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    65 | code{dfft(object, index=0)} on an object created from a forecast with 
       |     ^
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    22 | err_i = 1 - max_{k={1,\ldots,K}} P(Z_i=k|x_i)
       |                 ^
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    22 | err_i = 1 - max_{k={1,\ldots,K}} P(Z_i=k|x_i)
       |                    ^
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    33 | {MyTarget API Documenation}{https://target.my.com/doc/api/detailed/#resource_agency_clients}
       |                            ^
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--- re-building 'rnaCrosslinkOO.Rmd' using rmarkdown
File rnaCrosslinkProtocol.jpg not found in resource path
Error: processing vignette 'rnaCrosslinkOO.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'rnaCrosslinkOO.Rmd'

SUMMARY: processing the following file failed:
  'rnaCrosslinkOO.Rmd'

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installed size is 12.1Mb
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installed size is 11.3Mb
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/RobLoxBioC.Rcheck/00install.out' for details.
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    libs              1.3Mb
    simulationStudy   1.6Mb
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    18 | other object type that does not fail in code{model.frame(object)}.}
       |                                             ^
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Found the following significant warnings:
  RODBC.c:294:31: warning: format '%d' expects argument of type 'int', but argument 3 has type 'SQLINTEGER' {aka 'long int'} [-Wformat=]
  RODBC.c:1078:59: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'SQLULEN' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/RODBC.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
'LazyData' is specified without a 'data' directory
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 ?
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GNU make is a SystemRequirements.
installed size is  6.0Mb
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    R         3.2Mb
    extdata   2.7Mb
GNU make is a SystemRequirements.
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    16 | in \code{updated_tidy_data} (names) and the table {features, samples,
       |                                                   ^
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No news entries found.
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    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}".}
       |                                                                                                                                                                                                                                                                                                                                                               ^
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/ROracle.Rcheck/00install.out' for details.
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    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                ^
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                       ^
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                                  ^
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
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    R      2.0Mb
    data   2.7Mb
    libs   1.4Mb
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installed size is  7.7Mb
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    R      4.8Mb
    help   1.1Mb
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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.
       |                                                                                                                                                                                                         ^
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    60 | An example is: onRefresh=htmlwidgets::JS("function(config) { Shiny.onInputChange('myPivotData', config); }")
       |                                                            ^
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    17 |   \item{method}{Method to determine width of columns that represent classes: \dQuote{weight} (subject weight in class) or dQuote{binary} (depth in tree).}
       |                                                                                                                                 ^
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    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  5.1Mb
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    17 | \item{output}{Can be any or a combination of the input terms {'author', 'title', 'lines', 'linecount'}. If NULL, all
       |                                                              ^
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/RPostgreSQL.Rcheck/00install.out' for details.
installed size is  7.1Mb
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installed size is  5.4Mb
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    18 | Renames the \code{class(tg)["name"]} attribute and sets {class(tg)["type"] <- "TextGrid"} (if it is not already set)
       |                                                         ^
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    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  5.4Mb
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installed size is 14.2Mb
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checkRd: (-1) ex.Rd:20: Lost braces
    20 | Execute a ops-dag using `code{wrap()}` data as values.
       |                              ^
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    29 | \item{expand_braces}{logical if TRUE use {col} notation to ensure {col} is a column name.}
       |                                          ^
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    29 | \item{expand_braces}{logical if TRUE use {col} notation to ensure {col} is a column name.}
       |                                                                   ^
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    37 | \code{R2_lik()} is also computed for LMMs and GLMMs in the {MuMIn} package.
       |                                                            ^
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    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.
       |                                                                                                            ^
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    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()}
       |                                                                                                            ^
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    72 |  The average deviation rating $dev_{ij}$ between co-rated items is defined by:
       |                                    ^
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    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.
       |           ^
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    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.
       |                                                                              ^
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--- re-building 'benchmarks.Rmd' using rmarkdown
--- finished re-building 'benchmarks.Rmd'

--- re-building 'research_workflows.Rmd' using rmarkdown
File figure/unnamed-chunk-7-1.png not found in resource path
Error: processing vignette 'research_workflows.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'research_workflows.Rmd'

