:16: Lost braces; missing escapes or markup?
    16 | V A real number. The volume (in angstroms^3 or angstroms^{-3})
       |                                                          ^
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  all_functions.cpp:1382:11: warning: explicitly assigning value of variable of type 'arma::vec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/CSeQTL.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
installed size is 10.2Mb
  sub-directories of 1Mb or more:
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    libs   8.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.6Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   8.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 201.7Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    data    1.7Mb
    libs  196.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RTMBode’
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  19.1Mb
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘pbdMPI’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘TCGAbiolinks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 37.4Mb
  sub-directories of 1Mb or more:
    libs  37.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    doc    1.2Mb
    help   1.1Mb
    libs   4.7Mb
installed size is 29.1Mb
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    libs  28.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    docs          1.0Mb
    extdata       1.3Mb
    htmlwidgets   1.4Mb
checkRd: (-1) fit.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.Rd:39: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{  A small, positive scalar that determines when iterations
       |               ^
checkRd: (-1) fpiter.Rd:60-61: Lost braces
    60 |     \code{maxiter}{  An integer denoting the maximum limit on the number of
       |                   ^
checkRd: (-1) fpiter.Rd:63-65: Lost braces
    63 |     \code{trace}{  A logical variable denoting whether some of the intermediate
       |                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) formatScientificTeX.Rd:33: Lost braces; missing escapes or markup?
    33 | function will return  " 3.0\\\\times 10^{2}"
       |                                         ^
installed size is 39.0Mb
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installed size is  5.1Mb
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    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
installed size is  6.4Mb
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    R      2.0Mb
    help   2.6Mb
installed size is  7.6Mb
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installed size is  7.6Mb
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    doc    2.7Mb
    libs   4.6Mb
GNU make is a SystemRequirements.
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
       |     ^
installed size is  7.3Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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    data   5.3Mb
'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"}}
       |                    ^
Error(s) in re-building vignettes:
--- re-building ‘Details.Rnw’ using Sweave
Warning in initialize(value, ...) :
  There must be an even number of elements
Adding a ghost value
Loading required package: ggplot2
Loading required package: lattice
Error: processing vignette 'Details.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'Details.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm9): Font bbm9 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘Details.Rnw’

--- re-building ‘GettingStarted.Rnw’ using Sweave
Warning in initialize(value, ...) :
  There must be an even number of elements
Adding a ghost value
Warning in initialize(value, ...) :
  There must be an even number of elements
Adding a ghost value
Warning in initialize(value, ...) :
  There must be an even number of elements
Adding a ghost value
Loading required package: ggplot2
Loading required package: lattice
--- finished re-building ‘GettingStarted.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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    libs   1.8Mb
    po     1.5Mb
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) plot.mleBb.Rd:48: Lost braces
    48 |   \ code{size} is extracted from argument \code{x}.
       |         ^
checkRd: (-1) value_missing_table.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) value_missing_table.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CI_mc.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{i}{the row index of the interest entry X_{i,j}}
       |                                                ^
checkRd: (-1) CI_mc.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{j}{the row index of the interest entry X_{i,j}}
       |                                                ^
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
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    libs   7.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 84.0Mb
  sub-directories of 1Mb or more:
    libs  83.6Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  7.8Mb
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    data   1.9Mb
    libs   5.2Mb
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
installed size is  7.8Mb
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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}}
       |     ^
checkRd: (-1) plot.ddpcr_plate.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ddpcr_plate.Rd:138-139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ddpcr_plate.Rd:140-141: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.9Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
checkRd: (-1) deepNN-package.Rd:18: Lost braces
    18 | section{Dependencies}{
       |        ^
checkRd: (-1) deepNN-package.Rd:18-21: Lost braces
    18 | section{Dependencies}{
       |                      ^
checkRd: (-1) deepNN-package.Rd:23: Lost braces
    23 | section{Citation}{
       |        ^
checkRd: (-1) deepNN-package.Rd:23-25: Lost braces
    23 | section{Citation}{
       |                  ^
checkRd: (-1) deepNN-package.Rd:27-38: Lost braces
    27 | references{
       |           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'bGMYC', 'splits'
Packages unavailable to check Rd xrefs: ‘bGMYC’, ‘splits’
checkRd: (-1) deltaPlot.Rd:28: Lost braces
    28 |  \item{purify}{logical: should item purification be performed? (Default is code{FALSE}). See \bold{Details}.}
       |                                                                                ^
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checkRd: (-1) kin.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:53-61: Lost braces
    53 | {\itemize{
       | ^
checkRd: (-1) kin.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:59-67: Lost braces
    59 | {\itemize{
       | ^
checkRd: (-1) kin2sex.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
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There are ::: calls to the package's namespace in its code. A package
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  ‘.factorQ3’ ‘.factormax’ ‘.factormean’ ‘.factormedian’ ‘.factormin’
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    26 | \item{expr}{an expression that generates a {detourr} widget}
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    80 | supported using {crosstalk}. The set of interactive controls available are:
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    67 | supported using {crosstalk}. The set of interactive controls available are:
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    65 | supported using {crosstalk}. The set of interactive controls available are:
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    76 | supported using {crosstalk}. The set of interactive controls available are:
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    11 | Variables are evaluated using {tidyselect} syntax.}
       |                               ^
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See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/DFD.Rcheck/00install.out’ for details.
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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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       |                                                       ^
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       |                                       ^
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       |                                                       ^
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       |                    ^
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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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   272 | \item{name}{the name of the model {"GNG", "iNUDGE","NUDGE"} where
       |                                   ^
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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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    27 | udf <- function(x){
       |                   ^
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    Changes to previous versions
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    Previous Versions
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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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       |                          ^
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    10 | \item{...}{arguments goint to code{scale_color_manual()}}
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       |                                   ^
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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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     5 | \title{Tell {reticulate} to use Python Conda version available on Domino Data Lab.}
       |             ^
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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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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     9 | \item{occupancies}{Either a data frame containing two columns or an object of class \code{"upgrain"} from the \code{\link{upgrain}} function. If using a data frame the first column must be the grain sizes (cell area in squared units e.g. km^{2}). The second column is the proportion of occupancies at each grain size.}
       |                                                                                                                                                                                                                                                  ^
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    13 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
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    13 | \item{new.areas}{vector of grain sizes as cell area (in same units as cell.width but squared e.g. km^{2}) at fine scales for model prediction.}
       |                                                                                                      ^
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    10 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
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    43 |   emph{Generalized Linear Models}, 
       |       ^
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    18 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
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    16 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
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    11 | code{\link[DrDimont]{compute_correlation_matrices}}}
       |     ^
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Packages required but not available:
  'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Hsapiens.UCSC.hg38.knownGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Package suggested but not available for checking: ‘dsBaseClient’
Running ‘testthat.R’ [37s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DSMolgenisArmadillo)
  Loading required package: DSI
  Loading required package: progress
  Loading required package: R6
  Loading required package: MolgenisAuth
  > library(tibble)
  > 
  > test_check("DSMolgenisArmadillo")
  An object of class "ArmadilloCredentials"
  Slot "access_token":
  [1] "access456"
  
  Slot "expires_in":
  [1] 300
  
  Slot "expires_at":
  [1] "2025-08-18 21:18:02 NZST"
  
  Slot "id_token":
  [1] "id123"
  
  Slot "refresh_token":
  [1] "refresh123"
  
  Slot "token_type":
  [1] "Bearer"
  
  Slot "auth_type":
  [1] "keycloak"
  
  [ FAIL 2 | WARN 2 | SKIP 1 | PASS 396 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • I still don't get the .deparse arguments (1): 'test-utils.R:91:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-ArmadilloOAuth.R:86:3'): .refresh_token returns success message if new credentials are not null and option fusionauth ──
  DSMolgenisArmadillo:::.refresh_token(server, credentials_in) not equal to `credentials_out`.
  Attributes: < Component "expires_in": Mean relative difference: 0.3702278 >
  ── Failure ('test-ArmadilloOAuth.R:143:3'): .refresh_token returns success message if new credentials are not null and option keycloak ──
  DSMolgenisArmadillo:::.refresh_token(server, credentials_in) not equal to `credentials_out`.
  Attributes: < Component "expires_at": Mean absolute difference: 0.52771 >
  
  [ FAIL 2 | WARN 2 | SKIP 1 | PASS 396 ]
  Error: Test failures
  Execution halted
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    67 | parameter uncertainty. See Wood, Pya & S{\"a}fken (2016) for more
       |                                         ^
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   100 | Wood, S.N., Pya, N. and S{\"a}fken, B. (2016) Smoothing parameter and model
       |                          ^
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    22 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
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    21 |    \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                                ^
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    24 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
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    64 | The empiric model is specified as F(d, beta) = d^{exp(beta)}. The logistic model is
       |                                                  ^
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    27 |      For example, the order {a, b, c} implies that a > b, a  > c, and b > c.
       |                             ^
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    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                          ^
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    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                                                     ^
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    19 | \item{log_style}{is a {crayon::style()} that will colorize
       |                       ^
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    22 | \item{msg_style}{is a {crayon::style()} style that will gray scale the
       |                       ^
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    22 | \item{"sysname"} : {The operating system name.}
       |                    ^
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    23 | \item{"release"} : {The OS release.}
       |                    ^
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    24 | \item{"version"} : {The OS version.}
       |                    ^
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    25 | \item{"nodename"} : {A name by which the machine is known on the network (if any).}
       |                     ^
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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.}}
       |                       ^
GNU make is a SystemRequirements.
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    34 | if (require(incidence)) {
       |                         ^
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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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    48 | `{itemStyle: {color: 'red', fontBold: 'bold'}}`.
       |  ^
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    48 | `{itemStyle: {color: 'red', fontBold: 'bold'}}`.
       |              ^
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    51 | `{symbolSize: 4}`.
       |  ^
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or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
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    25 | minimization (most others). This function computes a factor from {-1, 1} for
       |                                                                  ^
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    30 | Kemp B., V\"{a}rri, A., Rosa, A.C., Nielsen, K.D. and Gade, J. (1992).
       |             ^
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO:
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GNU make is a SystemRequirements.
Package required but not available: ‘opGMMassessment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(EGRETci)
  > test_check("EGRETci")
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 15 ]
  
  ══ Skipped tests (10) ══════════════════════════════════════════════════════════
  • On CRAN (10): 'tests_boot_tests.R:57:3', 'tests_boot_tests.R:69:3',
    'tests_boot_tests.R:87:3', 'tests_boot_tests.R:131:3',
    'tests_boot_tests.R:150:3', 'tests_boot_tests.R:179:3', 'tests_kalman.R:4:3',
    'tests_kalman.R:21:3', 'tests_kalman.R:46:3', 'tests_kalman.R:71:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('tests_boot_tests.R:113:3'): paVector ──────────────────────────────
  `paIndexWinter` not equal to 11:13.
  Lengths differ: 4 is not 3
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 15 ]
  Error: Test failures
  Execution halted
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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)
       |                                          ^
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    92 |     J. Kotus and M. Urb\'{a}nski 2003.  \emph{Hausdorff dimension and Hausdorff
       |                          ^
Error(s) in re-building vignettes:
--- re-building ‘ellipticpaper.Rnw’ using Sweave

Attaching package: ‘elliptic’

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Loading required package: emulator
Loading required package: mvtnorm
Loading required package: calibrator
Error: processing vignette 'ellipticpaper.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'ellipticpaper.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm6): Font bbm6 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘ellipticpaper.Rnw’

--- re-building ‘residuetheorem.Rnw’ using Sweave

Attaching package: ‘elliptic’

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--- finished re-building ‘residuetheorem.Rnw’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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    80 | \code{\link{score}}, \link{elo.run.helpers}{elo.run helpers}, \code{\link{elo.calc}},
       |                                            ^
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GNU make is a SystemRequirements.
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  'IlluminaHumanMethylationEPICanno.ilm10b4.hg19',
  'IlluminaHumanMethylation450kanno.ilmn12.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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    25 |  \code{terms} the code{terms} object used.
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       |                       ^
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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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   124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
       |                                  ^
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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},
       |                                                        ^
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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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       |  ^
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    16 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then Sigma^{-1} 
       |                                                                         ^
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    17 | has the corresponding q-factor decomposition Sigma^{-1}=diag(phi)(I-theta theta')diag(phi), where theta is a mxq matrix and phi the vector of 
       |                                                    ^
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    21 | \item{iSB}{m x q matrix (diag(Psi)+BB')^{-1}B.}
       |                                         ^
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    15 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then the function returns a matrix Omega such that Sigma^{-1} = Omega Omega'. Equivalently,
       |                                                                                                                       ^
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    80 | \item{XtXlamIinv}{explicit value of (X'X + diag(penalty))^{-1}.  Useful
       |                                                           ^
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    12 | \item{orden}{Es un valor numérico que representa el orden del momento central (orden = {1,2,3,4,...})}
       |                                                                                        ^
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   138 | $j^{th}$ for all the observations.
       |    ^
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    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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    52 | \item{legend}{should a legend be added? Defaults to code{FALSE}}
       |                                                         ^
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    56 | \item{legend.pretty}{logical: should the legend values produced by \[base]{pretty}? Othewrwise they are exact. Defaults to \code{TRUE}}
       |                                                                           ^
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     5 |   Conducts a generalized likelihood ratio test testing whether {\eqn{\beta \in}  (-\code{c},\code{c})}. Covariates can be accommodated.
       |                                                                ^
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    34 |   This is a similar function to the main function \code{evian}. Instead of testing H0: \eqn{\beta}=0, it tests for whether H0:{\eqn{\beta \in} (-\code{c},\code{c})}.
       |                                                                                                                               ^
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   183 |  \item {nlumgammagpd} and {proflumgammagpd} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], sigmau, xi)}
       |                           ^
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   181 |  \item {nlumgammagpdcon} and {proflumgammagpdcon} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], xi)}
       |                              ^
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    87 | code{\link[evmix:kernels]{kd*}}  and \code{\link[evmix:kernels]{kp*}} give the
       |     ^
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    18 | Procrustes distance provides a measure of coincidence of two point sets {xi} and {yi}, i=1..N. For this purpose the variance of point deviations is calculated at the optimal superposition of the sets. It allows to characterize the shape proximity of a given simplex to shape of a reference one.
       |                                                                         ^
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    18 | Procrustes distance provides a measure of coincidence of two point sets {xi} and {yi}, i=1..N. For this purpose the variance of point deviations is calculated at the optimal superposition of the sets. It allows to characterize the shape proximity of a given simplex to shape of a reference one.
       |                                                                                  ^
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    42 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
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    41 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
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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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    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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    37 | where, \code{alpha(i)} is the intercept, \code{f(t)} is a {K x 1} vector of 
       |                                                           ^
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    82 | \item{las}{one of {0, 1, 2, 3} to set the direction of axis labels, same as
       |                   ^
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    39 | Returned object is of class {summary.ffm}.
       |                             ^
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    75 | (2001) proposed: "the smallest k such that gap(k) >= gap(k+1) - s_{k+1}". 
       |                                                                   ^
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    77 | SE.factor*s_{k+1}" where SE.factor is a numeric value which can be 1
       |             ^
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Problems with news in ‘NEWS.md’:
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    14 |                  code{Pretty happy} <  \code{Very happy}}
       |                      ^
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--- re-building ‘jss.Rmd’ using rmarkdown
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
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entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
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entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
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kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
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entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
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kpathsea: Appending font creation commands to missfont.log.
Error: processing vignette 'jss.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.4/fairadapt.Rcheck/vign_test/fairadapt/vignettes/jss.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips.
--- failed re-building ‘jss.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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    22 | A map of France as {sf} object. Can be used as dataset or for maps
       |                    ^
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    18 | \code{pi0}{The estimated proportion \code{pi0} of null hypotheses.}}
       |           ^
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GNU make is a SystemRequirements.
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    17 | The value of m^{-1}_{j,j}
       |                ^
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    17 | The value of m^{-1}_{j,j}
       |                     ^
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.run: no visible binding for global variable ‘init’
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Undefined global functions or variables:
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Note: information on .o files is not available
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GNU make is a SystemRequirements.
checkRd: (-1) Error-Classes.Rd:107-119: Lost braces
   107 |   \item \code{do_verbose(response, template)} {
       |                                               ^
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    33 |   \item \code{do(response, mssg)} {
       |                                   ^
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    25 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
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    27 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
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    34 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
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    36 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
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    31 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
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    33 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
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     5 | \title{Plots function for object of class{fbroc.conf}}
       |                                          ^
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    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                              ^
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    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                                           ^
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checkRd: (-1) NASAtemp.Rd:14: Lost braces in \itemize; meant \describe ?
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    30 | \item{adjust.method}{A string used to identify the p-value and false discovery rate adjustment method. Defaults to \code{BH}. Options are \code{BH}, \code{BY}, code{Bon},\code{Holm}, \code{Hoch}, and \code{Sidak}.}
       |                                                                                                                                                                     ^
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    19 | \item{exclui3pontos}{verify por ... ? in f<-function(a, ...){ }}
       |                                                             ^
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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}.
       |                               ^
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    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}.
       |                               ^
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Error(s) in re-building vignettes:
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown

Quitting from lines 22-24 [unnamed-chunk-1] (fitbitScraper-examples.Rmd)
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

SUMMARY: processing the following file failed:
  ‘fitbitScraper-examples.Rmd’

Error: Vignette re-building failed.
Execution halted
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    66 | \code{parA }{vector of the six "ABCDEF" coefficients
       |             ^
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    67 | \code{RSS }{'root sum square' figure of merit describing the relative fit quality}
       |            ^
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    68 | \code{iters }{number of iterations at convergence}
       |              ^
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    69 | \code{exitCode }{1 means ellipse, 2 means hyperbola, 3 means parabola.
       |                 ^
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    59 | For \code{xyrot} {a Nx2 array of the x,y coordinates of the rotated data set. }
       |                  ^
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Package suggested but not available for checking: ‘gridlayout’
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Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
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    14 | All standard distributions from {stats} package are covered. For a list
       |                                 ^
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    11 | The initial design, consisting of \code{d + 1} columns ({d} dimensions and
       |                                                         ^
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    31 |         \code{smoothed} of class {StatMixHMM}).
       |                                  ^
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    31 |         \code{smoothed} of class {StatMixHMMR}).
       |                                  ^
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     8 | This function summarizes a call to code{\link{flamCV}} and identifies the tuning parameter chosen by cross-validation.
       |                                        ^
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    53 | like those in package {MetricsWeighted}.}
       |                       ^
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    49 | {MetricsWeighted}.}
       | ^
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    45 | Experimental. Uses package {ggpubr} to rearrange the figure.
       |                            ^
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    96 | the `{.storyboard}` attribute to individual pages rather than using the
       |      ^
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    45 | If k = 0: (xi_1, ..., x_{C_i - 1}, omega)
       |                         ^
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    47 | If k = 1: (xi_1, ..., x_{C_i - 1}, omega, alpha1, tau1)
       |                         ^
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    49 | If k = 2: (xi_1, ..., x_{C_i - 1}, omega, alpha1, tau1, alpha2, tau2)
       |                         ^
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GNU make is a SystemRequirements.
installed size is 13.4Mb
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    30 | \item Don't forget to add {flow} to Suggests in your DESCRIPTION file.
       |                           ^
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    10 | \item{Flow}{Water flow, in m^{3}/s}
       |                              ^
Malformed Description field: should contain one or more complete sentences.
installed size is 26.8Mb
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GNU make is a SystemRequirements.
installed size is  7.6Mb
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checkRd: (-1) FMP.Rd:30: Lost braces; missing escapes or markup?
    30 | \eqn{m(\theta) = b_0 + b_1 \theta + b_2 \theta^2 + b_3 \theta^3}. Acceptable values of k = {0,1,2,3}. According to 
       |                                                                                            ^
checkRd: (-1) autoFMradio.Rd:46: Lost braces; missing escapes or markup?
    46 | Step 1 (regularized correlation matrix estimation) is performed using the \code{X}, \code{t}, and {fold} arguments.
       |                                                                                                   ^
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checkRd: (-1) Estable.Rd:40: Lost braces
    40 |   \code{dEstable}{ gives the density function;}
       |                  ^
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    41 |   \code{pEstable}{ gives the distribution function or its complement;}
       |                  ^
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    42 |   \code{qEstable}{ gives quantiles;}
       |                  ^
checkRd: (-1) Estable.Rd:43-56: Lost braces
    43 |   \code{tailsEstable}{ returns a list with the following components
       |                      ^
checkRd: (-1) FMstable.Rd:50: Lost braces
    50 |   \code{dFMstable}{ gives the density function;}
       |                   ^
checkRd: (-1) FMstable.Rd:51: Lost braces
    51 |   \code{pFMstable}{ gives the distribution function or its complement;}
       |                   ^
checkRd: (-1) FMstable.Rd:52: Lost braces
    52 |   \code{qFMstable}{ gives quantiles;}
       |                   ^
checkRd: (-1) FMstable.Rd:53-66: Lost braces
    53 |   \code{tailsFMstable}{  returns a list with the following components
       |                       ^
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checkRd: (-1) navbar_page.Rd:36: Lost braces in \itemize; meant \describe ?
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Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
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Package unavailable to check Rd xrefs: ‘cmdstanr’
checkRd: (-1) foreca.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
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Depends: includes the non-default packages:
  'doParallel', 'dplyr', 'fable', 'fabletools', 'fable.prophet',
  'feasts', 'fracdiff', 'ggplot2', 'gt', 'magrittr', 'parallel',
  'readr', 'tibble', 'tidyr', 'tsibble', 'urca'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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    28 | \item{pavd}{logical input to include Plant Area Volume Density Plot from {plot_pavd},
       |                                                                          ^
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checkRd: (-1) FGf.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) FourgameteP.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
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checkRd: (-1) plot_lines.Rd:66: Lost braces
    66 | moderator. By default it is equal to \8code{c(19, 17, 15, 8, 5, 4, 3, 1)}.}
       |                                            ^
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     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |     ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                        ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                              ^
checkRd: (-1) Fpop.Rd:9: Lost braces; missing escapes or markup?
     9 | m_{i+1}), where the indicator function I counts the number of
       |   ^
Package suggested but not available for checking: ‘bcp’
Package suggested but not available for checking: ‘RandomFields’
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checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) summary.frbs.Rd:32: Lost braces
    32 |                           \code{"GAUSSIAN"}, code{"TRIANGLE"}, \code{"TRAPEZOID"}, \code{"SIGMOID"}, and \code{"BELL"}.
       |                                                  ^
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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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checkRd: (-1) maximin.Rd:197: Lost braces
   197 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
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checkRd: (-1) NEWS.Rd:234: Escaped LaTeX specials: \_
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/fRLR.Rcheck/00install.out’ for details.
installed size is 55.2Mb
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checkRd: (-1) FSelector-package.Rd:14: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) FSelector-package.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:22: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘RTCGA.rnaseq’
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checkRd: (-1) report.Rd:18: Lost braces; missing escapes or markup?
    18 |         \item{las}{numeric in {0,1,2,3}; the style of axis labels (see \code{\link{par}}).}
       |                               ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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Malformed Description field: should contain one or more complete sentences.
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checkRd: (-1) plot.fd.Rd:72-77: Lost braces in \itemize; meant \describe ?
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/funMoDisco.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  7.3Mb
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checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                             ^
checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                                                     ^
checkRd: (-1) genmf.Rd:26: Lost braces; missing escapes or markup?
    26 | \item 'gbellmf' is c(\code{a, b, c}), where \code{a} denotes the width, \code{b} is usually positive and {c} locates the center of the curve.
       |                                                                                                          ^
Found the following significant warnings:
  Note: possible error in 'findInterval(null, ti, ': unused arguments (checkSorted = FALSE, checkNA = FALSE) 
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/fwb.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
norm_inter_invert: possible error in findInterval(null, ti, checkSorted
  = FALSE, checkNA = FALSE): unused arguments (checkSorted = FALSE,
  checkNA = FALSE)
Running ‘testthat.R’ [16s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(fwb)
  > 
  > test_check("fwb")
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 114 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-fwb.R:77:3', 'test-fwb.R:139:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-p-values.R:24:3'): p-values correctly invert CIs ───────────────
  Error in `findInterval(null, ti, checkSorted = FALSE, checkNA = FALSE)`: unused arguments (checkSorted = FALSE, checkNA = FALSE)
  Backtrace:
      ▆
   1. └─fwb:::check_p_value_okay(...) at test-p-values.R:24:3
   2.   ├─base::suppressWarnings(...) at tests/testthat/helpers.R:101:5
   3.   │ └─base::withCallingHandlers(...)
   4.   ├─base::summary(...) at tests/testthat/helpers.R:102:7
   5.   └─fwb:::summary.fwb(...)
   6.     └─fwb:::invert_ci(...)
   7.       └─base::apply(...)
   8.         └─fwb (local) FUN(newX[, i], ...)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 114 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    help   4.6Mb
Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’
Error(s) in re-building vignettes:
--- re-building ‘gaawr2.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'EnsDb.Hsapiens.v75''
running: bash  -c "export message=\"Hello, world!\"
echo \"print('\$message')\" > hello.R
R CMD BATCH hello.R
R --no-save -q < hello.R
R --no-save -q <<END
message <- Sys.getenv(\"message\"); print(message)
source(\"hello.R\")
END
echo \${message} | \\
Rscript -e '
message <- scan(\"stdin\", what=\"\", sep=\"\\n\", quiet=TRUE);
write.table(message, col.names=FALSE, row.names=FALSE,
            quote=FALSE)
' | \\
cat
rm hello.*"

Quitting from gaawr2.Rmd:409-415 [ensdb]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'metadata': object 'EnsDb.Hsapiens.v75' not found
---
Backtrace:
    ▆
 1. ├─ensembldb::metadata(EnsDb.Hsapiens.v75)
 2. └─base::.handleSimpleError(...)
 3.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'gaawr2.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'metadata': object 'EnsDb.Hsapiens.v75' not found
--- failed re-building ‘gaawr2.Rmd’

--- re-building ‘web.Rmd’ using rmarkdown
[WARNING] Citeproc: citation tsv not found
--- finished re-building ‘web.Rmd’

SUMMARY: processing the following file failed:
  ‘gaawr2.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 55.0Mb
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checkRd: (-1) vza_mean_and_var_rasters.Rd:20: Lost braces
    20 | of the paper on Wilson's warbler, this function computes $tilde{T}^{(mu)}$ (returned as
       |                                                                ^
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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
       |                                           ^
installed size is 25.3Mb
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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.  
       |                                                                                                                                                                                                                                         ^
'LazyData' is specified without a 'data' directory
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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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installed size is  6.9Mb
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installed size is  5.1Mb
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Package which this enhances but not available for checking: ‘doMPI’
checkRd: (-1) Gapfill.Rd:66-68: Lost braces in \itemize; \value handles \item{}{} directly
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    libs   3.8Mb
'LazyData' is specified without a 'data' directory
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    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                      ^
checkRd: (-1) read.ctable.Rd:19: Lost braces; missing escapes or markup?
    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                                      ^
checkRd: (-1) read.ctable.Rd:29: Lost braces; missing escapes or markup?
    29 | output array, {row,col}.names are not necessary \code{dimnames[[1]]} and
       |               ^
installed size is 11.8Mb
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    data   1.4Mb
    libs   9.7Mb
installed size is 112.1Mb
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    libs  111.6Mb
GNU make is a SystemRequirements.
installed size is 96.4Mb
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    extdata   1.6Mb
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installed size is  9.4Mb
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    R      2.0Mb
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checkRd: (-1) CompoundDensPlot.Rd:18: Lost braces
    18 |   \item{shape1, scale ,shape2, shape3}{numeric; positive parameters of the GB2 distribution. On the plot they are denotes as \code{a}, code{b}, \code{p}, \code{q} and \code{pl0} respectively.}
       |                                                                                                                                            ^
checkRd: (-1) CompoundVarest.Rd:58: Lost braces
    58 | \code{scoreU.cgb2} returns a \eqn{N \times (L-1)} matrix of scores <code{U}.
       |                                                                         ^
checkRd: (-1) Fisk.Rd:26: Lost braces
    26 | \value{\code{fisk} and \code{fiskh} return vectors of length 4 containing the estimated parameters \eqn{a}, eqn{b}, as well as \eqn{p=1} and \eqn{q=1}. 
       |                                                                                                                ^
checkRd: (-1) MLfullGB2.Rd:23: Lost braces
    23 |   \item{method}{numeric; the method to be used by \code{optim}. By default, code{method = }1 and the used method is BFGS. If \code{method = }2, method L-BFGS-B is used.}
       |                                                                                 ^
checkRd: (-1) MLprofGB2.Rd:16: Lost braces
    16 |   \item{method}{numeric; the method to be used by \code{optim}. By default, code{method = }1 and the used method is BFGS. If \code{method = }2, method L-BFGS-B is used.}
       |                                                                                 ^
installed size is  6.6Mb
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    libs   6.5Mb
Specified C++11: please drop specification unless essential
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  15.5Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘gputools’
Package suggested but not available for checking: ‘paleofire’
checkRd: (-1) listInverseBlocks.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                           ^
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    17 | List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                    ^
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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,
       | ^
Specified C++11: please drop specification unless essential
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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}).
       |                                    ^
installed size is 97.3Mb
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    30 | code{infile=}, indicating that the input file should be
       |     ^
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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).
       |            ^
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
Running examples in ‘GEC-Ex.R’ failed
The error most likely occurred in:

> ### Name: eep_optim
> ### Title: The Wrapper Function that Returns the Final Estimates from
> ###   Maximum Likelihood Estimation for EEP.
> ### Aliases: eep_optim
> 
> ### ** Examples
> 
> eep_optim(seq(1:100))
Error in stats::optim(init, lower = lower_bound, eep_nll, method = "L-BFGS-B",  : 
  L-BFGS-B needs finite values of 'fn'
Calls: eep_optim -> raw_est_eep -> <Anonymous>
Execution halted
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    17 | \item{y}{n-by-1 binary response vector sampled from {0,1}}
       |                                                     ^
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'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘GenomicRanges’

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘genderdata’
installed size is  9.4Mb
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checkRd: (-1) GeneF-internal.Rd:40: Lost braces; missing escapes or markup?
    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}}
       |                     ^
Specified C++11: please drop specification unless essential
installed size is 11.7Mb
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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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    70 | covariates included in \code{formula_l} or {formula_s} (required).}
       |                                            ^
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Specified C++11: please drop specification unless essential
installed size is  6.9Mb
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'LazyData' is specified without a 'data' directory
Package required but not available: ‘reactome.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) barto.Rd:15-18: Lost braces in \itemize; meant \describe ?
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Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) cfunc.new.Rd:57: Lost braces in \itemize; meant \describe ?
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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.}
       |                    ^
checkRd: (-1) gensvm.grid.Rd:127: Lost braces
   127 | GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                        ^
checkRd: (-1) gensvm.grid.Rd:129: Lost braces
   129 | section "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more 
       |                                        ^
checkRd: (-1) gensvm.grid.Rd:129: Lost braces
   129 | section "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more 
       |                                            ^
installed size is 46.8Mb
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Error(s) in re-building vignettes:
--- re-building ‘geoAr_geofacet.Rmd’ using rmarkdown
File figure/tucmap-1.png not found in resource path
Error: processing vignette 'geoAr_geofacet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘geoAr_geofacet.Rmd’

--- re-building ‘geoAr_leaflet.Rmd’ using rmarkdown
File figure/map-1.png not found in resource path
Error: processing vignette 'geoAr_leaflet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘geoAr_leaflet.Rmd’

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

SUMMARY: processing the following files failed:
  ‘geoAr_geofacet.Rmd’ ‘geoAr_leaflet.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
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checkRd: (-1) calvaria.Rd:8: Lost braces; missing escapes or markup?
     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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     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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Problems with news in ‘NEWS.md’:
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    33 |   {chisq_i = sum( (O_iz - E_iz)^2 / E_iz; z = 0, ..., C ), }
       |   ^
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    27 |   GUM-based probabilities just constrain alpha to a unit vector of length {I}
       |                                                                           ^
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    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}.
       |                                                                                                                                                                                                                                                                                                                                                                                                              ^
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    16 |         \item Now \code{AICc == Inf} when {n <= p + 1}.
       |                                           ^
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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}.}
       |                                                                                                                                                                                                                                                                                                                                                                                                          ^
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    16 |                          a factor with levels either \\code{F} (female) or code{M} (male)}
       |                                                            ^
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    16 |                          a factor with levels either \\code{F} (female) or code{M} (male)}
       |                                                                                ^
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     4 | \title{{Gal\'{a}pagos} Island species data}
       |              ^
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     6 |   The number of species on the {Gal\'{a}pagos} Islands
       |                                ^
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     6 |   The number of species on the {Gal\'{a}pagos} Islands
       |                                      ^
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    40 |    {Gal\'{a}pagos} (the endemics). 
       |    ^
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    40 |    {Gal\'{a}pagos} (the endemics). 
       |          ^
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    44 |   Species number and endemism: The {Gal\'{a}pagos} Archipelago revisited.
       |                                          ^
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    14 |   \item{object}{A fitted model object, of class \code{glm}, \code{lm} or code{glm.nb}}
       |                                                                              ^
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    14 | code{glmulti} finds what are the \code{n} best models (the confidence set of models) among all possible models (the candidate set, as specified by the user).
       |     ^
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    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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    24 | \item{g}{A formula as \code{y~z}, where code{y} is the response and
       |                                             ^
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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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--- re-building ‘GOxploreR.Rmd’ using rmarkdown