--- re-building 'rredlist.Rmd' using rmarkdown
--- finished re-building 'rredlist.Rmd'

SUMMARY: processing the following file failed:
  'research_workflows.Rmd'

Error: Vignette re-building failed.
Execution halted
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    46 |  \item \code{x-axis} {1st column: The names of the different institutions}
       |                      ^
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    47 |  \item \code{y-axis} {2nd column: The value to show completeness}
       |                      ^
Package suggested but not available for checking: 'rnaturalearthhires'
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    24 | \item{clustering}{A \code{List} that specifies a clustering of datapoint indexes {1, ..., n}. See \link{example_clustering} for details.}
       |                                                                                  ^
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    21 | \item{clustering}{A \code{List} that specifies a clustering of datapoint indexes {1, ..., n}.
       |                                                                                  ^
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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.
       |                                                                                                                                                          ^
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
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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",
       |                                 ^
'LazyData' is specified without a 'data' directory
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
GNU make is a SystemRequirements.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.4/Rserve/libs/x64/Rserve.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'R_Visible',
    'Rf_initialize_R', 'setup_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. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: 'gurobi'
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    help   1.6Mb
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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 19.8Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    4.7Mb
    libs  12.6Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib    1.9Mb
    libs   1.4Mb
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
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    91 |  distribution of \code{(u+v)/2}, where \code{u} and {v} are independent, each
       |                                                     ^
installed size is 18.2Mb
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    libs   2.3Mb
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installed size is 19.1Mb
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    libs  18.7Mb
installed size is 42.8Mb
  sub-directories of 1Mb or more:
    libs    1.0Mb
    swipl  41.6Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
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    libs   5.8Mb
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checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                              ^
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
installed size is 11.3Mb
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    rmarkdown  11.0Mb
GNU make is a SystemRequirements.
checkRd: (-1) tw_options.Rd:22: Lost braces in \itemize; meant \describe ?
installed size is  9.9Mb
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installed size is  9.5Mb
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    libs   7.7Mb
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installed size is  5.1Mb
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    R   5.0Mb
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 11.2Mb
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    doc    7.8Mb
    libs   2.5Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
installed size is 12.2Mb
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    data   1.5Mb
    libs   9.8Mb
GNU make is a SystemRequirements.
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    32 | If a name of a raster time series file is provided for the \code{x} argument, it acts the same as code{\link[rts]{read.rts}}.
       |                                                                                                       ^
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.1Mb
installed size is  5.7Mb
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    data   3.8Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) rules.Rd:24: Lost braces; missing escapes or markup?
    24 | \item Absent names are replaced with the 'rule__\\{ind\\}' where \\{ind\\} is the
       |                                                   ^
checkRd: (-1) rules.Rd:24: Lost braces; missing escapes or markup?
    24 | \item Absent names are replaced with the 'rule__\\{ind\\}' where \\{ind\\} is the
       |                                                                    ^
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  'nimble' 'nimbleAPT'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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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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installed size is  5.2Mb
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    include   5.2Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
    libs      5.2Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
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    15 | \code{x} filtered result (y 1_{|y|>t}).
       |                               ^
checkRd: (-1) SoftThresh.Rd:15: Lost braces; missing escapes or markup?
    15 | \code{x} filtered result (y 1_{|y|>t}).
       |                               ^
Package suggested but not available for checking: 'rWCVPdata'