Quitting from GOxploreR.Rmd:368-371 [unnamed-chunk-17]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Error: processing vignette 'GOxploreR.Rmd' failed with diagnostics:
Problem while converting geom to grob.
ℹ Error occurred in the 3rd layer.
Caused by error:
! vector memory limit of 16.0 Gb reached, see mem.maxVSize()
--- failed re-building ‘GOxploreR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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    65 |         least one root larger than one) on bootstrapped \verb{x} and {y}.
       |                                                                      ^
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       |                                                                      ^
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    71 |         least one root larger than one) on bootstrapped \verb{x}, \verb{y} and {z}.
       |                                                                                ^
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Specified C++11: please drop specification unless essential
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    help   2.2Mb
    libs   3.9Mb
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs  10.5Mb
Specified C++11: please drop specification unless essential
installed size is 18.5Mb
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    libs  16.1Mb
checkRd: (-1) MinimiseEPL.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MinimiseEPL.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MinimiseEPL.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MinimiseEPL.Rd:20: Lost braces in \itemize; meant \describe ?
installed size is 59.8Mb
  sub-directories of 1Mb or more:
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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:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:24: Lost braces
    24 | \item{code{figpos}:}{LaTeX figure environment position; default is \code{"htb!"}}
       |           ^
checkRd: (-1) setgreportOption.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:29: Lost braces in \itemize; meant \describe ?
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.8Mb
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    libs  38.5Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs                     5.6Mb
    supplementary_material   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Package required but not available: ‘org.Mm.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
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    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)}. }
       |                                                                                                                                                                                 ^
installed size is  5.0Mb
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    doc    1.6Mb
    libs   2.4Mb
installed size is  8.2Mb
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    help   1.9Mb
    libs   6.1Mb
checkRd: (-1) crossval.Rd:54: 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) spratt2016.Rd:29: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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checkRd: (-1) tumor.Rd:10: Lost braces in \itemize; meant \describe ?
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    98 | \code{left} and {right} for illustrative purpose), one would need a third variable (\code{status}) taking the value 0 
       |                 ^
installed size is 12.7Mb
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    extdata   4.5Mb
    libs      8.1Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   3.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    data   1.1Mb
    help   1.8Mb
'LazyData' is specified without a 'data' directory
installed size is 68.1Mb
  sub-directories of 1Mb or more:
    libs  67.2Mb
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))
       |                                  ^
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    38 |     \item{\code{summary_name}}{Name used for the run summary. Use '${run_id}' in the name to include the run ID.}
       |                                                                     ^
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    88 | \item{summary_name}{Name used for the run summary. Use '${run_id}' in the name to include the run ID.}
       |                                                          ^
installed size is  5.4Mb
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    extdata   2.5Mb
    libs      2.3Mb
installed size is  8.3Mb
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    htmlwidgets   8.2Mb
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},
       |                              ^
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    91 | \eqn{64} SNPs are in cluster {-}, \eqn{708} SNPs are in cluster \eqn{0},
       |                              ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs  25.6Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 275.7Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    help    1.0Mb
    java  272.1Mb
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
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    libs    1.5Mb
    shiny   4.3Mb
'LazyData' is specified without a 'data' directory
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    HaDeX   4.0Mb
    doc     3.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.5Mb
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’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    2.4Mb
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    2.7Mb
GNU make is a SystemRequirements.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is 85.3Mb
  sub-directories of 1Mb or more:
    libs  83.9Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is  5.6Mb
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    R         3.1Mb
    extdata   1.3Mb
GNU make is a SystemRequirements.
checkRd: (-1) deff.sigma.Rd:28: Lost braces in \itemize; meant \describe ?
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installed size is  5.9Mb
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    doc   5.3Mb
installed size is  5.5Mb
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    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
'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 ?
installed size is  8.1Mb
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    libs   5.5Mb
installed size is  7.3Mb
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    libs   6.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
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    libs   5.6Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
    libs   4.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Found the following significant warnings:
  /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppXsimd/include/xsimd/memory/xsimd_aligned_allocator.hpp:72:53: warning: 'allocator<void>' is deprecated [-Wdeprecated-declarations]
  /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppXsimd/include/xsimd/memory/xsimd_aligned_allocator.hpp:173:27: warning: 'allocator<void>' is deprecated [-Wdeprecated-declarations]
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/hdtg.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is 36.2Mb
  sub-directories of 1Mb or more:
    libs  35.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.7Mb
installed size is  6.3Mb
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    doc   5.3Mb
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  5.8Mb
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    doc   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
'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
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checkRd: (-1) marker_h2.Rd:96-97: Lost braces in \itemize; \value handles \item{}{} directly
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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
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    38 |   {b} and \code{m} to be lower (or greater) than \code{q}.
       |   ^
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.9Mb
    libs   1.8Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘Rmpi’
checkRd: (-1) hero.Rd:67-68: Lost braces
    67 | then \code{\link[pbapply]{pblapply}} is used. If code{package ==
       |                                                      ^
checkRd: (-1) hero.Rd:69: Lost braces
    69 | code{package == "Rmpi"}, then \code{\link[Rmpi]{mpi.applyLB}} is used.}
       |     ^
Package unavailable to check Rd xrefs: ‘Rmpi’
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  19.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      3.3Mb
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: \&
installed size is  5.2Mb
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    data   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    extdata   7.6Mb
Packages required but not available:
  'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene', 'org.Mm.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘diffHic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
installed size is  6.9Mb
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    data   2.0Mb
    libs   3.8Mb
Specified C++11: please drop specification unless essential
installed size is  8.7Mb
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    highlight   1.0Mb
    libs        7.5Mb
Package suggested but not available for checking: ‘INLA’
installed size is 57.5Mb
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    libs  57.3Mb
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
installed size is  6.9Mb
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    data   1.0Mb
    libs   4.9Mb
installed size is 83.3Mb
  sub-directories of 1Mb or more:
    libs  82.8Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘HadoopStreaming’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
mdffits:
  function(model, ...)
mdffits.mer:
  function(object, level, delete, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
installed size is  6.0Mb
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    help   2.3Mb
    libs   2.6Mb
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  7.8Mb
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    data   3.5Mb
    libs   4.0Mb
installed size is 11.5Mb
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    libs  10.6Mb
installed size is 113.0Mb
  sub-directories of 1Mb or more:
    article    3.0Mb
    doc        1.1Mb
    libs     108.3Mb
GNU make is a SystemRequirements.
Fdebug: multiple local function definitions for ‘deb’ with different
  formal arguments
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
installed size is 101.9Mb
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    libs  100.2Mb
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
       |                                                                            ^
installed size is  6.2Mb
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'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
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    app   1.7Mb
    doc   3.3Mb
installed size is 10.3Mb
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    libs   9.6Mb
'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
installed size is 16.9Mb
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    libs  16.6Mb
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  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
installed size is 90.0Mb
  sub-directories of 1Mb or more:
    libs  89.5Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.0Mb
    help   1.4Mb
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'hubExamples', 'hubVis'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
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
installed size is 50.6Mb
  sub-directories of 1Mb or more:
    libs  49.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘microViz’
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.7Mb
installed size is  5.3Mb
  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
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    extdata   5.7Mb
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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    libs   7.0Mb
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’
installed size is  5.2Mb
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    libs   1.0Mb
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  5.7Mb
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
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’
installed size is  5.8Mb
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checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
installed size is 19.3Mb
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Package suggested but not available for checking: ‘mixAK’
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
       |                             ^
installed size is  9.1Mb
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    data   3.0Mb
    libs   5.5Mb
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 ?
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checkRd: (-1) data.Rd:9: Lost braces in \itemize; meant \describe ?
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    doc    2.2Mb
    libs   2.7Mb
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Package suggested but not available for checking: ‘rggobi’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Note: possible error in 'SVT_SparseArray(dim = c(n_patients, ': unused argument (dim = c(n_patients, n_var, time)) 
  Note: possible error in 'SVT_SparseArray(dim = c(n_patients, ': unused argument (dim = c(n_patients, 1, time)) 
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/IDLFM.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
generate_data: possible error in SVT_SparseArray(dim = c(n_patients,
  n_var, time)): unused argument (dim = c(n_patients, n_var, time))
generate_data: possible error in SVT_SparseArray(dim = c(n_patients, 1,
  time)): unused argument (dim = c(n_patients, 1, time))
installed size is  5.2Mb
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    data   5.0Mb
Package suggested but not available for checking: ‘IFCdata’
installed size is  7.4Mb
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    R      2.0Mb
    libs   4.6Mb
Package required and available but unsuitable version: ‘utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 23.8Mb
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    R      2.1Mb
    doc    1.2Mb
    help   2.9Mb
    libs  17.1Mb
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)}.}
       |                  ^
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installed size is  8.0Mb
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Specified C++11: please drop specification unless essential
checkRd: (-1) lab.qcs.Rd:24: Lost braces
    24 | It develops an object of \code{lab.qcs}-code{link{class}} to perform statistical quality control.
       |                                             ^
checkRd: (-1) lab.qcs.Rd:24: Lost braces
    24 | It develops an object of \code{lab.qcs}-code{link{class}} to perform statistical quality control.
       |                                                  ^
checkRd: (-1) define_target_function.Rd:41: Lost braces; missing escapes or markup?
    41 | be done either as a single vector of values (e.g. `function(x) { ... }`), or individual inputs for each parameter
       |                                                                ^
checkRd: (-1) define_target_function.Rd:42: Lost braces; missing escapes or markup?
    42 | (e.g. `function(x1, x2) { ... }`). If a single vector is used, all parameters will be passed to the target function as
       |                         ^
checkRd: (-1) image_contour_detector.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_contour_detector.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_contour_detector.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) image_line_segment_detector.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_line_segment_detector.Rd:66-72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_line_segment_detector.Rd:73-76: Lost braces in \itemize; \value handles \item{}{} directly
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installed size is 28.6Mb
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    doc       3.7Mb
    extdata   1.0Mb
    include   3.3Mb
    libs     18.5Mb
checkRd: (-1) imagesToKerasInput.Rd:23: Lost braces
    23 | \item{grayscale}{logical. Defines color channels of images: 1 if code{TRUE}, 3 if \code{FALSE}.}
       |                                                                      ^
'LazyData' is specified without a 'data' directory
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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
       |                 ^
installed size is  5.8Mb
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    data   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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    data   3.4Mb
    doc    1.6Mb
checkRd: (-1) stringCSSRule.Rd:22: Lost braces
    22 | using the {{placeholder}} convention.
       |           ^
checkRd: (-1) stringTemplate.Rd:23: Lost braces
    23 | placeholders are marked using the {{placeholder}} convention.
       |                                   ^
checkRd: (-1) stringTemplate.Rd:12: Lost braces
    12 | {{placeholder}} format.}
       | ^
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Package suggested but not available for checking: ‘accdata’
'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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checkRd: (-1) imptree_params.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imptree_params.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imptree_params.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.imptree.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
installed size is 93.2Mb
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    libs  92.5Mb
GNU make is a SystemRequirements.
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs  12.1Mb
checkRd: (-1) kmpp.Rd:27: Lost braces
    27 |   \item{call}{a string containing the matched function call that generates this sQuote{inaparc} object.}
       |                                                                                       ^
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Specified C++11: please drop specification unless essential
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
GNU make is a SystemRequirements.
checkRd: (-1) make_likelihood_matrix.Rd:16: Lost braces; missing escapes or markup?
    16 | This function creates a matrix such that P[t, s] = P(C = t | I = s) = theta_{t-s} for s <= t and 0 otherwise.
       |                                                                             ^
Packages required but not available: 'Rfastp', 'Rsubread'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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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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checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
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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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Package suggested but not available for checking: ‘INLA’
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Package unavailable to check Rd xrefs: ‘INLA’
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Package unavailable to check Rd xrefs: ‘INLA’
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
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    44 | menu in the {utils} package, yesno in the {devtools} package.
       |             ^
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    44 | menu in the {utils} package, yesno in the {devtools} package.
       |                                           ^
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    25 | This function is useful for saveVideo() in the {animation} package.
       |                                                ^
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    27 | This function is useful for saveSWF() in the {animation} package.
       |                                              ^
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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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installed size is  7.2Mb
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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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GNU make is a SystemRequirements.
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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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installed size is  9.9Mb
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checkRd: (-1) intRvals-package.Rd:60: Lost braces
    60 | B\'{e}dard, J. & Gauthier, G. 1986. Assessment of faecal output in geese. Journal of Applied Ecology, 23, 77-90.
       |    ^
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    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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checkRd: (-1) cox_cure_net.Rd:132: Lost braces
   132 | \code{surv_lambda} (or code{cure_lambda}) that produces all-zero
       |                            ^
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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/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
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    47 | \code{conv_plot}: code{ipm} invisibly.
       |                       ^
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'LazyData' is specified without a 'data' directory
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installed size is  7.1Mb
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Package suggested but not available for checking: ‘Rmpi’
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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.}
       |     ^
checkRd: (-1) CLM.Rd:30: Lost braces
    30 | item{tau0}{the mean circular Kendall Tau of the initial order with the data.}
       |           ^
installed size is  6.2Mb
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checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
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checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
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installed size is 93.5Mb
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    doc    2.3Mb
    libs  88.2Mb
GNU make is a SystemRequirements.
installed size is 15.5Mb
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    doc    1.6Mb
    libs  13.6Mb
installed size is  6.3Mb
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    data   6.1Mb
checkRd: (-1) is_israd_database.Rd:19: Lost braces in \itemize; meant \describe ?
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    17 | \item{pi}{the matrix E[XZ']E[ZZ']^{-1}}
       |                                   ^
checkRd: (-1) sTslsSplines.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{pi}{matrix, corresponds to E[XZ']E[ZZ']^{-1}, the first stage
       |                                               ^
Specified C++11: please drop specification unless essential
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checkRd: (-1) jaccard.test.Rd:41: Lost braces; missing escapes or markup?
    41 | The {bootstrap} method uses resampling with replacement binary vectors to compute a p-value (see optional arguments).
       |     ^
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installed size is 19.7Mb
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    libs          17.3Mb
GNU make is a SystemRequirements.
installed size is 35.7Mb
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    libs  35.2Mb
Packages suggested but not available for checking: 'lfa', 'gcatest'
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
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    libs   8.7Mb
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
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installed size is  6.2Mb
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Package suggested but not available for checking: ‘clonevol’
installed size is 102.5Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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    libs      1.7Mb
installed size is  7.4Mb
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checkRd: (-1) jointLPM.Rd:298: Lost braces; missing escapes or markup?
   298 | following transformation b_1 + b_2*I_1(Y(t)) + ... + b_{n+2}*I_{n+1}(Y(t)),
       |                                                        ^
checkRd: (-1) jointLPM.Rd:298: Lost braces; missing escapes or markup?
   298 | following transformation b_1 + b_2*I_1(Y(t)) + ... + b_{n+2}*I_{n+1}(Y(t)),
       |                                                                ^
checkRd: (-1) jointLPM.Rd:299: Lost braces; missing escapes or markup?
   299 | where I_1,...,I_{n+1} is the basis of quadratic I-splines. To constraint the
       |                 ^
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installed size is 10.7Mb
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Specified C++11: please drop specification unless essential
installed size is  8.3Mb
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Specified C++11: please drop specification unless essential
installed size is  5.9Mb
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checkRd: (-1) jmdem.control.Rd:42: Lost braces; missing escapes or markup?
    42 |     The control argument of \code{jmdem} is by default passed to the control argument of {jmdem.fit}, which uses its elements as arguments to {jmdem.control}: the latter provides defaults and sanity checking.
       |                                                                                          ^
checkRd: (-1) jmdem.control.Rd:42: Lost braces; missing escapes or markup?
    42 |     The control argument of \code{jmdem} is by default passed to the control argument of {jmdem.fit}, which uses its elements as arguments to {jmdem.control}: the latter provides defaults and sanity checking.
       |                                                                                                                                               ^
installed size is 40.0Mb
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'LazyData' is specified without a 'data' directory
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installed size is  6.6Mb
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    data   1.1Mb
    libs   5.4Mb
installed size is  8.3Mb
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    R      4.0Mb
    i18n   4.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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    libs   3.9Mb
Package suggested but not available for checking: ‘remMap’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
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installed size is 34.2Mb
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checkRd: (-1) jSDM_binomial_probit_long_format.Rd:45: Lost braces
    45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr 
       |                                             ^
checkRd: (-1) jSDM_binomial_probit_long_format.Rd:45: Lost braces; missing escapes or markup?
    45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr 
       |                                                ^
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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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    14 | The {kdist} functions dk, pk, qk and rk, calculates the K-distribution
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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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    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
       |                        ^
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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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! LaTeX Error: Command \gather already defined.
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See the LaTeX manual or LaTeX Companion for explanation.
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       |                                                        ^
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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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    60 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion.
       |                                    ^
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       |                                    ^
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       |                                    ^
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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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   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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       |         ^
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       |                                                        ^
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       |                                                        ^
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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'},
       |                                                                                                                                               ^
checkRd: (-1) clusterDistance.details.Rd:28-29: Lost braces
    28 | \code{approach} indicates the algorithm used to get the value. \code{distance} indicates the distance used to get the value. Possible values: {\code{'MAX'},
       |                                                                                                                                               ^
checkRd: (-1) clusterDistanceByApproach.Rd:24-25: Lost braces
    24 | \code{approach} indicates the algorithm used to get the value. Possible values: {\code{'MAX'},
       |                                                                                 ^
checkRd: (-1) clusterDistanceByApproach.details.Rd:24-25: Lost braces
    24 | \code{approach} indicates the algorithm used to get the value. Possible values: {\code{'MAX'},
       |                                                                                 ^
'LazyData' is specified without a 'data' directory
installed size is 38.2Mb
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'LazyData' is specified without a 'data' directory
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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}).
       |                                                                   ^
checkRd: (-1) sample.quantile.Rd:20: Lost braces; missing escapes or markup?
    20 | \code{sample.quantile} computes a estimation of different quantiles, given a sample {x}, using order statistics.
       |                                                                                     ^
installed size is 74.7Mb
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    doc    2.5Mb
    libs  70.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
GNU make is a SystemRequirements.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
installed size is  5.5Mb
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    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 48.5Mb
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    help   1.1Mb
    libs  45.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hash_sentiment_slangsd.Rd:28-37: Lost braces
    28 | article{DBLP:journals/corr/Wu-etal16,
       |        ^
checkRd: (-1) hash_sentiment_slangsd.Rd:29: Lost braces; missing escapes or markup?
    29 |   author    = {Liang Wu and Fred Morstatter and Huan Liu},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:30-31: Lost braces
    30 |   title     = {SlangSD: Building and Using a Sentiment Dictionary of Slang 
       |               ^
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    32 |   journal   = {CoRR},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:33: Lost braces; missing escapes or markup?
    33 |   volume    = {abs/1608.05129},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:34: Lost braces; missing escapes or markup?
    34 |   year      = {2016},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:35: Lost braces; missing escapes or markup?
    35 |   url       = {http://arxiv.org/abs/1608.05129},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:36: Lost braces; missing escapes or markup?
    36 |   timestamp = {Wed, 17 Aug 2016 23:32:57 GMT}
       |               ^
checkRd: (-1) sw_python.Rd:32: Lost braces; missing escapes or markup?
    32 | * Neither the name of the {organization} nor the names of its
       |                           ^
installed size is 11.4Mb
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checkRd: (-1) flowunit.Rd:30: Lost braces; missing escapes or markup?
    30 | Usually flow units are of dimension $L^3 T^{-1}$. Currently a length $l$ can be on of \code{c("metre", "cm", "centimetre" "litre")}, whereas time $T$ can be one in \code{c("days", "hours", "mins", "secs")}, possibly abbreviated. The numerator of the fraction (everything before the literal \code{"/"}) is interpreted as the length (superscripts like \code{"^3"} are discarded), the denominator as time. E.g. valid units would be \code{"cm^3/s"}, \code{"m^3/day"} or \code{"litre/sec"}.
       |                                            ^
checkRd: (-1) seasindex.Rd:30: Lost braces
    30 | Laaha, G. and Bl{\"o}schl, G. (2006), Seasonality indices for regionalizing
       |                 ^
checkRd: (-1) seasindex.Rd:34: Lost braces
    34 | Mitteilungen, Inst. f{\"u}r Wasserbau u. Ingenieurhydrologie,
       |                      ^
checkRd: (-1) seasratio.Rd:31: Lost braces
    31 | Laaha, G. and Bl{\"o}schl, G. (2006), Seasonality indices for regionalizing low flows. Hydrol. Process., 20
       |                 ^
installed size is 115.7Mb
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checkRd: (-1) prior_to_num.Rd:13: Lost braces; missing escapes or markup?
    13 |   {'uniform', 'normal', 'student-t', 'gamma', 'inv-gamma', 'log-normal'}
       |   ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lgrExtra)
  > 
  > test_check("lgrExtra")
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 103 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • '/var/log/syslog' is not readable (1): 'test_AppenderSyslog.R:24:3'
  • Cannot establish connection (3): 'test_AppenderDbi.R:126:5',
    'test_AppenderDbi.R:126:5', 'test_AppenderDbi.R:126:5'
  • SQLite doesn't support schemas (2): 'test_AppenderDbi.R:223:7',
    'test_AppenderDbi.R:254:7'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_DynatraceLayout.R:23:3'): DynatraceLayout.format_event() - with default settings - format event correctly ──
  res$timestamp not identical to "2018-11-02 17:19:33".
  1/1 mismatches
  x[1]: "2018-11-03 05:19:33"
  y[1]: "2018-11-02 17:19:33"
  
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 103 ]
  Error: Test failures
  Execution halted
GNU make is a SystemRequirements.
installed size is 43.5Mb
  sub-directories of 1Mb or more:
    libs  43.3Mb
GNU make is a SystemRequirements.
installed size is 10.7Mb
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    data      1.1Mb
    include   1.0Mb
    lib       4.8Mb
    libs      3.6Mb
GNU make is a SystemRequirements.
checkRd: (-1) isingdata.Rd:14: Lost braces; missing escapes or markup?
    14 |     \item{X}{a 5000-by-100 matrix, each entry is in {-1,1}.}
       |                                                     ^
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
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checkRd: (-1) lx_list_lights.Rd:27: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
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installed size is 68.8Mb
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checkRd: (-1) likelihood_calculation.Rd:24: Lost braces
    24 | For eqn{i = 1\dots N} independent observations in a vector \var{X}, with individual observations \eqn{x_i}{xi}, and a set of parameter values \eqn{\theta}:
       |        ^
checkRd: (-1) simulated_annealing_algorithm.Rd:17: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) simulated_annealing_algorithm.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:27: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘org.Mm.eg.db’
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 22-30 [unnamed-chunk-2] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'org.Mm.eg.db'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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installed size is  5.3Mb
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    libs   4.8Mb
'LazyData' is specified without a 'data' directory
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checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
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checkRd: (-1) ld_build_html_site.Rd:41: Lost braces
    41 | directory specified by `rmd_dir`. Note that this is an {{rmarkdown}}
       |                                                        ^
checkRd: (-1) ld_create_doc.Rd:29: Lost braces
    29 | directory specified by `rmd_dir`. Note that this is an {{rmarkdown}}
       |                                                        ^
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
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checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) vcov.liu.Rd:20: Lost braces
    20 | A list of matrix of estimated covariances in the linear Liu regression model for scalar or vector biasing parameter \code{d}{d} is produced. Each list element has row and column names corresponding to the parameter names given by the \code{coef(mod)}. List items are named correspond to values of biasing parameter \eqn{d}{d}.}
       |                                                                                                                             ^
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
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    testdata   1.3Mb
checkRd: (-1) relLik.Rd:16: Lost braces
    16 | \item{AIC(x), BIC(x) }{The \code{AIC} or ]code{BIC} value of the first model object.}
       |                                               ^
checkRd: (-1) relLik.Rd:17: Lost braces
    17 | \item{AIC(y), BIC(y) }{The \code{AIC} or ]code{BIC} value of the second model object.}
       |                                               ^
checkRd: (-1) bootstrap_pvals.Rd:78: Lost braces; missing escapes or markup?
    78 | $(n_{extreme} + 1) / (B + 1)$.
       |     ^
installed size is 99.6Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
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    R              2.1Mb
    doc-overview   2.2Mb
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Specified C++11: please drop specification unless essential
checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cauchypoly.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) normpoly.Rd:38: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) normpoly.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) lmomPi-Package.Rd:9: Lost braces
     9 | {\code{\link{cdf}}}{: generic distribution function;  }  
       |                    ^
checkRd: (-1) lmomPi-Package.Rd:10: Lost braces
    10 | {\code{\link{qua}}}{: generic quantile function;  } 
       |                    ^
checkRd: (-1) lmomPi-Package.Rd:11: Lost braces
    11 | {\code{\link{pel}}}{: fitting of probability distribution function through L-moments. }
       |                    ^
checkRd: (-1) lmomPi-Package.Rd:27: Lost braces; missing escapes or markup?
    27 | The function  \code{\link{spi.cdf}()} is compared against \code{SPEI::spi()} in SPEI package (\url{https://cran.r-project.org/package=SPEI}). The differences in SPI extimation have order of magnitude averagely about 10^{-8},  due to  the different fitting methods implemented in the two packages. 
       |                                                                                                                                                                                                                            ^
checkRd: (-1) vcov.Rd:20: Lost braces
    20 | A list of matrix of estimated covariances in the linear ridge regression model for scalar or vector biasing parameter \code{K}{K} is produced. Each list element has row and column names corresponding to the parameter names given by the \code{coef(mod)}. List items are named correspond to values of biasing parameter \eqn{K}{K}.}
       |                                                                                                                               ^
Specified C++11: please drop specification unless essential
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
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    libs   5.2Mb
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Author
    Maintainer
Specified C++11: please drop specification unless essential
installed size is 65.4Mb
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checkRd: (-1) mte_tilde_at.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
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installed size is 33.1Mb
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Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error in ls.problem(model.text.lsp) : 
  has.localsolver(ls.path) is not TRUE
Calls: ls.problem -> stopifnot
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘localsolver.Rmd’ using knitr
sh: localsolver: command not found

Quitting from lines 66-68 [unnamed-chunk-3] (localsolver.Rmd)
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
--- failed re-building ‘localsolver.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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    15 |     { } \tab {or \code{FBConcuss}=football player with concussion history} \cr
       |     ^
checkRd: (-1) HappyPlanetIndex.Rd:14: Lost braces; missing escapes or markup?
    14 |     { } \tab {\code{5}=South Asia, \code{6}=East Asia, \code{7}=former Communist countries}\cr
       |     ^
checkRd: (-1) RockandRoll2012.Rd:17: Lost braces; missing escapes or markup?
    17 |     { } \tab {\code{Lifetime Achievement}, \code{Sideman}} \cr
       |     ^
checkRd: (-1) RockandRoll2015.Rd:17: Lost braces; missing escapes or markup?
    17 |     { } \tab {\code{Lifetime Achievement}, \code{Sideman}} \cr
       |     ^
checkRd: (-1) StudentSurvey.Rd:12: Lost braces; missing escapes or markup?
    12 |     \item{\code{Sex}}{code {F}=female or \code{M}=male}
       |                            ^
checkRd: (-1) SynchronizedMovement.Rd:16: Lost braces; missing escapes or markup?
    16 |     { } \tab {for High/Low Synchronization + High/Low Exertion}\cr
       |     ^
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
installed size is 27.9Mb
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Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’
Specified C++11: please drop specification unless essential
Depends: includes the non-default packages:
  'adabag', 'arm', 'brnn', 'C50', 'car', 'corrplot', 'Cubist',
  'doParallel', 'dplyr', 'e1071', 'gam', 'gbm', 'ggplot2', 'ggplotify',
  'gridExtra', 'gt', 'ipred', 'klaR', 'MachineShop', 'magrittr',
  'MASS', 'mda', 'parallel', 'pls', 'pROC', 'purrr', 'randomForest',
  'ranger', 'reactable', 'reactablefmtr', 'readr', 'rpart', 'scales',
  'tidyr', 'tree', 'xgboost'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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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}.
       |                                                                                                                                                                                                                                                                                                  ^
checkRd: (-1) logdensity_fft.Rd:33: Lost braces; missing escapes or markup?
    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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checkRd: (-1) loon.shiny.Rd:93-102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loon.shiny.Rd:95-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loon.shiny.Rd:97: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) loon.shiny.Rd:103-108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loon.shiny.Rd:105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loon.shiny.Rd:106: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scio’
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
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘kerdiest’
checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
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Error: package or namespace load failed for ‘LSTbook’:
 .onLoad failed in loadNamespace() for 'LSTbook', details:
  call: loadNamespace(name)
  error: there is no package called ‘mosaicData’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) spectral.density.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) k.Rd:27: Lost braces
    27 |  code{\link{ACSPlan-class}}, 
       |      ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) Upload_to_db.Rd:43: Lost braces
    43 | lucas]{Connect_to_db}
       |       ^
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checkRd: (-1) LVGP_fit.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) LVGP_predict.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) math_example.Rd:21: Lost braces
    21 | Data are sampled from the modified math function based on the first example in the paper listed in code{references}.
       |                                                                                                        ^
Specified C++11: please drop specification unless essential
checkRd: (-1) StEM_pcirt.Rd:11: Lost braces; missing escapes or markup?
    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.}
       |                                          ^
Package suggested but not available for checking: ‘depth’
checkRd: (-1) geom_lv.Rd:101: Lost braces; missing escapes or markup?
   101 | determines whether the width of the box for letter value LV(i) should be proportional to i (linear), proportional to $2^{-i}$ (height), or  whether
       |                                                                                                                         ^
checkRd: (-1) geom_lv.Rd:102: Lost braces; missing escapes or markup?
   102 | the area of the box should be proportional to $2^{-i}$ (area).}
       |                                                  ^
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) examinee-class.Rd:61: Lost braces; missing escapes or markup?
    61 | \item{\code{routing_based_on}}{a vector containing the routing was based on \code{estimated_theta_by_phase} or {estimated_theta_by_test} at each module position.}
       |                                                                                                                ^
Package suggested but not available for checking: ‘rnaturalearthhires’
installed size is  7.4Mb
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installed size is 38.1Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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installed size is 55.5Mb
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'LazyData' is specified without a 'data' directory
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Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error: package or namespace load failed for 'testthat' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
   there is no package called 'R6'
  Execution halted
Packages suggested but not available for checking: 'lumi', 'beadarray'
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checkRd: (-1) RepLOptim.Rd:21: Lost braces; missing escapes or markup?
    21 |         \item{gr}{A function to return the gradient for the \dQuote{nlminb}, \dQuote{BFGS}, \dQuote{CG} and {L-BFGS-B} methods.  If it is \sQuote{NULL}, a finite-difference approximation will be used. For the \dQuote{SANN} method it specifies a function to generate a new candidate point.  If it is \sQuote{NULL} a default Gaussian Markov kernel is used.}
       |                                                                                                             ^
checkRd: (-1) Robda-methods.Rd:69: Lost braces
    69 | \seealso{\code{\link{lda}}, \code{\link{qda}}, \code{\link{snda}}, \code{\linkS4class{IData}}, \code{\linkS4class{RobEstControl}},code{\link{ConfMat}} }
       |                                                                                                                                       ^
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Package unavailable to check Rd xrefs: ‘INLA’
installed size is 10.5Mb
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checkRd: (-1) create_terminal_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                              ^
checkRd: (-1) create_terminal_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                                                   ^
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    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                              ^
checkRd: (-1) full_repo_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                                                   ^
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checkRd: (-1) manet.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) MangroveTree.Rd:37: Lost braces
    37 |       An object of class \\code{\link[Mangrove]{MangrovePed}}
       |                                ^
installed size is 10.1Mb
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Specified C++11: please drop specification unless essential
checkRd: (-1) manipulateWidget.Rd:113-117: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) EEGwide.Rd:30-33: Lost braces
    30 |   if(requireNamespace("ggplot2")){ 
       |                                  ^
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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Package suggested but not available for checking: ‘INLA’
installed size is  5.0Mb
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Package unavailable to check Rd xrefs: ‘INLA’
installed size is 33.5Mb
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installed size is 22.2Mb
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installed size is  5.8Mb
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installed size is  8.5Mb
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    R   8.4Mb
Specified C++11: please drop specification unless essential
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/mappoly.Rcheck/00install.out’ for details.
installed size is  5.4Mb
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installed size is  6.1Mb
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GNU make is a SystemRequirements.
installed size is  8.9Mb
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checkRd: (-1) locate_shift.Rd:29: Lost braces
    29 | \code{\link{quickfit}}, code{\link{locator}}
       |                             ^
checkRd: (-1) marcher-package.Rd:14: Lost braces; missing escapes or markup?
    14 | 1. \code{\link{estimate_shift}} {Estimate a range shift process.}
       |                                 ^
checkRd: (-1) marcher-package.Rd:16: Lost braces; missing escapes or markup?
    16 | 2. \code{\link{simulate_shift}} {Simulate a range shift process.}
       |                                 ^
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    18 | 3. \code{\link{plot.shiftfit}} {Visualize a range shift process.}
       |                                ^
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    20 | 4. \code{\link{test_rangeshift}} {Test whether a range shift occurred.}
       |                                  ^
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    22 | 5. \code{\link{test_return}} {Test whether a migration was a return migration.}
       |                              ^
checkRd: (-1) marcher-package.Rd:24: Lost braces; missing escapes or markup?
    24 | 6. \code{\link{test_stopover}} {Test whether a stopover occurred during a migration.}
       |                                ^
checkRd: (-1) quickfit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) test_rangeshift.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
installed size is 26.2Mb
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installed size is  6.4Mb
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checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
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    28 | ( if(is.ts(DATA)) { DATA <- as.matrix(data.frame(DATA)) } and a message
       |                   ^
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
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    17 | \item{inputId}{The code{input} slot that will be used to access the value.}
       |                        ^
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checkRd: (-1) moduleMarkdownInput.Rd:72-73: Lost braces in \enumerate; meant \describe ?
'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 10.9Mb
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GNU make is a SystemRequirements.
checkRd: (-1) Markovchart.Rd:154: Lost braces
   154 | If either \code{h} or \code{k} have length greater than 1, then the \code{G-value} (weighted average of average cost and cost standard deviation) is calculated for all given values without optimisation. The value of the function in this case is a data frame of class code{Markov_grid} with \code{length(h)*length(k)} number of rows and three columns for \code{h}, \code{k} and the \code{G-value}.
       |                                                                                                                                                                                                                                                                                ^
checkRd: (-1) marqLevAlg-package.Rd:14: Lost braces; missing escapes or markup?
    14 | (GH^{-1}G).
       |     ^
installed size is  6.0Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘marssTMB’
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Packages suggested but not available for checking:
  'BSgenome.Hsapiens.NCBI.GRCh38', 'org.Mm.eg.db', 'wiggleplotr'
installed size is 18.9Mb
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checkRd: (-1) focalCompare.Rd:14: Lost braces
    14 | \item{fun}{The function fun should take multiple numbers, and return a single number. For example mean, modal, min or max. It should also accept a na.rm argument (or ignore it, e.g. as one of the 'dots' arguments. For example, length will fail, but function(x, ...){na.omit(length(x))} works. (Specifications from `raster::focal`)}
       |                                                                                                                                                                                                                                                                          ^
installed size is 49.1Mb
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checkRd: (-1) hr_levels.Rd:9-12: Lost braces
     9 | kernelBiweight <- function(x, mean = 0, sd = 1) {
       |                                                 ^
checkRd: (-1) hr_levels.Rd:33-36: Lost braces
    33 | kernelCosine <- function(x, mean = 0, sd = 1) {
       |                                               ^
checkRd: (-1) hr_levels.Rd:41-44: Lost braces
    41 | kernelEpanechnikov <- function(x, mean = 0, sd = 1) {
       |                                                     ^
checkRd: (-1) hr_levels.Rd:58-61: Lost braces
    58 | kernelOptCosine <- function(x, mean = 0, sd = 1) {
       |                                                  ^
checkRd: (-1) hr_levels.Rd:65-68: Lost braces
    65 | kernelRectangular <- function(x, mean = 0, sd = 1) {
       |                                                    ^
checkRd: (-1) hr_levels.Rd:72-75: Lost braces
    72 | kernelSquaredCosine <- function(x, mean = 0, sd = 1) {
       |                                                      ^
checkRd: (-1) hr_levels.Rd:79-82: Lost braces
    79 | kernelTriangular <- function(x, mean = 0, sd = 1) {
       |                                                   ^
checkRd: (-1) hr_levels.Rd:86-89: Lost braces
    86 | kernelTricube <- function(x, mean = 0, sd = 1) {
       |                                                ^
checkRd: (-1) hr_levels.Rd:93-96: Lost braces
    93 | kernelTriweight <- function(x, mean = 0, sd = 1) {
       |                                                  ^
checkRd: (-1) hr_levels.Rd:100-103: Lost braces
   100 | kernelUniform <- function(x, mean = 0, sd = 1) {
       |                                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) CF2004.Rd:8: Lost braces; missing escapes or markup?
     8 |   \item{X2}{an optional second variable with same length as \code{X}, should the equation be multiple (see Details) {in mm}}
       |                                                                                                                     ^
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checkRd: (-1) Rand.index.Rd:22: Lost braces; missing escapes or markup?
    22 | The two vectors \code{x} and \code{y} must have equal length. Given a set \eqn{S} and two partitions \eqn{X} and \eqn{Y} of \eqn{S}, the Rand index is the proportion of pairs of elements in \eqn{S} (out of all pairs) that are either concordant in both \eqn{X} and \eqn{Y} (i.e., they belong to the same member of \eqn{X} and to the same member of \eqn{Y}) or discordant (i.e., not concordant) in both \eqn{X} and {Y}.  
       |                                                                                                                                                                                                                                                                                                                                                                                                                              ^
checkRd: (-1) predict.matchFeat.Rd:21: Lost braces
    21 | The function \code{predict.matchFeat} finds the best matching for new feature vectors relative to an existing set of cluster/class centers. If code{object} results from a call to \code{\link{match.gaussmix}}, the same function is used for prediction (with fixed mean vectors and covariance matrices). In other cases, the function \code{\link{match.template}} is used for prediction. 
       |                                                                                                                                                    ^
installed size is 13.2Mb
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    java   3.3Mb
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Specified C++11: please drop specification unless essential
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installed size is  9.1Mb
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    doc    1.3Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) Match.Rd:90: Lost braces; missing escapes or markup?
    90 | expression in braces. For example, the condition "{[ab]*}" is equivalent
       |                                                   ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) Matrix_eQTL_main.Rd:31: Lost braces; missing escapes or markup?
    31 |     {genepos} in the call of \code{Matrix_eQTL_main} function.
       |     ^
checkRd: (-1) Matrix_eQTL_main.Rd:35: Lost braces; missing escapes or markup?
    35 |     the data frames \code{snpspos} and {genepos}.
       |                                        ^
installed size is 11.3Mb
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'LazyData' is specified without a 'data' directory
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Matrix’
A package should be listed in only one of these fields.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.0Mb
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GNU make is a SystemRequirements.
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checkRd: (-1) MaxentVariableSelection-package.Rd:46: Lost braces; missing escapes or markup?
    46 | \tab Tyberghein L, Verbruggen H, Pauly K, Troupin C, Mineur F and {De Clerck}, O (2012)\cr
       |                                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
checkRd: (-1) findDescendingTrans.Rd:29: Lost braces
    29 |    Foster, S.D., Hosack, G.R., J. Monk, Lawrence, E., Barrett, N.S., Williams, A. and Przeslawski, P. (2020) Spatially-Balanced Designs for Transect-Based Surveys. Methods in Ecology and Evolution. emph{11}: 95--105
       |                                                                                                                                                                                                           ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) SIGMAS.Rd:17: Lost braces; missing escapes or markup?
    17 | Sigmahat =  (Y^{T} Y)/n;
       |                ^
checkRd: (-1) SIGMAS.Rd:18: Lost braces; missing escapes or markup?
    18 | Sigmahat_fit = (Y^{T}  P_fx  Y)/n;
       |                   ^
checkRd: (-1) matpower.Rd:17: Lost braces; missing escapes or markup?
    17 | The function computes M^{power} for a symmetric matrix M. }
       |                         ^
checkRd: (-1) satisfaction.Rd:28: Lost braces
    28 | Della Valle E (2010) Della Valle E 2010 Analisi Multidimensionale dei Dati: la Qualit\'{a} del Lavoro nelle Cooperative Sociali. 
       |                                                                                        ^
checkRd: (-1) satisfaction.Rd:29: Lost braces
    29 | Unpublished thesis, Seconda Universit\'{a}  degli Studi di Napoli, Capua Italy.
       |                                        ^
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
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checkRd: (-1) MCbound.precalc1.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
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installed size is 20.0Mb
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installed size is 22.3Mb
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Specified C++11: please drop specification unless essential
checkRd: (-1) ess.Rd:14: Lost braces
    14 | \code{g} should take a vector input only. Ifcode{g} is \code{NULL}, \code{g} is set to be identity, which is estimation
       |                                                 ^
installed size is  7.4Mb
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Package suggested but not available for checking: ‘cmdstanr’
installed size is  5.9Mb
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'LazyData' is specified without a 'data' directory
checkRd: (-1) eigp.Rd:34: Escaped LaTeX specials: \&
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial version.
checkRd: (-1) mcvis.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) mcvis.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) get_mdgc.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^
Package suggested but not available for checking: ‘RGtk2’
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checkRd: (-1) mdp_example_forest.Rd:36: Lost braces; missing escapes or markup?
    36 | Let {1, ... S} be the states of the forest. the Sth state being the oldest.
       |     ^
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GNU make is a SystemRequirements.
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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
       |     ^
checkRd: (-1) strings-internal.Rd:21: Lost braces
    21 | code{checkFuzzy}: check for "close" string matches
       |     ^
installed size is 52.8Mb
  sub-directories of 1Mb or more:
    libs  51.5Mb
'LazyData' is specified without a 'data' directory
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
ADPopSel: no visible global function definition for ‘%dorng%’
ADRand: no visible global function definition for ‘%dorng%’
ADSSMod: no visible global function definition for ‘%dorng%’
ADTreatSel: no visible global function definition for ‘%dorng%’
ClustRand: no visible global function definition for ‘%dorng%’
EventPred: no visible global function definition for ‘%dorng%’
FutRuleNCores: no visible global function definition for ‘%dorng%’
MultAdj1NCores: no visible global function definition for ‘%dorng%’
MultAdj2NCores: no visible global function definition for ‘%dorng%’
MultAdj3NCores: no visible global function definition for ‘%dorng%’
Undefined global functions or variables:
  %dorng%
checkRd: (-1) MED.Rd:25: Lost braces
    25 | The vector of treatment assignments of length \eqn{n}. Must be coded as \eqn{\{0,1} {{0,1}}.
       |                                                                                     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 155.5Mb
  sub-directories of 1Mb or more:
    libs  154.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
installed size is  5.2Mb
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    libs   3.6Mb
'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 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
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    libs   5.4Mb
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
installed size is 129.7Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
checkRd: (-1) CVLasoelacox.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
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'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  6.2Mb
  sub-directories of 1Mb or more:
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    help   2.3Mb
checkRd: (-1) datagenerator.Rd:17: Lost braces; missing escapes or markup?
    17 | Returns data frame with \code{n*K} rows (if \code{n} is a scalar), or \code{sum(n)} rows (if \code{n} is a \code{K}-element vector). The data frame contains columns "y", "x1", \dots, "x_{p-1}" and "group" if \code{family="gaussian"}, \code{"binomial"} or \code{"poisson"}; or contains columns "time", "status", "x1", \dots, "x_{p-1}" and "group" if \code{family="cox"}.
       |                                                                                                                                                                                           ^
checkRd: (-1) datagenerator.Rd:17: Lost braces; missing escapes or markup?
    17 | Returns data frame with \code{n*K} rows (if \code{n} is a scalar), or \code{sum(n)} rows (if \code{n} is a \code{K}-element vector). The data frame contains columns "y", "x1", \dots, "x_{p-1}" and "group" if \code{family="gaussian"}, \code{"binomial"} or \code{"poisson"}; or contains columns "time", "status", "x1", \dots, "x_{p-1}" and "group" if \code{family="cox"}.
       |                                                                                                                                                                                                                                                                                                                                        ^
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data       3.0Mb
    examples  10.3Mb
checkRd: (-1) rland.graph.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
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Packages suggested but not available for checking:
  'hgu133plus2.db', 'hgu133a.db', 'hgu95av2.db'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   4.9Mb
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.5Mb
installed size is 91.3Mb
  sub-directories of 1Mb or more:
    libs  90.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
  sub-directories of 1Mb or more:
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    help   2.0Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  12.6Mb
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    3.5Mb
    libs  22.2Mb
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.5Mb
'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  5.9Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs  20.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) readFastq.Rd:62: Lost braces
    62 | code{\link{readFasta}}.
       |     ^
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    lib    9.1Mb
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘midfielddata’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
checkRd: (-1) miive.Rd:120-239: Lost braces in \itemize; meant \describe ?
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   426 | \link{MIIVsem}{miivs}
       |               ^
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    60 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
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    62 | Kelly Sovacool, {sovacool@umich.edu}
       |                 ^
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    30 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
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    58 | Kelly Sovacool, {sovacool@umich.edu}
       |                 ^
checkRd: (-1) set_hparams_glmnet.Rd:16: Lost braces; missing escapes or markup?
    16 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
Package suggested but not available for checking: ‘gurobi’
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) milr.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
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'LazyData' is specified without a 'data' directory
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    14 |   \item{BROADBND}{Cellular data plan for a smartphone or other mobile device}{1 yes 2 no}
       |                                                                              ^
checkRd: (-1) acs2016.Rd:21: Lost braces
    21 |   \item{MHP}{Mobile home costs}{$, yearly}
       |                                ^
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  27.5Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  22.4Mb
installed size is 42.4Mb
  sub-directories of 1Mb or more:
    libs  41.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    libs        1.4Mb
    redengine  39.6Mb
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checkRd: (-1) sim.data.Rd:27: Lost braces in \enumerate; meant \describe ?
installed size is 164.7Mb
  sub-directories of 1Mb or more:
    libs  164.0Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   7.5Mb
Packages suggested but not available for checking: 'mixAK', 'BRugs'
Package unavailable to check Rd xrefs: ‘mixAK’
checkRd: (-1) sumKeepAttr.Rd:19: Lost braces
    19 |       (only relevant if code{x} has only one element).}
       |                             ^
Specified C++14: please drop specification unless essential
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
installed size is  5.4Mb
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    doc       2.4Mb
    extdata   1.2Mb
    libs      1.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
checkRd: (-1) PV.Rd:14: Lost braces
    14 | plausible value in turn; with code{rewrite=FALSE} a new data set is
       |                                   ^
installed size is  7.1Mb
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Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
Package which this enhances but not available for checking: ‘pbdMPI’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
installed size is 41.3Mb
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    libs  41.0Mb
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installed size is 11.9Mb
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    libs  11.6Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
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    libs   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is 40.6Mb
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    libs  40.3Mb
'LazyData' is specified without a 'data' directory
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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
       |                                                                                   ^
Package suggested but not available for checking: ‘IlluminaHumanMethylation450kmanifest’
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  'ueadata6', 'ueadata7', 'ueadata8'
installed size is 245.7Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘polars’
Package unavailable to check Rd xrefs: ‘polars’
Package listed in more than one of Depends, Imports, Suggests, Enhances:
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A package should be listed in only one of these fields.
Package suggested but not available for checking: ‘mlr3proba’
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   119 | Notes in Computer Science, ISBN 978-3-642-37139-4, pp. 756{770,
       |                                                           ^
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GNU make is a SystemRequirements.
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    21 | \item{fim}{the Fisher Information Matrix estimated by Monolix. fim={"sa", "lin"} (default="sa")}
       |                                                                    ^
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    62 | \item Probability of attribution of each unknown individual to each source $p_{u,s}$
       |                                                                               ^
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    69 |   \item{obj$M}{Number of total observations sum_{i=1}^N(pi)}
       |                                                 ^
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     6 | These function takes the output of pgls.iter and uses its list of objects { model fits, optimzations (e.g.AICc)} and performs a weighted average on the ctoefficients estimated in the former by weighting by the latter. The parameters can also optionally be converted to binary by specifying "binary=FALSE" or just running the alias wraper function for assessing evidence of variable importance (Burnham & Anderson 2000).
       |                                                                           ^
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    26 | d_ND(x,y) = sqrt{ k(x,x) - 2k(x,y) + k(y,y)}.
       |                 ^
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    34 | d_n(x,y) = 1 - k(x,y)/sqrt{ k(x,x)k(y,y)},
       |                           ^
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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)}
       |                     ^
Package required but not available: ‘doMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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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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    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
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    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
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    60 | \item{lnconst}{When inequality constraints are present, \code{lnconst} serves as an adjustment of code{lnInt}. It estimates the logarithm of the proportion of parameter space [0,1]^S that satisfies those inequality constraints, and the log integral term is given by \code{lnInt+lnconst}.
       |                                                                                                       ^
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    38 | The labels on the x-axis. Default is \code{Tree 1} to code{Tree n}.
       |                                                           ^
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    33 |         \item{LogTimes}{Magnification of {-log10(P-value)}; the default is
       |                                          ^
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    35 |     \item{LODTimes}{Magnification of {LOD score}; the default is 1.2.}
       |                                      ^
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    10 |            log E(Y_{t+1} | A_t = 0, I_t = 1) = alpha_0 + alpha_1 * time / total_T
       |                    ^
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    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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--- re-building ‘multipol.Rnw’ using Sweave
Loading required package: multipol
Loading required package: abind

Attaching package: ‘multipol’

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Loading required package: polynom
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Running 'texi2dvi' on 'multipol.tex' failed.
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!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
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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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--- re-building ‘cias.Rnw’ using Sweave

Attaching package: ‘multivator’

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--- finished re-building ‘cias.Rnw’

--- re-building ‘multivator.Rnw’ using Sweave

Attaching package: 'multivator'

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Error: processing vignette 'multivator.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'multivator.tex' failed.
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!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
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    74 | \code{\link{glm1path}}, \\code{\link{glm1}}, \code{\link{glm}}, \code{\link{family}}
       |                               ^
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    16 | {Provides a test of multivariate normality of a sample which does not require estimation of the nuisance parameters, the mean      vector and covariance matrix.  Rather, a sequence of transformations removes these nuisance parameters, resulting in a set of    sample matrices that are positive definite.  If, and only if the original data is multivariate normal, these matrices are       uniformly distributed on the space of positive definite matrices in the unit hyper-rectangle.  The package performs a goodness    of fit test of this hypothesis. In addition to the test, functions in the package give visualizations of the  support region    of positive definite matrices for p equals 2.
       | ^
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    22 | @source {Simulated to serve as an example}
       |         ^
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    15 | for(i in 1:50){
       |               ^
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    17 |   for(j in 1:50){
       |                 ^
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    31 | for(i in 1:20){
       |               ^
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    33 |   for(j in 1:20){
       |                 ^
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    10 | for(i in 1:200){
       |                ^
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    12 |   for(j in 1:200){
       |                  ^
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    26 | for(i in 1:20){
       |               ^
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    28 |   for(j in 1:20){
       |                 ^
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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 (2018-01-22)
    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. 
       |                                                                                                                                              ^
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    33 | A label vector of size n x 1 with elements in {1,2,...,K}
       |                                               ^
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    20 |  \item{las}{numeric in {0,1,2,3}; the style of chromosome labels. 0, always parallel to the track [default]; 1, always horizontal; 2, always perpendicular to the track; 3, always vertical.}
       |                        ^
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    56 | with a matrix response {y}. \code{x1} and \code{x2} are used as
       |                        ^
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   278 | \code{AgeFirstMarij}{Age participant first tried marijuana. Reported for participants aged 18 to 59 years.}
       |                     ^
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Package which this enhances but not available for checking: ‘jpndistrict’
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    44 | training sample), psi (the value of this observations Psihat(P_{n,B_n}^0)),
       |                                                                ^
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    49 | training sample), psi (the value of this observations Psihat(P_{n,B_n}^0)),
       |                                                                ^
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    19 |   Returns an object of class code{anova}.  These objects represent
       |                                  ^
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    14 |   \item{shape}{either \code{wide} or {long}. Default \code{wide}. See Details.}
       |                                      ^
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    75 |     \item{\code{GetTrace()}:}{retrieve all traced iterations. Returns a list with all the parameters set using the method SetTrace(). See description of snapshot{reference} method for a description of the parameters.  }
       |                                                                                                                                                                  ^
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    35 |               code{plot.type="circle"} and \code{x} is the output of \code{\link{kern.reg.circ.lin}}) or to \code{\link{lines3d}} (if \code{plot.type="circle"})
       |                   ^
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   148 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
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    73 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
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    21 | \code{MSM.fit} returns an object of class code{MSM.lm} or \code{MSM.glm}, depending on the input model.
       |                                               ^
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    25 | observation at current time step. It should return {xx} (the samples xt) and
       |                                                    ^
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    26 | {logww} (their corresponding log weight).}
       | ^
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    31 |    \item Finally, code{T} is rotated an angle \code{z} about its NEWEST z-axis.
       |                       ^
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    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
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    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
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    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |        ^
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    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |                  ^
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    35 |  function(x, lambda){const_hazard(x, lambda=100)}
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       |            ^
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Running ‘testthat.R’ [5s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("OhdsiReportGenerator")
  Loading required package: OhdsiReportGenerator
  Connecting using SQLite driver
  [ FAIL 3 | WARN 2 | SKIP 2 | PASS 417 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test-Helpers.R:89:1'
  • skip prediction report due to odd linux error (1):
    'test-PredictionReport.R:5:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-Backwards.R:9:5'): generatePresentationMultiple old works ──────
  Error in `testthat::skip_on_cran("Quarto not found so skipping old generate presentation multiple")`: unused argument ("Quarto not found so skipping old generate presentation multiple")
  ── Error ('test-Generate.R:8:5'): generatePresentation ─────────────────────────
  Error in `testthat::skip_on_cran("Quarto not found so skipping generate presentation")`: unused argument ("Quarto not found so skipping generate presentation")
  ── Error ('test-Generate.R:64:5'): generateFullReport ──────────────────────────
  Error in `testthat::skip_on_cran("Quarto not found so skipping generate full report")`: unused argument ("Quarto not found so skipping generate full report")
  