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installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
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File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
'LazyData' is specified without a 'data' directory
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installed size is  6.3Mb
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    data   2.1Mb
    doc    3.9Mb
installed size is  5.1Mb
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    data   5.0Mb
Malformed Title field: should not end in a period.
checkRd: (-1) wtss_to_ts.Rd:31: Lost braces; missing escapes or markup?
    31 | This period can be either {"month", "week", "day"}, 
       |                           ^
checkRd: (-1) wtss_to_ts.Rd:32: Lost braces; missing escapes or markup?
    32 | {"months", "weeks", "days"} or
       | ^
checkRd: (-1) wtss_to_ts.Rd:33: Lost braces; missing escapes or markup?
    33 | {12, 52, 365}. This function creates a new time series with the required 
       | ^
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    libs      4.7Mb
checkRd: (-1) plot.eff.ridge.Rd:6: Lost braces
     6 |  emph{Single Interior Knot} at the MSE Optimal m-Extent of Shrinkage. The
       |      ^
Specified C++11: please drop specification unless essential
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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}.}
       |                                                                                                                                                   ^
checkRd: (-1) ZigZagLogistic.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                                 ^
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    13 | \item{dataY}{Vector of length n containing {0, 1}-valued observations of the dependent variable y.}
       |                                            ^
checkRd: (-1) ciReg.Rd:10: Lost braces
    10 | \item{fit}{an object of class{lm}, i.e. the output from \code{\link{lm}}.}
       |                              ^
Specified C++14: please drop specification unless essential
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checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
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installed size is 15.3Mb
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    libs  13.4Mb
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installed size is  7.5Mb
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    doc    2.3Mb
    help   3.4Mb
    libs   1.3Mb
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    37 |         class {StatHMMR}).
       |               ^
Package suggested but not available for checking: 'networkTomography'
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installed size is  6.6Mb
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    bin   5.8Mb
installed size is  5.0Mb
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    doc    1.7Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
installed size is  6.3Mb
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    extdata   1.1Mb
installed size is  5.2Mb
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checkRd: (-1) gen.ds.Rd:43-48: Lost braces in \itemize; meant \describe ?
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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.
       |         ^
checkRd: (-1) gen.ds.Rd:66: Lost braces
    66 |    \item{the list \code{asy} of asymmetric weights \eqn{\beta_{i,b}} for \eqn{b \in B}  and \eqn{i \in b}. When missing, these coefficients are obtained from independent standard uniform sampling followed by renormalization in order to satisfy the sum-to-one constraints.}
       |         ^
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    42 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
checkRd: (-1) OTC.Rd:83: Lost braces; missing escapes or markup?
    83 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
checkRd: (-1) OTHist.Rd:29: Lost braces; missing escapes or markup?
    29 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
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    72 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
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Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
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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.}
       |                              ^
checkRd: (-1) PermBiclust.beta.ks.Rd:30: Lost braces
    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.}
       |                              ^
checkRd: (-1) PermBiclust.sigclust.Rd:33: Lost braces
    33 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
checkRd: (-1) PermBiclust.sigclust_stop.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.sigclust_stop.Rd:36: Lost braces
    36 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
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installed size is 16.8Mb
  sub-directories of 1Mb or more:
    cppad     9.5Mb
    include   4.7Mb
    libs      1.9Mb
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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)
       |                                                  ^
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                                         ^
checkRd: (-1) geom_flat_violin.Rd:7: Lost braces
     7 | url{https://gist.github.com/dgrtwo/eb7750e74997891d7c20}
       |    ^
checkRd: (-1) sdc_extabs.Rd:59: Lost braces
    59 | (including ]code{forcelist} variables) that can be used to form tables.}
       |                 ^
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.7Mb
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Error(s) in re-building vignettes:
--- re-building 'sdmvspecies.Rnw' using Sweave
Loading required package: sp
Warning: `D:\RCompile\CRANpkg\lib\4.4\sdmvspecies\external\env\bio1.bil' not recognized as being in a supported file format. (GDAL error 4)