  [ FAIL 3 | WARN 2 | SKIP 2 | PASS 417 ]
  Error: Test failures
  Execution halted
  Closing database connection
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    15 | \item{service}{One of {"locations", "deployments", "deviceCategories", "devices",
       |                       ^
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    18 | \item{method}{One of {"get", "getTree"}}
       |                      ^
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    19 | (numeric) Result code from {0: done, -1: error, -2: fileExists}
       |                            ^
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    40 | In two sided or one sided interval estimation of \code{sigma^2} of one normal sample, {side} is a parameter used to control whether to compute two sided or one sided interval estimation. When computing the one sided upper limit, input \code{side = -1}; when computing the one sided lower limit, input \code{side = 1}; when computing the two sided limits, input \code{side = 0} (default).
       |                                                                                       ^
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/OpenMx.Rcheck/00install.out’ for details.
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Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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    14 | number of individual records. An \code{n} x code{2} dataframe can
       |                                                 ^
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    23 | N is computed from \code{p} length. M is code{10^4} by default.
       |                                              ^
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    24 | [GNU Command Line Standards]{http://www.gnu.org/prep/standards/standards.html}
       |                             ^
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    74 | matrix of covariates \code{X} and a vector of outcomes 'code{Y} to the \code{orf}
       |                                                             ^
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    44 | \item{print}{Level of verbosity in Fortran (may not be visible on all terminals); should be an integer between {range, range}, Default: 3}
       |                                                                                                                ^
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    41 | \item{start}{Starting point generation method, see vignettes for details; should be an integer between {range,range}, Default: 2}
       |                                                                                                        ^
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    90 | \item \link{optimise_OSLintervals}: {Approximates the optimal integration intervals. Uses the global
       |                                     ^
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    92 | \item \link{decompose_OSLcurve}: {Calculates component intensities for \strong{all} \code{record_type} measurements.
       |                                  ^
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    97 | fitting with the \emph{RSS_{K-1}} value of the previous fitting and calculates
       |                            ^
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    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                ^
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    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                                ^
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    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
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    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
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    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
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   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
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    15 | \item outcome: codes {I, P, R, NC, O, UH, UO, eUH, eUO, NE}
       |                      ^
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    24 | The input parameters given by the user are {I, P, R, NC, O, UH, UO} and
       |                                            ^
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    25 | the parameter 'e'. The parameter e is multiplied by {UH, UO} internally so as to
       |                                                     ^
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    26 | produce {eUH, eUO}.
       |         ^
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    14 | \item \strong{code:} one of the outcome codes {I, P, R, NC, O, UH, UO, UH, UO, NE}
       |                                               ^
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Problems with news in ‘NEWS.md’:
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    Changes
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   112 | \item `"{exp(estimate) * std.error}"
       |         ^
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       |         ^
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    11 |     \item{\code{roof_tile}}{a numeric vector, roof_tile}{dummy, roof made out of tiles =1}
       |                                                         ^
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    25 |     \item{\code{railways}}{a numeric vector, railways}{distance to nearest railway in meters}
       |                                                       ^
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    26 |     \item{\code{nature_SLD}}{a numeric vector, nature_SLD}{distance to nearest nature area in meters}
       |                                                           ^
Specified C++11: please drop specification unless essential
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    21 |   \item{...}{Other options including {type} which refers to the
       |                                      ^
Malformed Description field: should contain one or more complete sentences.
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    30 |     {\code{bin model}}{\cr Zhiqiu Hu, Zhiquan Wang, and Shizhong Xu (2012) An infinitesimal model for quantitative trait genomic value prediction. PloS ONE 7: e41336.}
       |                       ^
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Package required and available but unsuitable version: ‘ggkegg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: possible error in 'findInterval(c(i - 0.5, ': unused argument (checkSorted = FALSE) 
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/PathwaySpace.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
.find_nn_positions : .find_positions: possible error in
  findInterval(c(i - 0.5, i + 0.5), x_sorted, left.open = TRUE,
  rightmost.closed = TRUE, checkSorted = FALSE): unused argument
  (checkSorted = FALSE)
Running examples in ‘PathwaySpace-Ex.R’ failed
The error most likely occurred in:

> ### Name: circularProjection,PathwaySpace-method
> ### Title: Spatial Projection of Graph-Associated Signals
> ### Aliases: circularProjection,PathwaySpace-method circularProjection
> 
> ### ** Examples
> 
> # Load a demo igraph
> data('gtoy1', package = 'RGraphSpace')
> 
> # Create a new PathwaySpace object
> ps <- buildPathwaySpace(gtoy1, nrc = 100)
Validating arguments...
Validating the 'igraph' object...
Creating a 'PathwaySpace' object...
> # note: adjust 'nrc' to increase image resolution
> 
> # Set '1s' as vertex signal
> vertexSignal(ps) <- 1
> 
> # Create a 2D-landscape image
> ps <- circularProjection(ps)
Validating arguments...
Using circular projection...
Mapping 'x' and 'y' coordinates...
Running signal convolution...
Error in findInterval(c(i - 0.5, i + 0.5), x_sorted, left.open = TRUE,  : 
  unused argument (checkSorted = FALSE)
Calls: circularProjection ... .find_nn_positions -> lapply -> FUN -> .find_positions
Execution halted
Package required but not available: ‘reactome.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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checkRd: (-1) plotHeat.Rd:113: Lost braces
   113 | code{\link[patternize]{patPCA}}, as 'one' when visualizing single image or as 'multi' for multi
       |     ^
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/pbdMPI.Rcheck/00install.out’ for details.
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    31 |     \code{pars2[1]} {set the conditioning on non-extinction of the clade (1) or not (0) \cr \cr}
       |                     ^
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    32 |     \code{pars2[2]} {sets whether the likelihood is for the branching times (0) or the phylogeny (1) \cr \cr}
       |                     ^
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    33 |     \code{pars2[3]} {sets whether the first element of the branching times is the stem (1) or the crown (2) age \cr \cr}
       |                     ^
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    34 |     \code{pars2[4]} {sets whether the parameters and likelihood should be shown on screen (1) or not (0) \cr \cr}
       |                     ^
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    35 |     \code{pars2[5]} {sets which method should be used in the ode-solver. Default is 'lsoda'. See package deSolve for details. \cr \cr}
       |                     ^
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    36 |     \code{pars2[6]}{Sets the lower bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}
       |                    ^
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    37 |     \code{pars2[7]}{Sets the upper bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}  
       |                    ^
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Malformed Description field: should contain one or more complete sentences.
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No news entries found.
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--- re-building ‘tutorial.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.4/pcSteiner.Rcheck/vign_test/pcSteiner/vignettes/tutorial.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See tutorial.log for more info.
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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    42 | set {X, y} and cross-validation.
       |     ^
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    42 | set {X, y} and cross-validation.
       |     ^
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    63 | \cite{C18}{pdSpecEst} for more details. Note that this comes at the cost of increased computation time in comparison to one
       |           ^
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    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
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    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
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    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
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    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
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    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
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    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
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    94 | Method \code{"b"} was proposed by \doi{10.1016/0098-3004(95)00095-X}{Jian et al. (1996)} and
       |                                                                     ^
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    98 | \doi{10.1016/j.cageo.2008.10.011}{Hiemstra et al. (2009)}.
       |                                  ^
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   100 | Method \code{"d"} was developed by \doi{10.1007/s11004-012-9434-1}{Desassis & Renard (2012)}.
       |                                                                   ^
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Problems with news in ‘NEWS.md’:
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    Fixed issues
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    15 | A code{\link{marked_petrinet}}
       |       ^
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   100 | "Result": {
       |           ^
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       |                  ^
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    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
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    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^
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    11 | code{l2df}: convert list to data.frame
       |     ^
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       |     ^
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       |     ^
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       |     ^
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Problems with news in ‘NEWS.md’:
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    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                       ^
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    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                                 ^
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    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                                              ^
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   127 | rank skipped. For example {1, 0, 2, 1}, ranks the first and fourth items in
       |                           ^
installed size is 28.9Mb
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   125 | function serves for the purpose of spot-testing for any pre-specified {n,
       |                                                                       ^
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    19 |     \item{RNAMES}{code{row.names} if \code{x} is a matrix or data.frame,
       |                       ^
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   103 | {'ALL', 'AFF', 'UNAFF', 'ALL(QT)', 'ALL(NP)'}), A1 (Allele 1; usually minor),
       | ^
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    21 | delta_k = log(a_k - a_{k+1})
       |                       ^
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    29 | logical. If code{TRUE} all the q variable are assumed to have the same mean.
       |                 ^
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    15 | When \\code{y0} is not specified, the lowest value of the y-axis is used.}
       |            ^
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    24 | \\code{\\link[graphics]{par}}.}
       |       ^
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    24 | \\code{\\link[graphics]{par}}.}
       |                        ^
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   129 |  in factors are are shown as a special factor level code{"?"}. They can be
       |                                                         ^
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    29 | code{\link{help}}
       |     ^
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    32 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    20 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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Package unavailable to check Rd xrefs: ‘ggmanh’
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installed size is  5.3Mb
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    16 | Additional arguments are replaced with "{n} more".
       |                                         ^
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Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                              ^
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   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                                                         ^
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    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                   ^
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    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                              ^
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   106 | \item{lookupDF}{A data frame containing a lookup table for node labels. By default, {plot_scm} will use the PSN model names. If a lookup table containing the fields `Model` and `Alias` is provided, model names in `Model` will be replaced in the output plots by mtaching labels in `Alias`.}
       |                                                                                     ^
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Problems with news in ‘NEWS.md’:
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    34 | \item{bw}{function describing bandwidth selection (see ?gmm for alternatives). Standard is that the bandwidth depends on the sample length $T$ by $m(T)=T^{1/5}$.}
       |                                                                                                                                                           ^
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    94 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
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    95 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
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    81 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
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    82 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
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    14 | Number {25, 50, 75}
       |        ^
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    31 |   the weight vectors \bold{{w}^{i}} corresponds to class \eqn{i}{i}.
       |                                ^
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    33 | We set \eqn{{\bold{{w}}^{h}} = 0} and the parameters to be learned are the weight vectors \bold{{w}^{i}}
       |                                                                                                     ^
installed size is 19.4Mb
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installed size is 63.0Mb
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GNU make is a SystemRequirements.
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Problems with news in ‘NEWS.md’:
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    22 | the \code{conflict} argument of {powerjoin}'s join functions. \code{coalesce_xy()} is
       |                                 ^
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    67 | \item{by}{As in {dplyr}, but extended so user can supply a formula or a list
       |                 ^
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    79 | \item{keep}{A boolean for compatibility with {dplyr}, or a value among "left",
       |                                              ^
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    37 | only be used in the \code{x} and \code{y} arguments of {powerjoin} join functions. No
       |                                                        ^
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    26 | \item{model}{Determines of model fit is such that there are p_{it}s (model=1) or
       |                                                               ^
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   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
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   143 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
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   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
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   145 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
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   147 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each sujbects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’
Error(s) in re-building vignettes:
--- re-building ‘pQTLdata.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'EnsDb.Hsapiens.v75''

Quitting from pQTLdata.Rmd:125-153 [refdata]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'metadata': object 'EnsDb.Hsapiens.v75' not found
---
Backtrace:
    ▆
 1. ├─ensembldb::metadata(EnsDb.Hsapiens.v75)
 2. └─base::.handleSimpleError(...)
 3.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'pQTLdata.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'metadata': object 'EnsDb.Hsapiens.v75' not found
--- failed re-building ‘pQTLdata.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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     8 | Given an hypothetical value of effect size, {PRDA} performs a prospective
       |                                             ^
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    22 | In {PRDA} there are two main functions:
       |    ^
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    51 | Alternatively, {PRDA} allows users to specify a distribution of plausible
       |                ^
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    39 | \item wrapping a function argument in two curly braces (e.g. `{{arg}} > 0) means
       |                                                               ^
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    20 | the (pre)registration form specification (in {preregr} format), see the
       |                                              ^
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    23 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
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    26 | For an introduction to working with {preregr} (pre)registrations,
       |                                     ^
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    75 | This function creates an R Markdown template from a {preregr}
       |                                                     ^
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    77 | Sheet holding the (pre)registration form specification (in {preregr}
       |                                                            ^
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    81 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
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    20 | The user does not put these directly into this function, but rather uses code{ode} in the \code{deSolve} package.
       |                                                                              ^
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    20 | \item{lower.v}{logical, if TRUE the specified percentile.value is the upper limit for the mean (or the median or the mode) at the specified confidence level (percentile). If {FALSE} the specified percentile.value is the lower limit for the mean (or the median or the mode) at the specified confidence level (percentile). The default is FALSE.}
       |                                                                                                                                                                               ^
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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    91 |     \code{OSME} \tab Output-oriented scale-mix efficiency score \emph{(code{orientation = "out"})}\cr
       |                                                                            ^
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     9 |                 \item{CD}{}{Character disorder scale score}
       |                            ^
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    40 |   by the code{kcachegrind} program available on some operating
       |              ^
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    32 | \item{global}{Logical. If \code{TRUE} ({default}), a global density plot is
       |                                        ^
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    12 | \item{model}{the item model to use. Accepts \code{grm} or {gpcm}.}
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    15 | \item{value}{code{data.frame} or code{data.table}}
       |                  ^
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    15 | \item{value}{code{data.frame} or code{data.table}}
       |                                      ^
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    21 | response variable. Vector of length emph{n}, assumed to be quantitative.
       |                                         ^
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    20 | Implementation of the {SnowballC} stemmer. Note that punctuation and capital letters 
       |                       ^
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    20 | Implementation of the {SnowballC} stemmer. Note that punctuation and capitals letters 
       |                       ^
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     7 | See the {rfeel} package now: http://github.com/ColinFay/rfeel}
       |         ^
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    20 | See the {rfeel} package now: http://github.com/ColinFay/rfeel
       |         ^
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    43 | S{Sulewski, P. (2020). \emph{Normal Distribution with Plasticizing Component,} Communications in Statistics ? Theory and Method 51(11), 3806-3835.}
       |  ^
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    14 | The data set from {AbouRizk, S.M., Halpin, D.W., Wilson, J. R. (1994). \emph{Fitting beta distributions based on sample data.} Journal of Construction Engineering and Management 120(2), 288–305.}
       |                   ^
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    14 | The data set presents the height of 99 five-year-old British boys in cm downloaded from {http://www.mas.ncl.ac.uk/njnsm/medfac/docs/intro.pdf.}
       |                                                                                         ^
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    14 | The first data set from {Sulewski, P. (2017) \emph{A new test for independence in 2x2 contingency tables,} Acta Universitatis Lodziensis. Folia Oeconomica, 4(330), 55–75}
       |                         ^
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    14 | The third data set from {Sulewski, P. (2021). \emph{Logarithmic Minimum Test for Independence in Three Way Con-tingency Table of Small Sizes.} Journal of Statistical Computation and Simulation 91(13), 2780-2799}
       |                         ^
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    39 |                                                         continuous = function(Xytrain){ #defalt is OLS regression
       |                                                                                       ^
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    43 |                                                         incidence = function(Xytrain){ #default is logistic regression
       |                                                                                      ^
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    48 |                                                         survival = function(Xytrain){ #default is Weibull regression
       |                                                                                     ^
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    66 |                                         function(mod, Xyleftout){
       |                                                                 ^
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    74 |                                         function(results, indices_1_1, indices_0_0, indices_0_1, indices_1_0){
       |                                                                                                              ^
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    20 | @Article{Bloemberg2010,
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    30 | Article{Wehrens2015,
       |        ^
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    62 | \item{yi}{Numeric vector of length code{k} with observed effect size
       |                                        ^
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    65 | \item{vi}{Numeric vector of length code{k} with sampling variances.}
       |                                        ^
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     5 | \title{PubMed wordcloud using function 'wordcloud' of package {wordcloud}}
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    32 | This function just call 'wordcloud' from package {wordcloud}. See package {wordcloud} for more details about the parameters.
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    32 | This function just call 'wordcloud' from package {wordcloud}. See package {wordcloud} for more details about the parameters.
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    10 | \format{the \code{PvarQuantileDF} is a \code{data.frame} with fields \code{prob} an {Qaunt}. 
       |                                                                                     ^
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    42 | \item{no_zi_idx}{List of pairs {(i, j)} where zero inflation is not allowed. To
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    35 | \item{no_zi_idx}{List of pairs {(i, j)} where zero inflation is not allowed. To
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    10 |   \item{listRanef}{{\emph{ranef(model)}} object where {\emph{model}} is an { \emph{lmer}} object.}
       |                                                                            ^
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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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installed size is  9.3Mb
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installed size is 123.6Mb
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GNU make is a SystemRequirements.
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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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GNU make is a SystemRequirements.
installed size is  5.1Mb
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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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installed size is  5.7Mb
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Malformed Description field: should contain one or more complete sentences.
installed size is  5.4Mb
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Error(s) in re-building vignettes:
--- re-building ‘ragtop_convertibles_in_r.Rmd’ using rmarkdown

Quitting from ragtop_convertibles_in_r.Rmd:424-461 [twitter_cb_via_BondValuation]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (index_LIPD >= 1) ...`:
! argument is of length zero
---
Backtrace:
    ▆
 1. └─BondValuation::AnnivDates(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ragtop_convertibles_in_r.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘ragtop_convertibles_in_r.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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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 | where the vector dimension is 2^{response.number}.}
       |                                 ^
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    48 | \\env{$XDG_CACHE_HOME} if defined
       |      ^
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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. }
       |                           ^
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    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. }
       |                              ^
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    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}}.}
       |                                ^
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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}
       |                             ^
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checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
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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  7.2Mb
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installed size is 13.8Mb
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installed size is  5.4Mb
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GNU make is a SystemRequirements.
installed size is 65.2Mb
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GNU make is a SystemRequirements.
installed size is 66.1Mb
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GNU make is a SystemRequirements.
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installed size is 14.3Mb
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Specified C++11: please drop specification unless essential
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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}
       |                   ^
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    31 | \item post retirement: {a4, lambda4}
       |                        ^
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    29 | if(resolution == "300m"){
       |                         ^
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    33 | if(resolution == "1km"){
       |                        ^
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checkRd: (-1) Rchoice.Rd:159: Lost braces; missing escapes or markup?
   159 |  \code{ranp}. If the parameters are assumed to be normally distributed \eqn{\beta_i ~ N(\beta, \Sigma)}, then the random parameter are constructed as: \deqn{\beta_{ir}=\beta+L\omega_{ir}} where \eqn{LL'=\Sigma} and \eqn{\omega_{ir}} is the {r}-th draw from standard normal distribution for individual \eqn{i}. 
       |                                                                                                                                                                                                                                                 ^
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Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
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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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installed size is  7.6Mb
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Package suggested but not available for checking: ‘hgu133plus2.db’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/Rcplex.Rcheck/00install.out’ for details.
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Problems with news in ‘NEWS.md’:
No news entries found.
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/RcppMeCab.Rcheck/00install.out’ for details.
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installed size is  6.9Mb
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Specified C++14: please drop specification unless essential
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    45 | there is a linear map \eqn{f:R^N} to {R^n} such that
       |                                      ^
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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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Installation failed.
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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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    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}.)
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}} and \code{\link[graphics]{matplot}}). 
       |                                ^
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    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}}.
       |                                ^
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    26 | {Pd = sqrt(sum(p_j*(x_j-mean(x_p))/4.5)^2)}
       | ^
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    37 | The set of divisors is formed by the odd numbers, that is {1,3,..,2n+1}.
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   121 | \item Single or multiple covariates, time varying: For \code{CovSnd}, \code{CovRec}, or \code{CovInt}, an \code{m} by \code{p} by {n} array whose respective dimensions index time (i.e., event number), covariate, and actor.  For \code{CovEvent}, a \code{m} by \code{p} by \code{n} by \code{n} array, whose dimensions are analogous to the previous case.
       |                                                                                                                                   ^
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    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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    44 | ## chunk "item 1" {
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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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    52 |     \item B. Bollob\'{a}s, 1998.  \emph{Modern Graph Theory}.  Springer.
       |                      ^
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    44 | \item{perl}{Use perl-like regex? Defaults to {FALSE}.}
       |                                              ^
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    39 | \code{"fastfloyd"}{ (default) uses an iterative variant of the Floyd-Warshall algorithm, in which the check of consistency of the current observation with a given cluster is done in a single step of the Floyd-Warshall algorithm. Much faster than \code{"floyd"}.}
       |                   ^
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    41 | \code{"floyd"}{ uses the algorithm described in Crawford and Pendakur (2013): at each step the complete Floyd-Warshall algorithm is run to check whether each cluster can accomodate the current observation.}
       |               ^
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Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg38’

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    12 | \item{use_wd}{logical - If TRUE, the history will be prepended by setwd({'users current working directory'}). This function will set the script's working directory to
       |                                                                         ^
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    76 | \\code{\link{fs_auth}} \code{\link{fs_browse}}
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    21 | {data}{Population of data}
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    23 | {data}{Sample of data}
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   450 | if (reticulate::py_module_available("geomstats")) {
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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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    35 |    \item{pam_cluster_64_7_5715},{N=64, seven clusters with 5715 vectors per
       |                                 ^
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checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
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"}
       |                                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
'LazyData' is specified without a 'data' directory
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  23.7Mb
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 12.0Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   9.4Mb
'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-arm64/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.
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
installed size is 56.0Mb
  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 27.8Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
installed size is 44.8Mb
  sub-directories of 1Mb or more:
    libs  44.2Mb
'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   8.8Mb
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 161.2Mb
  sub-directories of 1Mb or more:
    libs  160.2Mb
GNU make is a SystemRequirements.
installed size is 71.6Mb
  sub-directories of 1Mb or more:
    include   7.3Mb
    lib      37.7Mb
    libs     26.2Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘reactome.db’
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
checkRd: (-1) basic_GS.Rd:42: Lost braces; missing escapes or markup?
    42 | \eqn{L} and {U} are strictly lower/upper triangular matrix respectively.
       |             ^
checkRd: (-1) basic_SOR.Rd:45: Lost braces; missing escapes or markup?
    45 | \eqn{L} and {U} are strictly lower/upper triangular matrix respectively.
       |             ^
checkRd: (-1) basic_SSOR.Rd:45: Lost braces; missing escapes or markup?
    45 | \eqn{L} and {U} are strictly lower/upper triangular matrix respectively.
       |             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rnaturalearthhires’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
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  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
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-arm64/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 ?
installed size is 143.2Mb
  sub-directories of 1Mb or more:
    libs  142.8Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘bridgestan’
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-arm64/results/4.4/RmecabKo.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   5.7Mb
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfft-class.Rd:65: Lost braces
    65 | code{dfft(object, index=0)} on an object created from a forecast with 
       |     ^
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R          1.0Mb
    libs       1.1Mb
    minizinc   3.3Mb
Specified C++11: please drop specification unless essential
installed size is 44.3Mb
  sub-directories of 1Mb or more:
    libs  43.3Mb
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
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 ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 84.5Mb
  sub-directories of 1Mb or more:
    libs  83.9Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
GNU make is a SystemRequirements.
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    libs  30.2Mb
checkRd: (-1) myTarGetClientList.Rd:33: Lost braces
    33 | {MyTarget API Documenation}{https://target.my.com/doc/api/detailed/#resource_agency_clients}
       |                            ^
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
Package suggested but not available for checking: ‘rnaturalearthhires’
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
checkRd: (-1) rncl.Rd:53-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:59-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:65-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:73-78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:80-84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:86-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:92-93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:98-99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:101-102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:107-110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:112-115: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:117-119: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:121-124: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
Packages which this enhances but not available for checking:
  'pbdMPI', 'Rmpi'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
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  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is 119.5Mb
  sub-directories of 1Mb or more:
    extdata    2.0Mb
    libs     117.3Mb
'LazyData' is specified without a 'data' directory
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    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
checkRd: (-1) fData.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) outliergram.Rd:45-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:55-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:59-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:63-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:66-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) outliergram.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) outliergram.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R  11.4Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  18.3Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 40.5Mb
  sub-directories of 1Mb or more:
    libs  40.3Mb
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'beadarrayExampleData',
  'illuminaHumanv3.db'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 95.9Mb
  sub-directories of 1Mb or more:
    libs  95.1Mb
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 22.6Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
Specified C++11: please drop specification unless essential
installed size is 38.8Mb
  sub-directories of 1Mb or more:
    libs  38.2Mb
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  9.7Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              5.6Mb
    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
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  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'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 17.5Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
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-arm64/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
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    data   2.7Mb
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installed size is 16.0Mb
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    help   1.0Mb
    libs   9.6Mb
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 ?
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checkRd: (-1) rp.pos.Rd:43: Lost braces in \itemize; meant \describe ?
installed size is 88.8Mb
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GNU make is a SystemRequirements.
installed size is  8.0Mb
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installed size is 27.7Mb
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installed size is  5.5Mb
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'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  5.3Mb
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installed size is  9.9Mb
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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
       |                                                              ^
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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.
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checkRd: (-1) check_node.Rd:11: Lost braces
    11 | \item{x}{\\code{list}, the node to check}
       |                ^
installed size is 33.6Mb
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'LazyData' is specified without a 'data' directory
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installed size is 103.5Mb
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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) 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 ?
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checkRd: (-1) lateformeeting.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) regrad.Rd:46: Lost braces; missing escapes or markup?
    46 |  \item \code{x-axis} {1st column: The names of the different institutions}
       |                      ^
checkRd: (-1) regrad.Rd:47: Lost braces; missing escapes or markup?
    47 |  \item \code{y-axis} {2nd column: The value to show completeness}
       |                      ^
Package suggested but not available for checking: ‘rnaturalearthhires’
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 ?
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Package suggested but not available for checking: ‘polars’
installed size is  5.0Mb
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Package unavailable to check Rd xrefs: ‘polars’
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  5.7Mb
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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",
       |                                 ^
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installed size is 20.0Mb
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GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/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_Outputfile’,
    ‘R_TempDir’, ‘R_Visible’, ‘getInputHandler’, ‘ptr_R_Busy’,
    ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’, ‘ptr_R_ReadConsole’,
    ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’, ‘ptr_R_WriteConsole’,
    ‘ptr_R_WriteConsoleEx’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
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installed size is 28.6Mb
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installed size is  7.2Mb
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    libs   6.2Mb
installed size is  6.1Mb
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    libs   5.5Mb
Specified C++11: please drop specification unless essential
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installed size is 10.2Mb
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    libs   9.5Mb
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Package suggested but not available for checking: ‘INLA’
installed size is  6.4Mb
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    R      4.7Mb
    help   1.5Mb
Specified C++11: please drop specification unless essential
installed size is 46.6Mb
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installed size is 12.5Mb
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    libs  11.8Mb
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'LazyData' is specified without a 'data' directory
installed size is 311.3Mb
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    R       2.0Mb
    doc     4.7Mb
    libs  303.8Mb
GNU make is a SystemRequirements.
installed size is 94.7Mb
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    libs  94.4Mb
GNU make is a SystemRequirements.
installed size is 57.3Mb
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    libs  56.6Mb
GNU make is a SystemRequirements.
installed size is 49.5Mb
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    exec   1.7Mb
    lib   34.2Mb
    libs  11.7Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
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
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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
       |                                                     ^
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installed size is 28.7Mb
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installed size is 26.7Mb
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GNU make is a SystemRequirements.
Package unavailable to check Rd xrefs: ‘Rglpk’
'LazyData' is specified without a 'data' directory
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                              ^
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                                    ^
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    libs   4.9Mb
installed size is 11.4Mb
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GNU make is a SystemRequirements.
checkRd: (-1) tw_options.Rd:22: Lost braces in \itemize; meant \describe ?
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Specified C++11: please drop specification unless essential
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installed size is 122.6Mb
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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 29.4Mb
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    doc    7.8Mb
    libs  20.7Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 160.3Mb
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    data    1.5Mb
    libs  158.0Mb
GNU make is a SystemRequirements.
Running examples in ‘RtsEva-Ex.R’ failed
The error most likely occurred in:

> ### Name: tsEvaTransformSeriesToStatSeasonal_ciPercentile
> ### Title: tsEvaTransformSeriesToStatSeasonal_ciPercentile
> ### Aliases: tsEvaTransformSeriesToStatSeasonal_ciPercentile
> 
> ### ** Examples
> 
> timeAndSeries <- ArdecheStMartin
> timeStamps <- ArdecheStMartin[,1]
> series <- ArdecheStMartin[,2]
> #select only the 5 latest years
> yrs <- as.integer(format(timeStamps, "%Y"))
> tokeep <- which(yrs>=2015)
> timeStamps <- timeStamps[tokeep]
> series <- series[tokeep]
> timeWindow <- 365 # 1 year
> percentile <- 90
> result <- tsEvaTransformSeriesToStatSeasonal_ciPercentile(timeStamps,
+ series, timeWindow, percentile)
computing trend...
trend on the 90 percentile
computing trend seasonality...
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.
computing the slowly varying 90th percentile...
computing standard deviation seasonality...
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$trendSeries)
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.
installed size is  7.6Mb
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    extdata   1.0Mb
    libs      5.3Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.5Mb
'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  6.3Mb
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installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) 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) }
       |                                                                                   ^
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Problems with news in ‘NEWS.md’:
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    15 | \code{x} filtered result (y 1_{|y|>t}).
       |                               ^
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    15 | \code{x} filtered result (y 1_{|y|>t}).
       |                               ^
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    31 | This period can be either {"month", "week", "day"}, 
       |                           ^
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    32 | {"months", "weeks", "days"} or
       | ^
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    33 | {12, 52, 365}. This function creates a new time series with the required 
       | ^
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     6 |  emph{Single Interior Knot} at the MSE Optimal m-Extent of Shrinkage. The
       |      ^
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    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                   ^
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    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                                 ^
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    13 | \item{dataY}{Vector of length n containing {0, 1}-valued observations of the dependent variable y.}
       |                                            ^
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    10 | \item{fit}{an object of class{lm}, i.e. the output from \code{\link{lm}}.}
       |                              ^
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    37 |         class {StatHMMR}).
       |               ^
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installed size is  5.3Mb
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GNU make is a SystemRequirements.
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    64 |    \item{the dependence parameter \code{dep} or the vector of dependence parameters \code{dep}. When missing, these coefficients are obtained from independent standard uniform sampling.
       |         ^
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    66 |    \item{the list \code{asy} of asymmetric weights \eqn{\beta_{i,b}} for \eqn{b \in B}  and \eqn{i \in b}. When missing, these coefficients are obtained from independent standard uniform sampling followed by renormalization in order to satisfy the sum-to-one constraints.}
       |         ^
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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    42 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
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    83 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
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    29 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
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    72 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
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    Updated help pages with examples
    Updated conjugate model sampler
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    51 |   code{\link[deSolve]{events}}
       |       ^
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   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       | ^
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   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       |                                              ^
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    29 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
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    30 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
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    32 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
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    33 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
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    35 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
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    36 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
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    19 | \item{ndim}{the maximum dimension of the space which the data are to be represented in; must be in {1, 2, \ldots, n-1}.}
       |                                                                                                    ^
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    18 | \item{distance_method}{A character string indicating which correlationcoefficient (or covariance) is to be computed. One of "pearson", "spearman" (default), or "cosine". Domain: {spearman, pearson, cosine}. Default: spearman. Format: character.}
       |                                                                                                                                                                                   ^
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    30 | \item{smoother}{\code{principal_curve} parameter; choice of smoother. Domain: {smooth_spline, lowess, periodic_lowess}. Default: smooth_spline. Format: character.}
       |                                                                               ^
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     5 | \title{Get location of script in a fashion analagous to ${BASH_SOURCE[0]}}
       |                                                          ^
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    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
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    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                                         ^
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     7 | url{https://gist.github.com/dgrtwo/eb7750e74997891d7c20}
       |    ^
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    59 | (including ]code{forcelist} variables) that can be used to form tables.}
       |                 ^
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    17 | \item{c}{denotes the expected range of eqn{f} .}
       |                                           ^
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    17 | \item{u}{numeric, maximum number of projections. The default is 10. This is used for \code{type="seed1"}, \code{type="seed2"} and {tyepe="pls"}.}
       |                                                                                                                                   ^
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--- 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:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
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--- re-building ‘SemiCompRisks.ltx’ using tex
Error: processing vignette 'SemiCompRisks.ltx' failed with diagnostics:
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!pdfTeX error: pdflatex (file bbm8): Font bbm8 at 600 not found
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   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
       |                                                               ^
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       |                                                                                          ^
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   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                              ^
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   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                                                     ^
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   127 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
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       |                                          ^
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       |                                          ^
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       |                                          ^
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    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.
       |                                                                                                                                                                                   ^
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    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.
       |                                                                                                                                                                                                                                                                                                        ^
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    15 | \item{plot}{Should the results be plotted? (/code{TRUE/FALSE})}
       |                                                  ^
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       |                                                     ^
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       |                              ^
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    37 |     See code{\link{shiftrPermBinary}} function and the respective example.
       |             ^
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    14 | \item{choices}{link{pickCheckboxInput} choices list.}
       |                    ^
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    19 | See the {gargle} package to manage authentication, and especially
       |         ^
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    20 | \href{https://gargle.r-lib.org/articles/articles/managing-tokens-securely.html}{this vignette from {gargle} package} to manage the process.
       |                                                                                                    ^
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     7 | \title{Modify {shinymanager} labels to use custom text}
       |               ^
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     5 | \title{Use {shinymanager} labels}
       |            ^
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    13 | A string `"{tagId}-shinyreforms-validation"`.
       |            ^
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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)}
       |                                                                                                                   ^
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    59 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.'
       |                       ^
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    36 |   \code{drr} {is Rosin - Rammler probability density function}\cr
       |              ^
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    37 |   \code{urr} {is Rosin - Rammler cumulative distribution function (CDF) representing undersize mass fraction}\cr
       |              ^
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    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
       |              ^
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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))}
       |                                                     ^
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    25 | convert_xlsx_to_csv<-function(xlsx_file){
       |                                         ^
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    33 |   for (i in Sheetnames) {
       |                         ^
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    67 |  \code{within.SD} to be extremely small (e.g., $1 * 10^{-7}$) and all corresponding correlations in matrix
       |                                                        ^
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    15 | For example, in latex it would take "2" and output "{\\bf 2}"; in html
       |                                                     ^
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    20 |   \item{distr.type}{school district type (constructed for illustration purposes; (values={"A", "B", "C", "D"})).}
       |                                                                                          ^
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    61 | \item{replacementUnitsFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "replacementUnits.csv"}
       |                                                                    ^
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    63 | \item{subUnitTableFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "subUnitTable.csv"}
       |                                                                ^
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    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                  ^
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    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                                                                                  ^
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    26 | \item{alpha}{The eqn{\\alpha} error used to compute the \eqn{100*(1-\\alpha)\%} confidence interval}
       |                     ^
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    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |     ^
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    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |                 ^
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    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                            ^
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    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                                        ^
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GNU make is a SystemRequirements.
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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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    24 | sum(x' V^{-1} (y - x beta)) = 0 as the covariance V tends from V[, , 1] +
       |          ^
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     6 | A subset of world.cities{maps}. Extracted in order to shink number of dependencies. 
       |                         ^
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    17 |     \item{\code{resp}}{a factor indicating the transport mode choice, and \code{B} denotes taking the bus, code{D} denotes driving one's own vehicle, \code{F} denotes getting a ride with a friend, \code{O} denotes other, and \code{W} denotes walking}
       |                                                                                                                ^
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/smer.Rcheck/00install.out’ for details.
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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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--- re-building ‘smm.Rnw’ using Sweave
Error: processing vignette 'smm.Rnw' failed with diagnostics:
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LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘smm.Rnw’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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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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Problems with news in ‘NEWS.md’:
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checkRd: (-1) SnakesAndLaddersGame.Rd:25: Lost braces; missing escapes or markup?
    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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   101 | data. Default value for code{which} is \code{2:4} if \code{p>1}, otherwise
       |                             ^
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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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Warning in microbenchmark::get_nanotime() :
  less accurate nanosecond times to avoid potential integer overflows

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

Probably some imports need to be declared in the NAMESPACE file.
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    20 | \code{a1, a2, a3}, then code{sdf_explode(df, a)} will produce output with each record replicated
       |                             ^
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    54 | \item{triangle=TRUE}{Input \code{rows} and {cols} represent lower
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    59 | \item{triangle=FALSE}{Input \code{rows} and {cols} represent a full
       |                                             ^
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     5 | \title{Solve the equation X = AQ^{-1}t(A) under permutations}
       |                                  ^
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    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |    ^
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    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |             ^
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    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                      ^
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    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                   ^
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    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                            ^
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    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                                     ^
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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    43 | \env{select}{
       |             ^
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    47 | \env{printit}{
       |              ^
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    50 | \env{stage}{
       |            ^
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Package suggested but not available for checking: ‘INLA’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/spaths.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘INLA’
installed size is 95.1Mb
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    40 |   matrix and weight matrix (plus a matrix with {eID} identifiers
       |                                                ^
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GNU make is a SystemRequirements.
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
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  '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.
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  'spatstat.data', 'spatstat.univar', 'spatstat.sparse',
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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
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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.
       |                                                              ^
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    Roadmap of specklestar package
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    23 |       p(y|ens) = 1 / K * sum {dnorm(y, z.i, s)} \cr
       |                              ^
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    25 | The default compilation is that of \ code {speech_build (., compiler = TRUE}).
       |                                           ^
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    61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc}, 
       |                                                   ^
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    14 | code{adaptIntegrateBallPolar()} will likely miss these abrupt changes and give
       |     ^
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   118 | rfcv{randomForest} and gbm
       |     ^
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   108 | variable and anisotropy parameters. see notes vgm{gstat} for details.
       |                                                  ^
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Problems with news in ‘NEWS.md’:
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    updates of 10th May 2021
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    42 | and a matching \code{Qres} list attribute if {Q} was given.
       |                                              ^
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   158 |   the matrix of regressors, of order \emph{(Nxp_{g})}. Moreover, 
       |                                                 ^
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    67 | \item{het}{default {FALSE}: if {TRUE} uses the methods 
       |                    ^
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    67 | \item{het}{default {FALSE}: if {TRUE} uses the methods 
       |                                ^
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    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                   ^
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    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                              ^
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    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                                             ^
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   248 | and code{port} arguments of sqldf.
       |         ^
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    55 |     \code{tol}{ - a small, positive scalar that determines when iterations 
       |               ^
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    60 |     \code{maxiter}{ - an integer denoting the maximum limit on the number of 
       |                   ^
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    63 |     \code{trace}{ - a logical variable denoting whether some of the intermediate 
       |                 ^
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    67 |     \code{intermed}}{ - a logical variable denoting whether the intermediate 
       |                     ^
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   134 |       along with the corresponding log-likelihood value.  When the code{objfn} is not specified it will return the fixed-point residual instead of the objective function values. 
       |                                                                        ^
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    83 |   \item \code{X1_sto_shared} (default \code{TRUE}): {logical}; if \code{TRUE}, the stochastic environmental effect included in the environmental effect x1 will be shared between individuals. If \code{FALSE}, each individual will experience a different stochastic environmental effect x1 (i.e. a new stochastic environmental effect is generated for each individual).
       |                                                     ^
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GNU make is a SystemRequirements.
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Problems with news in ‘NEWS.md’:
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   100 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
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   109 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
Problems with news in ‘NEWS.md’:
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    42 |     always use code{"none"}.}
       |                    ^
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    25 |     always use code{"none"}.}
       |                    ^
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    20 | \code{Fsts}{a matrix of pairwise Fst values between populations}
       |            ^
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    21 | \code{Pvalues}{a matrix of p-values for each of the pairwise Fst values containined in the 'Fsts' matrix}
       |               ^
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    22 | \code{Bootstraps}{a dataframe of each Fst value generated during Bootstrapping and the associated confidence intervals}
       |                  ^
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    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                ^
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    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                                           ^
installed size is 17.0Mb
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GNU make is a SystemRequirements.
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    27 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
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    34 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
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    67 |    \item $S_{275-295}$ slope between 275 and 295 nm calculated with nonlinear regression
       |             ^
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    68 |    \item $S_{350-400}$ slope between 350 and 400 nm calculated with nonlinear regression
       |             ^
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    69 |    \item $S_{300-700}$ slope between 275 and 295 nm calculated with nonlinear regression
       |             ^
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    70 |    \item SR slope ratio, calculated by $S_{275-295}$/$S_{350-400}$
       |                                           ^
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    70 |    \item SR slope ratio, calculated by $S_{275-295}$/$S_{350-400}$
       |                                                         ^
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    71 |    \item E2:E3 ratio $a_{250}$/$a_{365}$
       |                         ^
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    71 |    \item E2:E3 ratio $a_{250}$/$a_{365}$
       |                                   ^
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    72 |    \item E4:E6 ratio $a_{465}$/$a_{665}$
       |                         ^
checkRd: (-1) abs_parms.Rd:72: Lost braces; missing escapes or markup?
    72 |    \item E4:E6 ratio $a_{465}$/$a_{665}$
       |                                   ^
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    73 |    \item $a_{254}$ absorbance at 254 nm
       |             ^
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    74 |    \item $a_{300}$ absorbance at 300 nm
       |             ^
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   229 |   \item{report}{a character string containing only elements of {\code{"v"}, \code{"c"}, \code{"s"},\code{"t"}, \code{"p"}, \code{"*"}} that determines whether, and in which order, variable names (\code{"v"}), coefficients (\code{"c"}), standard errors/confidence intervals (\code{"s"}), test statistics (\code{"t"}) and p-values (\code{"p"}) should be reported in regression tables. If one of the aforementioned letters is followed by an asterisk (\code{"*"}), significance stars will be reported next to the corresponding statistic.}
       |                                                                ^
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   246 |   \item{table.placement}{a character string containing only elements of {\code{"h"}, \code{"t"},\code{"b"}, \code{"p"}, \code{"!"}, \code{"H"}} that determines the table placement in its LaTeX floating environment.}
       |                                                                         ^
Package suggested but not available for checking: ‘starsdata’
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checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
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    16 |     \code{Side} \tab {Side of vehicle: code{1}=right or \code{2}=left}\cr
       |                                            ^
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    22 | \code{statcan_data()} function has 2 arguments to fulfill to get data: {tableNumber} & {lang}.
       |                                                                        ^
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    22 | \code{statcan_data()} function has 2 arguments to fulfill to get data: {tableNumber} & {lang}.
       |                                                                                        ^
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    18 | The \code{statcan_search()} function has 2 arguments to fulfill to find a database: {keywords} and {lang}.
       |                                                                                     ^
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    18 | The \code{statcan_search()} function has 2 arguments to fulfill to find a database: {keywords} and {lang}.
       |                                                                                                    ^
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installed size is  9.8Mb
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Package suggested but not available for checking: ‘asreml’
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Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: ‘networksis’
unable to reach CRAN