Error: processing vignette 'sdmvspecies.Rnw' failed with diagnostics:
 chunk 2 (label = niche_Synthsis_Method) 
Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer",  : 
  Cannot create a RasterLayer object from this file.

--- failed re-building 'sdmvspecies.Rnw'

SUMMARY: processing the following file failed:
  'sdmvspecies.Rnw'

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
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    17 | \item{c}{denotes the expected range of eqn{f} .}
       |                                           ^
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'MuSiC', 'seAMLessData'
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R   7.8Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    css_data   8.7Mb
checkRd: (-1) seas.check.Rd:48-49: Lost braces in \itemize; meant \describe ?
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installed size is 19.2Mb
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    extdata  18.0Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs   2.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running examples in 'seeclickfixr-Ex.R' failed
The error most likely occurred in:

> ### Name: list_places
> ### Title: Query sub-city neighborhoods in which issues can be reported.
> ### Aliases: list_places
> 
> ### ** Examples
> 
> list_places("Boston, MA",limit = 5)
Error: lexical error: invalid char in json text.
                                       <!DOCTYPE html><html lang="en-U
                     (right here) ------^
Execution halted
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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"}.}
       |                                                                                                                                   ^
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    www  34.4Mb
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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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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
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'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:
    libs     3.3Mb
    models   1.6Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                               ^
checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                                                          ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                              ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                                                     ^
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
GNU make is a SystemRequirements.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    help   1.3Mb
    libs   3.9Mb
GNU make is a SystemRequirements.
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
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installed size is  8.3Mb
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    R     1.2Mb
    doc   6.4Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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    doc   5.1Mb
installed size is 113.1Mb
  sub-directories of 1Mb or more:
    doc      2.2Mb
    gdal     3.0Mb
    libs    94.2Mb
    proj     9.0Mb
    sqlite   1.5Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) bisee.Rd:127: Lost braces
   127 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) hisee.Rd:101: Lost braces
   101 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) isee.Rd:116: Lost braces
   116 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) see.Rd:98: Lost braces
    98 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
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    data   6.7Mb
checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                   ^
checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) changept.Rd:17-19: Lost braces in \itemize; meant \describe ?
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'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
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    doc    4.4Mb
    libs   1.3Mb
Package suggested but not available for checking: 'rCOSA'
Package unavailable to check Rd xrefs: 'rCOSA'
Package suggested but not available for checking: 'hydromad'
checkRd: (-1) age_corr.Rd:15: Lost braces
    15 | \item{plot}{Should the results be plotted? (/code{TRUE/FALSE})}
       |                                                  ^
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    17 | \item{agecorrection}{Correct for jumps in age (/code{TRUE}) or
       |                                                     ^
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    18 | only for starting time (/code{FALSE})}
       |                              ^
installed size is  6.3Mb
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    doc       1.7Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) shiftrPrepare.Rd:37: Lost braces
    37 |     See code{\link{shiftrPermBinary}} function and the respective example.
       |             ^
installed size is  7.7Mb
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Package suggested but not available for checking: 'cmdstanr'
installed size is  9.5Mb
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installed size is 20.5Mb
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checkRd: (-1) js_calls.Rd:63: Lost braces in \itemize; meant \describe ?
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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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installed size is  5.5Mb
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    tutorials   3.6Mb
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'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
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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
checkRd: (-1) shiny_pivot_table.Rd:58: Lost braces in \itemize; meant \describe ?
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'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is 13.3Mb
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    www  10.1Mb
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checkRd: (-1) addValidationSuffix.Rd:13: Lost braces; missing escapes or markup?
    13 | A string `"{tagId}-shinyreforms-validation"`.
       |            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) add_class.Rd:18: Lost braces; missing escapes or markup?
    18 | Custom function for adding a CSS class used in {shinysurveys}.
       |                                                ^
checkRd: (-1) disable_element.Rd:16: Lost braces; missing escapes or markup?
    16 | Custom function for disabling an HTML element in {shinysurveys}.
       |                                                  ^
checkRd: (-1) enable_element.Rd:16: Lost braces; missing escapes or markup?
    16 | Custom function for disabling an HTML element in {shinysurveys}.
       |                                                  ^
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    12 | \item{extension}{A shiny input type not natively supported by {shinysurveys}. See the examples section for more information.}
       |                                                               ^
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    15 | default, and the built-in {shinysurveys} userID will be used.}
       |                           ^
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    18 | \item{...}{Additional arguments specific to {shinysurveys} required questions.}
       |                                             ^
checkRd: (-1) remove_class.Rd:18: Lost braces; missing escapes or markup?
    18 | Custom function for removing a CSS class used in {shinysurveys}.
       |                                                  ^
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    18 | Custom function for toggling enable/disable state of HTML element in {shinysurveys}.
       |                                                                      ^
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    24 | \item{contype}{A character string; the type of consensus tree calculated from the posterior distribution of trees}{either "halfcompat" (majority-rule consensus tree) or "allcombat" (strict consensus tree)}
       |                                                                                                                   ^
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    59 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.'
       |                       ^
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    41 | where \emph{dist(i,j)} represents the distance between populations \emph{i} and \emph{j}, \emph{m} and \emph{n} are the number of sequences in populations \emph{i} and \emph{j}, respectively, and \emph{dist(H_{ki},H_{lj})} is the distance between the \emph{k-th} sequence found in population \emph{i} and the \emph{l-th} sequence found in population \emph{j}. 
       |                                                                                                                                                                                                                  ^
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    41 | where \emph{dist(i,j)} represents the distance between populations \emph{i} and \emph{j}, \emph{m} and \emph{n} are the number of sequences in populations \emph{i} and \emph{j}, respectively, and \emph{dist(H_{ki},H_{lj})} is the distance between the \emph{k-th} sequence found in population \emph{i} and the \emph{l-th} sequence found in population \emph{j}. 
       |                                                                                                                                                                                                                         ^
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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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See 'd:/Rcompile/CRANpkg/local/4.4/SIGN.Rcheck/00install.out' for details.
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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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    27 | individual curves, adjusted for {abcd} to lie on top of (i.e. be
       |                                 ^
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   110 | \code{\link{nlme}}) (default {nlmeControl(returnObject = TRUE)}).}
       |                              ^
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    20 |   \item{distr.type}{school district type (constructed for illustration purposes; (values={"A", "B", "C", "D"})).}
       |                                                                                          ^
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    61 | \item{replacementUnitsFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "replacementUnits.csv"}
       |                                                                    ^
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    63 | \item{subUnitTableFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "subUnitTable.csv"}
       |                                                                ^
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    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                  ^
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    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                                                                                  ^
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    26 | \item{alpha}{The eqn{\\alpha} error used to compute the \eqn{100*(1-\\alpha)\%} confidence interval}
       |                     ^
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    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |     ^
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    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |                 ^
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    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                            ^
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    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                                        ^
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    44 |   \item I.cov.rob - The matrix (V'GnV)^{-1} used to compute the statistics to detect the idiosyncratic outliers.
       |                                        ^
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    22 | https://i.cdn.turner.com/nba/nba/.element/img/4.0/global/logos/512x512/bg.white/svg/{team_short_name}.svg
       |                                                                                     ^
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    24 | sum(x' V^{-1} (y - x beta)) = 0 as the covariance V tends from V[, , 1] +
       |          ^
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     6 | A subset of world.cities{maps}. Extracted in order to shink number of dependencies. 
       |                         ^
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    17 |     \item{\code{resp}}{a factor indicating the transport mode choice, and \code{B} denotes taking the bus, code{D} denotes driving one's own vehicle, \code{F} denotes getting a ride with a friend, \code{O} denotes other, and \code{W} denotes walking}
       |                                                                                                                ^
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    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                  ^
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    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                            ^
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    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                          ^
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    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                                    ^
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    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                              ^
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    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                        ^
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    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                      ^
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    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                                ^
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Running examples in 'smiles-Ex.R' failed
The error most likely occurred in:

> ### Name: DoTSA
> ### Title: Trial sequential analysis.
> ### Aliases: DoTSA
> 
> ### ** Examples
> 
> ## Not run:
> # 1. Import a dataset of study by Fleiss (1993)
> library(meta)
Loading required package: metadat
Loading 'meta' package (version 8.1-0).
Type 'help(meta)' for a brief overview.
> data("Fleiss1993bin")
> 
> # 2. Perform trial sequential analysis
> DoTSA(Fleiss1993bin, study, year,
+       r1 = d.asp, n1 = n.asp,
+       r2 = d.plac, n2 = n.plac,
+       measure = "RR", RRR = 0.2,
+       group = c("Aspirin", "Control"))
Error in if (lgcMAAdj) { : the condition has length > 1
Calls: DoTSA
Execution halted
Error(s) in re-building vignettes:
--- re-building 'An_overview_on_pakcage_smiles.Rmd' using rmarkdown

Quitting from An_overview_on_pakcage_smiles.Rmd:170-184 [result-DoTSA]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (lgcMAAdj) ...`:
! the condition has length > 1
---
Backtrace:
    ▆
 1. └─smiles::DoTSA(...)
 2.   └─base::suppressWarnings(...)
 3.     └─base::withCallingHandlers(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'An_overview_on_pakcage_smiles.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'An_overview_on_pakcage_smiles.Rmd'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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   115 |  is the empirical explained variance from \cite{Meinshausen and B{u}hlmann, 2015}.  See \cite{Lund et al., 2020} for more details and references.
       |                                                                  ^
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   170 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
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    44 | estimMk returns the transition probability matrix of size (S^{k})xS (with S = length(E)) 
       |                                                              ^
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    10 | or code{smoof_multi_objective_function}. Both single- and multi-objective functions share the following attributes.
       |        ^
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    25 | {Hector Haffenden} {haffendenh@cardiff.ac.uk}
       |                    ^
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    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                  ^
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    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                           ^
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    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                                      ^
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    40 | Operations with V^{-1} are computed using the factorization \code{fac} (see \code{sk_var}), or
       |                   ^
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    37 | \code{quad_form} is z^T V^{-1} z, for the observed response vector z, which is constructed
       |                           ^
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    41 | returns the quadratic form X^T V^{-1} X.
       |                                  ^
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    33 | either matrix \code{V}, or X^T V^{-1} X, or a factorization ('chol' or 'eigen')
       |                                  ^
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    32 | This function efficiently constructs group-knockoffs of {0,1,2} variables distributed
       |                                                         ^
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    11 | \item{X}{a {0,1,2} matrix of size n-by-p containing the original variables.}
       |            ^
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    29 | A {0,1,2} matrix of size n-by-p containing the knockoff variables.
       |   ^
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    26 | \item{call.rate}{\code{numeric}. Threshold for removing marker by missing genotype rate. SNP with \code{call rate} below threshold are removed from dataset. Must be between {0, 1}}
       |                                                                                                                                                                              ^
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    28 | \item{maf}{Threshold for removing SNP by minor allele frequency. Must be between {0, 1}}
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    82 | \link{guides}, \link{theme} and link{guide_legend} functions from the
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    99 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
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    35 | \link{soc.csa}, \link{map.csa.all}, link{map.csa.mca.array}
       |                                         ^
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    85 | \link{guides}, \link{theme} and link{guide_legend} functions from the
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    80 | \link{guides}, \link{theme} and link{guide_legend} functions from the
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       |                          ^
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       |                                                        ^
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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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Loading required package: quickPlot
Loading required package: reproducible

It looks like this package (or one of its dependent packages) has an
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declared in DESCRIPTION.
See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package.  All dependencies must be
declared in DESCRIPTION.
See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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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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     5 | \title{Solve the equation X = AQ^{-1}t(A) under permutations}
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    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
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    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                            ^
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       |                          ^
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    25 | \env{xlabel}{
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       |         ^
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    47 | \env{printit}{
       |              ^
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    50 | \env{stage}{
       |            ^
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    40 |   matrix and weight matrix (plus a matrix with {eID} identifiers
       |                                                ^
Running 'testthat.R' [1s]
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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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    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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       |     ^
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       |                                                  ^
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    42 | and a matching \code{Qres} list attribute if {Q} was given.
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       |                                                 ^
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       |                    ^
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       |                                ^
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    55 |     \code{tol}{ - a small, positive scalar that determines when iterations 
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       |                     ^
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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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installed size is  5.7Mb
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installed size is  6.8Mb
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GNU make is a SystemRequirements.
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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 14.1Mb
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    include  11.3Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
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    27 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
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    34 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
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    67 |    \item $S_{275-295}$ slope between 275 and 295 nm calculated with nonlinear regression
       |             ^
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    68 |    \item $S_{350-400}$ slope between 350 and 400 nm calculated with nonlinear regression
       |             ^
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    69 |    \item $S_{300-700}$ slope between 275 and 295 nm calculated with nonlinear regression
       |             ^
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    70 |    \item SR slope ratio, calculated by $S_{275-295}$/$S_{350-400}$
       |                                           ^
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    70 |    \item SR slope ratio, calculated by $S_{275-295}$/$S_{350-400}$
       |                                                         ^
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    71 |    \item E2:E3 ratio $a_{250}$/$a_{365}$
       |                         ^
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    71 |    \item E2:E3 ratio $a_{250}$/$a_{365}$
       |                                   ^
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    72 |    \item E4:E6 ratio $a_{465}$/$a_{665}$
       |                         ^
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    72 |    \item E4:E6 ratio $a_{465}$/$a_{665}$
       |                                   ^
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    73 |    \item $a_{254}$ absorbance at 254 nm
       |             ^
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    74 |    \item $a_{300}$ absorbance at 300 nm
       |             ^
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   229 |   \item{report}{a character string containing only elements of {\code{"v"}, \code{"c"}, \code{"s"},\code{"t"}, \code{"p"}, \code{"*"}} that determines whether, and in which order, variable names (\code{"v"}), coefficients (\code{"c"}), standard errors/confidence intervals (\code{"s"}), test statistics (\code{"t"}) and p-values (\code{"p"}) should be reported in regression tables. If one of the aforementioned letters is followed by an asterisk (\code{"*"}), significance stars will be reported next to the corresponding statistic.}
       |                                                                ^
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   246 |   \item{table.placement}{a character string containing only elements of {\code{"h"}, \code{"t"},\code{"b"}, \code{"p"}, \code{"!"}, \code{"H"}} that determines the table placement in its LaTeX floating environment.}
       |                                                                         ^
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    16 |     \code{Side} \tab {Side of vehicle: code{1}=right or \code{2}=left}\cr
       |                                            ^
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    22 | \code{statcan_data()} function has 2 arguments to fulfill to get data: {tableNumber} & {lang}.
       |                                                                        ^
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    22 | \code{statcan_data()} function has 2 arguments to fulfill to get data: {tableNumber} & {lang}.
       |                                                                                        ^
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    18 | The \code{statcan_search()} function has 2 arguments to fulfill to find a database: {keywords} and {lang}.
       |                                                                                     ^
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    18 | The \code{statcan_search()} function has 2 arguments to fulfill to find a database: {keywords} and {lang}.
       |                                                                                                    ^
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Found the following possibly unsafe calls:
File 'statnet.common/R/control.utilities.R':
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: 'networksis'
unable to reach CRAN

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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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    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                        ^
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    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                                                                  ^
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    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                                                                      ^
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    43 | sampling from the standard normal distribution. Another example is defining func=function(n){rchisq(n=n, df=3, ncp=2)}
       |                                                                                             ^
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    19 |   \code{rows}{ every row corresponds to a different plot or community} \cr
       |              ^
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    20 |   \code{columns}{ every column corresponds to a different species.} \cr
       |                 ^
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    25 |   \code{rows}{ every row corresponds to a different species} \cr
       |              ^
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    26 |   \code{columns}{ the first column contains the name of the species, every consecutive column corresponds to a different trait} \cr
       |                 ^
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    16 |             - \code{DA}{ a vector containing the posterior distribution for the parameter dispersal assembly} \cr
       |                        ^
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    17 |             - \code{HF}{ a vector containing the posterior distribution for the parameter habitat filtering} \cr
       |                        ^
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    18 |             - \code{LS}{ a vector containing the posterior distribution for the parameter limiting similarity} \cr
       |                        ^
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    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
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    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
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    10 |   \item{semilandmark.pattern}{a regular expression pattern passed to \code{sub()} for identifying and grouping curve points. The default is landmark names ending in one or more numbers. To disable grouping, set to code{''}.}
       |                                                                                                                                                                                                                           ^
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    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("config")}
       | ^
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    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_container")}
       | ^
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    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("image")}
       | ^
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    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("plugin")}
       | ^
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