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
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    48 | Pooled standard deviation= \code{sp} = sqrt{((n1 - 1) sigma1^2 +(n2 - 1) sigma2^2) / (n1 + n2 - 2)}
       |                                            ^
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installed size is 25.5Mb
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    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
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    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
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    10 |   \item{semilandmark.pattern}{a regular expression pattern passed to \code{sub()} for identifying and grouping curve points. The default is landmark names ending in one or more numbers. To disable grouping, set to code{''}.}
       |                                                                                                                                                                                                                           ^
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    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("config")}
       | ^
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    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_container")}
       | ^
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    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("image")}
       | ^
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    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("plugin")}
       | ^
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    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("service")}
       | ^
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    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_task")}
       | ^
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GNU make is a SystemRequirements.
installed size is  5.3Mb
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installed size is  7.8Mb
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installed size is 47.5Mb
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Malformed Title field: should not end in a period.
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installed size is 10.9Mb
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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 10.2Mb
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checkRd: (-1) StrathE2E2-package.Rd:70: Lost braces; missing escapes or markup?
    70 | {Basic model operations:} \cr
       | ^
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    79 | {Parameter estimation:} \cr
       | ^
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    88 | {Sensitivity and Monte Carlo analyses:} \cr
       | ^
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    98 | {Compare model runs:} \cr
       | ^
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   105 | {Fishery yield analysis:} \cr
       | ^
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   111 | {Visualize model inputs:} \cr
       | ^
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   117 | {Visualize model outputs:} \cr
       | ^
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installed size is 13.7Mb
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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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 34.7Mb
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installed size is 10.0Mb
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'LazyData' is specified without a 'data' directory
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efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
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installed size is  5.3Mb
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    22 | \item{quant}{numeric quantile to calculate {0,1}, default 0.95.}
       |                                            ^
checkRd: (-1) cmss.Rd:21: Lost braces
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                        ^
checkRd: (-1) cmss.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                            ^
checkRd: (-1) cmss.Rd:21: Lost braces
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                        ^
checkRd: (-1) cmss.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                            ^
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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},
       |                                ^
checkRd: (-1) BiclustSet-class.Rd:19: Lost braces
    19 |     \item{\code{Number}:}{code{"numeric"}, number of biclusters in the set}
       |                               ^
Package suggested but not available for checking: ‘velocyto.R’
checkRd: (-1) plot.Rd:42: Lost braces; missing escapes or markup?
    42 |  \item{color.off}{color code; specifying the color for set(s) which are "{absent}" for an intersection.}
       |                                                                          ^
installed size is  7.9Mb
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Package suggested but not available for checking: ‘extraTrees’
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installed size is  5.6Mb
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checkRd: (-1) getFittedProbs.Rd:6-8: Lost braces
     6 | getFittedValues <- function(object) {
       |                                     ^
checkRd: (-1) getFittedProbs.Rd:14-16: Lost braces
    14 | getFittedValues <- function(object) {
       |                                     ^
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/SurfRough.Rcheck/00install.out’ for details.
installed size is  6.7Mb
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installed size is 63.5Mb
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GNU make is a SystemRequirements.
installed size is 71.1Mb
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GNU make is a SystemRequirements.
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installed size is  6.8Mb
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    24 | \item{mpl_h0t}{MPL estimates of the baseline hazard for T, i.e. h_{0T}(x_i)}
       |                                                                   ^
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    25 | \item{mpl_h0c}{MPL estimates of the baseline hazard for C, i.e. h_{0C}(x_i)}
       |                                                                   ^
checkRd: (-1) coxph_mpl_dc.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{mpl_H0t}{MPL estimates of the baseline cumulative hazard for T, i.e. H_{0T}(x_i)}
       |                                                                              ^
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    27 | \item{mpl_H0c}{MPL estimates of the baseline cumulative hazard for C, i.e. H_{0c}(x_i)}
       |                                                                              ^
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    28 | \item{mpl_S0t}{MPL estimates of the baseline survival for T, i.e. S_{0T}(x_i)}
       |                                                                     ^
checkRd: (-1) coxph_mpl_dc.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{mpl_S0c}{MPL estimates of the baseline survival for C, i.e. S_{0C}(x_i)}
       |                                                                     ^
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    66 | A {data.table} which is stored as an attribute of
       |   ^
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GNU make is a SystemRequirements.
checkRd: (-1) coxDT.Rd:76: Lost braces; missing escapes or markup?
    76 | The estimation procedure here is performed using coxph {survival} and inserting these estimated
       |                                                        ^
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checkRd: (-1) koInstall.Rd:24: Lost braces; missing escapes or markup?
    24 | set, svKomodo loads {svSocket}, starts the socket server listening to the
       |                     ^
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    18 | Komodo and (2) the present {svKomodo} R package that work hand in hand to
       |                            ^
checkRd: (-1) svKomodo-package.Rd:28: Lost braces; missing escapes or markup?
    28 | Nevertheless, the SciViews-K Komodo addin and the {svKomodo} R package
       |                                                   ^
checkRd: (-1) svKomodo-package.Rd:31: Lost braces; missing escapes or markup?
    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                          ^
checkRd: (-1) svKomodo-package.Rd:31: Lost braces; missing escapes or markup?
    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                                         ^
checkRd: (-1) svKomodo-package.Rd:37: Lost braces; missing escapes or markup?
    37 | Both SciViews-K and {svKomodo} should be considered archived items. I keep
       |                     ^
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    32 | \code{\link[survey:surveysummary]{survey::svymean()}} and related functions from the {survey}
       |                                                                                      ^
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checkRd: (-1) swDsn.Rd:28: Lost braces
    28 | numeric (scalar or vector): Relative treatment effect upon crossing over from control. Note that this is not the treatment effect (the treatment effect is specified in the call to other functions such as \code{swPwr} or \code{swSim})!  If \code{tx.effect.frac} is set to a scalar with value of 1, the standard SW CRT treatment effect will be presumed. If code{tx.effect.frac} is set to a scalar with a fractional value between 0 and 1, then only the first time point upon crossing over from control will have fractional relative treatment effect; the remaining exposure times will have a relative treatment effect of 1. If a vector of fractional treatment effect is specified, each element of the vector corresponds to the (fractional) treatment effect upon crossing over from control; if the length of the vector is less than total number of exposure times, the remaining time points will have a relative treatment effect value of 1; if the length of the vector is greater than total number of time points after crossing over, not all elements of \code{tx.effect.frac} will be used. The default value is (scalar) 1.
       |                                                                                                                                                                                                                                                                                                                                                                        ^
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Package suggested but not available for checking: ‘swephRdata’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
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checkRd: (-1) hyph.support.en.Rd:19: Lost braces in \itemize; meant \describe ?
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Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
checkRd: (-1) kRp.hyphen-methods.Rd:84: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) manage.hyph.pat.Rd:53: Lost braces in \itemize; meant \describe ?
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    18 |   \item{epsilon}{positive convergence tolerance \emph{e}; the iterations converge when |fit - fit_{old}|/|fit| < \emph{e}. Default is \emph{e=1e-04}.}
       |                                                                                                   ^
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installed size is 45.5Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) coord2dist.Rd:14: Lost braces; missing escapes or markup?
    14 | \code{n} x 4 matrix of coordinates consisting of {lat or y, lon or x} pairs for each each site
       |                                                  ^
checkRd: (-1) create_synthetic_example.Rd:10: Lost braces in \itemize; meant \describe ?
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Error: inferior call failed
Execution halted
Please remove or rename the files.
See section ‘Package subdirectories’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘inst/NEWS.Rd’:
  cannot open the connection
Fatal error: cannot create 'R_TempDir'
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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    68 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
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    67 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
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    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |   ^
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    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |                      ^
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   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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    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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    19 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
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    23 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
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    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
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    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
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    10 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
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    16 | \item{\code{func}}{prepared for objective functions like SYS_LSF$func <- function(x){return(x[1] + x[2])}}
       |                                                                                     ^
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    37 |  {The 2 in the first row means there are two cycles;}
       |  ^
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    38 |   {The second row means there is a cycle of length 2, with members  (1,3);}
       |   ^
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    39 |  {The third row means  there is a cycle of length 1, with member  (2);}
       |  ^
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    40 |  {The fourth row is redundant for this specific case.}
       |  ^
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    41 |  {One can read from the output of permucycle() to obtain cycle notation (13)(2) of the permutation, and other information.}
       |  ^
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    16 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variatioanl approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
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    26 | It is recommended to use link{sibp_param_search} instead of this function to search over multiple configurations of the most important parameters.  So long as only the training data is used, the analyst can freely experimient with as many parameter configurations as he likes without corrupting his causal inferences.  Once a parameter configuration is chosen, the user can then use \link{sibp_amce} on the test set to estimate the average marginal component effect (AMCE) for each treatment.}
       |                              ^
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    28 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variational approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
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    19 |   \item{sibp.amce}{The table returned by code{sibp_amce}.}
       |                                              ^
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    20 |  \\tabular{rrrrr}{
       |           ^
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       |                  ^
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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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    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                    ^
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       |                                           ^
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    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                                          ^
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     5 | \title{Install {timeseriesdb} System Functions}
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    17 | Installs functions needed to operated {timeseriesdb} in
       |                                       ^
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     5 | \title{Grant execute on {timeseriesdb} functions}
       |                         ^
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    17 | Grant execute on {timeseriesdb} functions
       |                  ^
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     5 | \title{Install {timeseriesdb} System Tables}
       |                ^
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    17 | Installs tables needed to operated {timeseriesdb} in
       |                                    ^
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     5 | \title{Install {timeseriesdb} Triggers}
       |                ^
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    20 | \item{cutoff}{Numeric. The value max(0, g_{i,j} - cutoff) so that there are <\code{.num_components}> components in the graph.}
       |                                           ^
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   332 |   If the input argument code{boxes} is \code{F}, the \code{lBox},
       |                             ^
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installed size is 46.8Mb
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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.
       |                                                 ^
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    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the season_id value found in the change entries.
       |                                                 ^
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     5 | \title{Format data as a JSON object (like this: {"x": "120"}).}
       |                                                 ^
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    18 | Format data as a JSON object (like this: {"x": "120"}).
       |                                          ^
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    21 | Recommended range is in {5, ..., 20}.}
       |                         ^
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    14 | \item{data}{data.table returned from function /code{tdtr}}
       |                                                    ^
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installed size is 222.9Mb
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    R          6.2Mb
    help       1.7Mb
    include    1.9Mb
    libs     212.5Mb
Package suggested but not available for checking: ‘toscaData’
installed size is  5.6Mb
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    data   5.2Mb
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 13.0Mb
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    data  13.0Mb
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    23 |     item{\code{estimates}: parameter estimates}
       |         ^
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    24 |     item{
       |         ^
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    29 |     item{\code{operators}: the BEAST2 MCMC operator
       |         ^
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    28 |     item{\code{estimates}: parameter estimates}
       |         ^
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    29 |     item{
       |         ^
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installed size is 69.1Mb
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    libs  66.2Mb
Package listed in more than one of Depends, Imports, Suggests, Enhances:
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A package should be listed in only one of these fields.
Subdirectory 'demo' contains invalid file names:
  ‘NAMI.Rout.save’ ‘SCI_ePolr.Rout.save’ ‘hcc.Rout.save’
  ‘mtram.Rout.save’ ‘npb.Rout.save’ ‘npn.Rout.save’ ‘stram.Rout.save’
  ‘survtram.Rout.save’ ‘tram.Rout.save’ ‘undernutrition.Rout.save’
Please remove or rename the files.
See section ‘Package subdirectories’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘fwelnet’
installed size is  5.1Mb
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    69 | numeric with two values {0,1} and gaussian(link = "identity") otherwise.
       |                         ^
Package suggested but not available for checking: ‘TreeDistData’
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installed size is 10.3Mb
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installed size is  6.2Mb
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installed size is  8.6Mb
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    doc    3.1Mb
    libs   5.0Mb
installed size is  6.2Mb
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installed size is 17.7Mb
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    doc       1.3Mb
    extdata  14.8Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 135.3Mb
  sub-directories of 1Mb or more:
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    libs  130.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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installed size is 52.9Mb
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    31 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
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    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
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    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
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    24 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
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    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
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    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
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    18 | data.frame with "{var_name}" column for the mean and
       |                  ^
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    19 | "{var_name}_{prob}" columns for each probability.
       |  ^
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    19 | "{var_name}_{prob}" columns for each probability.
       |             ^
GNU make is a SystemRequirements.
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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-arm64/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.
installed size is 34.4Mb
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installed size is 40.5Mb
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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  8.4Mb
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
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    16 | \item{matrix.logical}{With matrix=TRUE, the matrix is logical TRUE/FALSE or string "*"/code{" "}}
       |                                                                                            ^
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Error(s) in re-building vignettes:
--- re-building ‘tsglm.Rnw’ using Sweave
Error: processing vignette 'tsglm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tsglm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'tsglm.Rnw'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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installed size is 15.3Mb
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    libs  12.2Mb
GNU make is a SystemRequirements.
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installed size is  8.7Mb
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    data   4.6Mb
    libs   2.7Mb
GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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    28 | The final representation has length equal to floor(n / 2^{level}), where n is a length of original time series.
       |                                                          ^
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/TTR.PGM.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
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    74 |         doi{10.1093/biomet/74.2.221}
       |            ^
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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})
       |                                    ^
Problems with news in ‘NEWS.md’:
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installed size is  7.2Mb
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GNU make is a SystemRequirements.
installed size is 22.5Mb
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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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    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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GNU make is a SystemRequirements.
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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
       |                             ^
checkRd: (-1) UNPaC_num_clust.Rd:66: Lost braces; missing escapes or markup?
    66 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}}
       |                                  ^
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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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     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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    38 | Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
       |               ^
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installed size is 115.6Mb
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    libs  114.2Mb
GNU make is a SystemRequirements.
Package required and available but unsuitable version: ‘ENMeval’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
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installed size is  5.3Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) Session.Rd:146: Lost braces
   146 | sQuote{page load} timeout specifies a time to wait for the page loading
       |       ^
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installed size is 10.5Mb
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    client   9.4Mb
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installed size is 29.4Mb
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GNU make is a SystemRequirements.
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    15 | /href{https://crawdad.org/coppe-ufrj/RioBuses/20180319/}
       |      ^
Specified C++11: please drop specification unless essential
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    10 | integer/numeric with values all in {0=negative,1=positive} or
       |                                    ^
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    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       | ^
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    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       |                            ^
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   149 | Composite likelihood {E}{M} algorithm with applications to
       |                         ^
installed size is 12.6Mb
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installed size is  5.3Mb
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
installed size is 92.1Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
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    14 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
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installed size is 57.6Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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installed size is  8.7Mb
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installed size is  5.2Mb
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installed size is  5.4Mb
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installed size is  6.7Mb
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    libs   2.7Mb
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Malformed Description field: should contain one or more complete sentences.
installed size is  6.7Mb
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installed size is 12.8Mb
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installed size is 11.3Mb
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installed size is 11.5Mb
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installed size is 11.4Mb
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installed size is 43.3Mb
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Package suggested but not available for checking: ‘wmtsa’
Package listed in more than one of Depends, Imports, Suggests, Enhances:
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A package should be listed in only one of these fields.
installed size is  7.0Mb
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    extdata   2.5Mb
checkRd: (-1) createDemandSite.Rd:26: Lost braces
    26 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
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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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installed size is  7.1Mb
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    help   1.9Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
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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.
       | ^
checkRd: (-1) wtest.high.Rd:61-64: Lost braces
    61 | {When \code{w.order} > 2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
installed size is  7.3Mb
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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
       |                     ^
checkRd: (-1) produceAllManualPagesFromObject.Rd:14: Lost braces
    14 | See \emph{\bold{\\code{\link{ProcessingContext}}}}.}
       |                       ^
installed size is 15.9Mb
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installed size is 21.7Mb
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GNU make is a SystemRequirements.
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installed size is 31.7Mb
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   144 | Default {NULL} means the workbook will not be protected with a password}
       |         ^
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installed size is 25.2Mb
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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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GNU make is a SystemRequirements.
installed size is 53.8Mb
  sub-directories of 1Mb or more:
    libs  53.4Mb
GNU make is a SystemRequirements.
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installed size is 11.6Mb
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    R      3.1Mb
    libs   7.4Mb
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
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checkRd: (-1) glm.cons.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{method}{the method used in fitting the model. The default method "\code{glm.fit.cons}" uses function {nnnpls} from package nnls instead of \code{lm.fit} to impose the sign of the coefficients. As in \code{glm}, the alternative method "\code{model.frame}" returns the model frame and does no fitting.}
       |                                                                                                            ^
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GNU make is a SystemRequirements.
installed size is  6.0Mb
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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}.
       |                                              ^
installed size is  5.2Mb
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No news entries found.
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    libs   5.6Mb
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checkRd: (-1) Ehrenfest.Rd:19: Lost braces
    19 | In this experiment there are i balls in Urn I, and remaining 2n-i balls in Urn II. Then at any instance, the probability of selecting a ball from Urn I and placing it in Urn II is i/2n, and the other way of placing a ball from Urn II to Urn I is (2n-i)/2n. At each instant we let the number i of balls in the Urn I to be the state of the system. Thus, the state space is S = { 0, 1, 2, \ldots, 2n }. Then we can pass from state i only to either of the states i-1 or i+1.
       |                                                                                                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) Ehrenfest.Rd:20: Lost braces
    20 | Here, S = {0, 1, \ldots, 2n}. 
       |           ^
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
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    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
checkRd: (-1) est_S_Plus_Plus_MethodB.Rd:31: Lost braces; missing escapes or markup?
    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method B}
       |                                                          ^
checkRd: (-1) est_S_Star_Plus_MethodA.Rd:29: Lost braces; missing escapes or markup?
    29 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
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    29 |   \item{trt_diff}{Estimate of treatment difference for S_{*+} using Method B}
       |                                                          ^
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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}.
       |                                                                                                                                                                                                          ^
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    23 | and the best result from three values of v = {0.25, 0.5, 0.75}
       |                                              ^
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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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    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.
       |                                                                                                                                                                                                                                                                                              ^
Problems with news in ‘NEWS.md’:
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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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    42 | \item{basehaz}{: {baseline hazard structure including baseline
       |                  ^
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       |                  ^
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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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    25 | \item{parameters}{Parameter(s) to return data for. Choices are PM_{2.5}
       |                                                                   ^
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    61 |                                      names with the format {"Inferred1", "Inferred2", ...}.
       |                                                            ^
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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}}
       | ^
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    60 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
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    55 | Prior 1x1 covariance matrix for predicting x_t from x_{t-1}.
       |                                                       ^
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    65 | Prior 2x2 covariance matrix for predicting x_t from x_{t-1}.
       |                                                       ^
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   625 | group = function(...) {
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   172 |     the height of the area containing the panels and a margin of size code{100 * 0.1} 
       |                                                                           ^
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    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                              ^
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    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                                            ^
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    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       | ^
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    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       |                                 ^
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    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
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    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |   ^
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    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                  ^
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    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                                             ^
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installed size is  6.8Mb
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installed size is  6.2Mb
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    28 | code{NA} means the performance value is not available, possibly because the algorithm run was aborted.
       |     ^
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    40 |   code{NA} means the cost is not available, possibly because the feature computation was aborted.
       |       ^
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    47 |   code{NA} means the cost is not available, possibly because the feature computation was aborted.
       |       ^
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    55 |   code{NA} means the feature is not available, possibly because the feature computation was aborted.
       |       ^
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    62 |   code{NA} means the feature is not available, possibly because the feature computation was aborted.
       |       ^
installed size is 11.0Mb
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   199 |   yakka. (Note that \code{flap} stands for dQuote{function list
       |                                                  ^
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    34 |   always, the identifier has the format YYYY-NNNP{PP}, where YYYY is the year
       |                                                  ^
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    36 |   during year YYYY and P{PP} is a part specifier comprising 1 to 3 capital letters
       |                         ^
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    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.
       |                                                                       ^
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    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.
       |                                                                                                ^
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    14 | \item{x_discrete}{TRUE if the distribution of the covariate is uniform on {-3.0, -2.9, ..., 3.0} and
       |                                                                           ^
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    23 | \item{att_oracle}{the sample analog of E[D{Y(1) - Y(0)}|D=1]}
       |                                           ^
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    50 | \item \code{covars_data}   {The \code{data.frame} that is filtered out of \code{df} with only the selected \code{covars}}. The values of the
       |                            ^
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    53 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
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    40 | \item \code{multiplicative_bias}{The absolute log of the multiplicative bias term for each of the auto-selected prioritised covariates}
       |                                 ^
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    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}}
       |                           ^
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    27 | code{\link{help}}
       |     ^
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    25 | code{\link{help}}
       |     ^
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    22 | code{\link{help}}
       |     ^
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    29 | code{\link{help}}
       |     ^
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    32 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    20 | \item{fit}{See glm {stats}.}
       |                    ^
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    21 | \item{fit}{See glm {stats}.}
       |                    ^
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    21 | \item{host}{For \code{cosmos_mongo_endpoint}, the URL of the Cosmos DB MongoDB endpoint. Usually of the form "https://{account-name}.mongo.cosmos.azure.com:443/".}
       |                                                                                                                       ^
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installed size is  6.3Mb
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Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
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installed size is 91.4Mb
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installed size is 137.3Mb
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GNU make is a SystemRequirements.
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installed size is 105.5Mb
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GNU make is a SystemRequirements.
installed size is 97.3Mb
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘fdpbandsdata’
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    27 | read.dna() from package {ape} was used to obtain DNAbin object for unaligned non-coding barcodes.
       |                         ^
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installed size is 20.1Mb
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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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    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.}
       |                  ^
installed size is  7.4Mb
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    41 |  \item{namespaces}{code{character} with required packages to load via \code{\link[base]{requireNamespace}}.}
       |                        ^
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    31 | Algorithms are functions which get the code{data} part as well as the problem instance (the return value of the
       |                                            ^
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installed size is 105.8Mb
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GNU make is a SystemRequirements.
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    32 | plot{...} functions are generated programmatically so the function calls in
       |     ^
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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}.}
       |                                                                    ^
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    53 | online trajectories related to the state parameter, the simulated BOLD responses, \mjseqn{\hat{Y}}{ascii}.
       |                                                                                                   ^
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installed size is 17.5Mb
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installed size is 119.6Mb
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GNU make is a SystemRequirements.
installed size is 126.4Mb
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GNU make is a SystemRequirements.
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    18 |   \item{optim.method}{optimization method in \code{optim()}{stats}.}
       |                                                            ^
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installed size is 55.2Mb
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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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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.}
       |                                                                              ^
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    22 | A data frame where new rows have been inserted to regularize the \code{date} column. This results in values provided for \code{id}, \code{date}, and {dt} while inserting NAs for all other columns. Additionally, observations with duplicate date-times are removed.
       |                                                                                                                                                      ^
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
installed size is  5.5Mb
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Specified C++11: please drop specification unless essential
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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).
       |                                                                                        ^
'LazyData' is specified without a 'data' directory
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installed size is 44.6Mb
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    libs  43.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) goftype1.Rd:4: Lost braces
     4 | \description{The goodness-of-fit (GOF) measures consist of Anderson-Darling (\code{AD}) and Cram\'{e}er-von Misses (\code{CVM}) statistics for progressive type-I interval censoring scheme are given, respectively, by
       |                                                                                                   ^
installed size is  7.5Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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checkRd: (-1) WindowSweep.Rd:32: Lost braces
    32 | `code{\link{GetVT}}`.   Otherwise, any column (e.g. \code{"Depth"}) in the 
       |      ^
checkRd: (-1) WindowSweep.Rd:36: Lost braces
    36 | \code{T.mid}  from the output of the `code{\link{GetVT}}`.}
       |                                           ^
Package suggested but not available for checking: ‘BRugs’
Specified C++11: please drop specification unless essential
checkRd: (-1) gene_s.Rd:17: Lost braces; missing escapes or markup?
    17 | giving the virus access to the cell and thus facilitating the COVID-19 disease. The gene sequence is mapped to the alphabet {0,1,2,3} via the obvious map A->0, C->1, G->2, T->3.
       |                                                                                                                             ^
checkRd: (-1) sars_cov_2.Rd:16: Lost braces; missing escapes or markup?
    16 | It consists of n = 29903 base pairs. The gene sequence is mapped to the alphabet {0,1,2,3} via the obvious map A->0, C->1, G->2, T->3.
       |                                                                                  ^
'LazyData' is specified without a 'data' directory
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installed size is  5.2Mb
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installed size is 121.5Mb
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    libs  119.9Mb
GNU make is a SystemRequirements.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    java   8.5Mb
installed size is 51.5Mb
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    libs  50.0Mb
GNU make is a SystemRequirements.
installed size is 66.1Mb
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    libs  62.8Mb
GNU make is a SystemRequirements.
installed size is 14.5Mb
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    libs  13.5Mb
'LazyData' is specified without a 'data' directory
installed size is 56.1Mb
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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
installed size is 44.5Mb
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    libs  43.9Mb
GNU make is a SystemRequirements.
checkRd: (-1) sockeye.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sockeye.Rd:15-16: Lost braces in \itemize; meant \describe ?
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installed size is 64.4Mb
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GNU make is a SystemRequirements.
installed size is 32.4Mb
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    libs  31.4Mb
Specified C++11: please drop specification unless essential
installed size is 65.2Mb
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checkRd: (-1) gen.data.Rd:42: Lost braces
    42 | code{cortype = 2} denotes the constant structure, where the \eqn{(i,j)} entry of covariance
       |     ^
'LazyData' is specified without a 'data' directory
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Malformed Title field: should not end in a period.
checkRd: (-1) BETSsearch.Rd:56: Lost braces
    56 |        \item{To exclude whole expressions from the search, surround them with code{' '} and insert a \code{~} before each of them.
       |                                                                                   ^
checkRd: (-1) dummy.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{date}{a \code{list}. The periods for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                               ^
checkRd: (-1) dummy.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{from}{An \code{integer vector} The starting period of a sequence of perids for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                                                                         ^
checkRd: (-1) dummy.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{to}{The ending period of a sequence of perids for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                                            ^
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
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    doc    3.3Mb
    help   1.1Mb
    libs   7.9Mb
installed size is  5.0Mb
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    data   3.5Mb
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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 10.9Mb
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    doc    2.9Mb
    libs   6.5Mb
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Depends: includes the non-default packages:
  'coda', 'ggplot2', 'gridExtra', 'lpl', 'MASS', 'survival'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is 168.5Mb
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    include  168.4Mb
installed size is  5.3Mb
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    libs   4.6Mb
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) BiDimRegression.Rd:29: Lost braces; missing escapes or markup?
    29 | \item \code{euclidean.df1, affine.df1} -  degrees of freedom of the nominator used for the F-statistics propagated by Nakaya (1997); df1 = p-2, with p is the number of elements  needed to calculate the referring model: p=4 for the Euclidean and p=6 for the affine geometry {Nakaya, 1997, Table 1}.
       |                                                                                                                                                                                                                                                                                  ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   7.8Mb
Package suggested but not available for checking: ‘ffbase’
Package suggested but not available for checking: ‘INLA’
installed size is  5.6Mb
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    data   5.2Mb
installed size is  8.5Mb
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    data   1.4Mb
    libs   6.2Mb
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
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    libs   4.7Mb
Specified C++14: please drop specification unless essential
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checkRd: (-1) bdm.ptsne.Rd:47: Lost braces; missing escapes or markup?
    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                         ^
checkRd: (-1) bdm.ptsne.Rd:47: Lost braces; missing escapes or markup?
    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                                                                                   ^
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
installed size is  7.3Mb
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installed size is  9.0Mb
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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 30.4Mb
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Package required but not available: ‘pwalign’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.2Mb
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installed size is 12.4Mb
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installed size is  5.7Mb
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installed size is 19.3Mb
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    libs  17.7Mb
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
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installed size is  6.0Mb
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GNU make is a SystemRequirements.
installed size is  6.6Mb
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    R      1.0Mb
    libs   2.9Mb
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
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'LazyData' is specified without a 'data' directory
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installed size is 20.0Mb
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    libs  17.7Mb
GNU make is a SystemRequirements.
checkRd: (-1) calc_ed.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_pi.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
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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’
installed size is  5.3Mb
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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  8.2Mb
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installed size is  7.9Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 49.3Mb
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    libs     46.9Mb
GNU make is a SystemRequirements.
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installed size is  7.9Mb
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installed size is 56.6Mb
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GNU make is a SystemRequirements.
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installed size is 10.2Mb
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installed size is  6.7Mb
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Packages suggested but not available for checking: 'cmdstanr', 'blavsam'
installed size is 162.0Mb
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    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}
       |                                       ^
installed size is  7.7Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
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installed size is 13.7Mb
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installed size is 10.7Mb
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checkRd: (-1) durban.Rd:16: Lost braces; missing escapes or markup?
    16 | This data set was obtained from the durban.rowcol {agridat} example in package 'agridat' 
       |                                                   ^
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    25 | evenly spaced points between \code{min} and {max}.
       |                                             ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) bluebike.Rd:17: Lost braces
    17 | \item{\code{import_month_data}}\cr {Takes in numeric year/month values and imports data from \href{https://www.bluebikes.com/system-data}{Blue Bikes System Data} for the specified time}
       |                                    ^
checkRd: (-1) bluebike.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{\code{station_distance}}\cr {Returns stations with distance in ascending order given the user's current location}
       |                                   ^
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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}
       |                                 ^
checkRd: (-1) bluebike.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{\code{trip_distance}}\cr {Computes the geographical distance between the start and end stations}
       |                                ^
checkRd: (-1) bluebike.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{\code{trip_history_sample}} \cr {A sample of 1000 trip data entries from February 2022}
       |                                       ^
checkRd: (-1) bluebike.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{\code{station_data}} \cr {A dataset that includes identification, position, and other basic information about bluebike stations}
       |                                ^
Specified C++11: please drop specification unless essential
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    20 | Helper function for as.data.frame.{fitted, forecast}. Converts predictive array to data.frame.
       |                                   ^
GNU make is a SystemRequirements.
installed size is 118.5Mb
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GNU make is a SystemRequirements.
installed size is 66.7Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
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GNU make is a SystemRequirements.
installed size is  6.5Mb
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    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |               ^
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |                                             ^
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Packages suggested but not available for checking:
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installed size is 10.3Mb
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Depends: includes the non-default packages:
  'tseries', 'fGarch', 'timeSeries', 'timeDate', 'fBasics', 'geoR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is 13.2Mb
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installed size is 394.8Mb
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GNU make is a SystemRequirements.
installed size is 93.4Mb
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installed size is 38.9Mb
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installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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installed size is  5.7Mb
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installed size is  5.1Mb
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installed size is  5.0Mb
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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 | $$SD = sqrt(sum(x_{i+1} - xbar)^2/n-1)$$
       |                   ^
installed size is 53.6Mb
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GNU make is a SystemRequirements.
installed size is 10.0Mb
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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installed size is 46.3Mb
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GNU make is a SystemRequirements.
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installed size is  5.2Mb
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installed size is  9.0Mb
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installed size is  5.4Mb
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installed size is  7.7Mb
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installed size is 12.5Mb
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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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installed size is 32.2Mb
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installed size is 10.0Mb
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installed size is 15.6Mb
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installed size is 169.8Mb
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GNU make is a SystemRequirements.
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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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installed size is  9.9Mb
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installed size is 23.1Mb
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Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘doMPI’
Specified C++11: please drop specification unless essential
installed size is 20.9Mb
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installed size is 57.4Mb
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GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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installed size is  7.8Mb
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    24 | functions, and often the /code{cut()} function are relatively slow when working with tens of millions of rows or more.
       |                               ^
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    19 | \item{y}{response variable (in {0,1}).}
       |                                ^
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   112 | Stop recording images with {camcorder}.
       |                            ^
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    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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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
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    13 | The exit status code{R CMD build}, invisibly.
       |                     ^
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installed size is 12.2Mb
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GNU make is a SystemRequirements.
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    71 |   \item{states.samples}{(\code{niter}- \code{burn}) draws from p(alpha_t | Y_{1:T}).}
       |                                                                              ^
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    61 |   \item{states.samples}{(\code{niter}- \code{burn}) draws from p(alpha_t | Y_{1:T}).}
       |                                                                              ^
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installed size is  5.3Mb
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installed size is 19.2Mb
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installed size is 22.2Mb
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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}).
       |                                  ^
installed size is 24.0Mb
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Problems with news in ‘NEWS.md’:
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installed size is  6.5Mb
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installed size is  5.9Mb
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Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
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    36 | A code{data.frame} with the requested variables at the requested
       |       ^
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    22 | Centroid value C_{cen}(v) for node v defined as:
       |                  ^
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    23 | where the term f(c_{i}) accounts for the effect of i's local clustering and the term '+1' results from the contribution of \eqn{j}{j} itself. \cr
       |                    ^
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    31 |   {epsi}^{# regression coefficients} times the initial value,
       |   ^
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    31 |   {epsi}^{# regression coefficients} times the initial value,
       |          ^
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    23 | Assuming one-dimensional \code{p1} and \code{p2} for clarity, the algorithm calculates cumulative incidence function for cuase 1 using a recursive formula: \code{ci1[n+1] = ci1[n] + dci1[n]}, where \code{dci1[n] = 0.5*(p2[n] + p2[n+1])*(p1[n] - p1[n+1])}. The increment in cumulative incidence function for cause 2 is similarly calculated, \code{dci2[n] = 0.5*(p1[n] + p1[n+1])*(p2[n] - p2[n+1])}. These equations guarantee that \code{dci1[n] + dci2[n] = p1[n]*p2[n] - p1[n+1]*p2[n+1]}. Event-free probability is simply calculated as code{efp[n] = p1[n]*p2[n]}. Taken together, this numerical integration ensures that \code{efp[n+1] - efp[n] + dci1[n] + dci2[n] = 0}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           ^
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    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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checkRd: (-1) C316.amp.Rd:28-32: Lost braces
    28 |     40 x {
       |          ^
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    28 |     40 x {
       |          ^
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    63 |     40 x {
       |          ^
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     5 | \title{prepares Dy y_1 Dy_1 ... Dy_{nlag-1} for estimation}
       |                                    ^
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    15 | ymat contains the folloiwing columns {Dy y_1 Dy_1 ... Dy_{nlag-1}}
       |                                      ^
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    15 | ymat contains the folloiwing columns {Dy y_1 Dy_1 ... Dy_{nlag-1}}
       |                                                          ^
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    21 |              REM: alternative to "lead-lag" {dplyr} which applies to vector y
       |                                             ^
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  'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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checkRd: (-1) CIplot.Rd:58: Lost braces; missing escapes or markup?
    58 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.
       |                       ^
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    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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    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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Depends: includes the non-default packages:
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  'ggplot2', 'gt', 'ipred', 'MachineShop', 'magrittr', 'parallel',
  'pls', 'purrr', 'randomForest', 'ranger', 'reactable',
  'reactablefmtr', 'scales', 'tidyr', 'tree'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  9.6Mb
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Package required but not available: ‘pwalign’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
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    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
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    clhs_0.2-1
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    68 | \code{\link{cf_find_station}} and code{vignette("choose-station")} for
       |                                       ^
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   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                   ^
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   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                                 ^
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GNU make is a SystemRequirements.
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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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Error(s) in re-building vignettes:
--- re-building ‘createStreams.Rmd’ using knitr
--- finished re-building ‘createStreams.Rmd’

--- re-building ‘fisher.sim.Rmd’ using knitr
--- finished re-building ‘fisher.sim.Rmd’

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

Quitting from random_numbers.Rmd:62-96 [rnormGpu]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! ViennaCL: FATAL ERROR: CL_INVALID_PROGRAM_EXECUTABLE.
If you think that this is a bug in ViennaCL, please report it at viennacl-support@lists.sourceforge.net and supply at least the following information:
 * Operating System
 * Which OpenCL implementation (AMD, NVIDIA, etc.)
 * ViennaCL version
Many thanks in advance!
---
Backtrace:
    ▆
 1. ├─base::as.vector(clrng::rnormGpu(10, myStreamsGpu, verbose = 2))
 2. └─clrng::rnormGpu(10, myStreamsGpu, verbose = 2)
 3.   └─clrng:::gpuRnBackend(xVcl, streams, Nglobal, "normal", verbose)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'random_numbers.Rmd' failed with diagnostics:
ViennaCL: FATAL ERROR: CL_INVALID_PROGRAM_EXECUTABLE.
If you think that this is a bug in ViennaCL, please report it at viennacl-support@lists.sourceforge.net and supply at least the following information:
 * Operating System
 * Which OpenCL implementation (AMD, NVIDIA, etc.)
 * ViennaCL version
Many thanks in advance!
--- failed re-building ‘random_numbers.Rmd’

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) clr.Rd:24: Lost braces
    24 | the sense that its Karhunen-Lo\`{e}ve decomposition has qx terms only.}
       |                                 ^
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No news entries found.
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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
       |                                  ^
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
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    43 | \emph{Technometrics}, bold{60} (1), 48-60, DOI 10.1080/00401706.2017.1281846.\cr\cr
       |                           ^
checkRd: (-1) fwtnppermC.Rd:35: Lost braces
    35 | Given \eqn{n} points on a line, \env{x}, each with a corresponding env{f} value this function computes
       |                                                                       ^
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GNU make is a SystemRequirements.
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Package which this enhances but not available for checking: ‘rkward’
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checkRd: (-1) educFM.Rd:22: Lost braces in \itemize; meant \describe ?
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Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  6.0Mb
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Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘reactable’ ‘DT’
A package should be listed in only one of these fields.
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checkRd: (-1) getHistList.Rd:32: Lost braces; missing escapes or markup?
    32 | ({FALSE})? If a bin is empty, the center of the bin is returned as the
       |  ^
checkRd: (-1) imageClusterPipeline.Rd:82: Lost braces; missing escapes or markup?
    82 | of the bin ({FALSE})? If a bin is empty, the center of the bin is returned
       |             ^
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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.
checkRd: (-1) xsimplex.Rd:6: Lost braces; missing escapes or markup?
     6 |              Generates all points on a {p,n} simplex lattice (i.e. a p-part
       |                                        ^
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checkRd: (-1) BMD.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) BMD.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add.risk.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add.risk.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  14.5Mb
checkRd: (-1) count_pairs.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) score_log_nonparam.Rd:36: Lost braces; missing escapes or markup?
    36 | {0, 1}.
       | ^
checkRd: (-1) score_log_semiparam.Rd:40: Lost braces; missing escapes or markup?
    40 | values in {0, 1}.
       |           ^
checkRd: (-1) sort_pairs.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) sort_pairs.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    java   6.7Mb
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
checkRd: (-1) hmm.Rd:47-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:56-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:63-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:71-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:79-84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:85-89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:95-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:104-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:108-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:112-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:119-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:130-133: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘CAM’
Running examples in ‘CompareMultipleModels-Ex.R’ failed
The error most likely occurred in:

> ### Name: best_model_finder
> ### Title: Finding the Best Model Using Eight Metrics Values
> ### Aliases: best_model_finder
> 
> ### ** Examples
> 
> set.seed(123) # for reproducibility
> Y <- rnorm(100, 100, 10)
> model_1 <-CEEMDANML::carigaan(Y, ratio = 0.8, n_lag = 4)
Error in optim(init[mask], armafn, method = optim.method, hessian = TRUE,  : 
  non-finite finite-difference value [1]
Calls: <Anonymous> -> arima -> optim
Execution halted
checkRd: (-1) glass.Rd:10: Lost braces
    10 | \item{item}{factor}{200 levels - which item the measurements came from}
       |                    ^
checkRd: (-1) glass.Rd:11-12: Lost braces
    11 | \item{fragment}{factor}{4 levels - which of the four fragments from each item the observations were made
       |                        ^
checkRd: (-1) glass.Rd:13: Lost braces
    13 | \item{logNaO}{numeric}{log of sodium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:14: Lost braces
    14 | \item{logMgO}{numeric}{log of magnesium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:15: Lost braces
    15 | \item{logAlO}{numeric}{log of aluminium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:16: Lost braces
    16 | \item{logSiO}{numeric}{log of silicon concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:17: Lost braces
    17 | \item{logKO}{numeric}{log of potassium concentration to oxygen concentration}
       |                      ^
checkRd: (-1) glass.Rd:18: Lost braces
    18 | \item{logCaO}{numeric}{log of calcium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:19: Lost braces
    19 | \item{logFeO}{numeric}{log of iron concentration to oxygen concentration}
       |                       ^
installed size is 36.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  34.8Mb
checkRd: (-1) atomdeps.Rd:9: Lost braces
     9 |  \item{"tangle"}: {Dihedral angle defined by atoms A-B-C-D as described below. \code{NA}'s represent the free side chain dihedral angles \emph{chi} for that amino acid.}
       |                   ^
checkRd: (-1) atomdeps.Rd:10: Lost braces; missing escapes or markup?
    10 |  \item{"names"}: {The component atoms of the amino acid side chain.  Represents atom D in the dihedral.}
       |                  ^
checkRd: (-1) atomdeps.Rd:11: Lost braces; missing escapes or markup?
    11 |  \item{"matx"}: {The names of atoms A,B,C in the dihedral, with rows corresponding to the atoms in "names".}
       |                 ^
checkRd: (-1) atomdeps.Rd:12: Lost braces; missing escapes or markup?
    12 |  \item{"bangle"}: {Planar bond angle formed between B-C-D}
       |                   ^
checkRd: (-1) atomdeps.Rd:13: Lost braces; missing escapes or markup?
    13 |  \item{"blength"}: {Bond length between C-D}
       |                    ^
checkRd: (-1) keener.Rd:82: Lost braces; missing escapes or markup?
    82 | a_{ij} = (S_ij + 1) / (S_ij + S_ji + 2). This step should make comparing
       |   ^
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
Specified C++11: please drop specification unless essential
checkRd: (-1) concstats_hhi.Rd:13: Lost braces; missing escapes or markup?
    13 | value is required. Ranges from {0, 1} and often used for comparison over
       |                                ^
checkRd: (-1) KCI.Rd:44: Lost braces
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                ^
checkRd: (-1) KCI.Rd:44: Lost braces
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                      ^
checkRd: (-1) KCI.Rd:44: Lost braces; missing escapes or markup?
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                                    ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) binary_class_cm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) NetStats.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) NetStats.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly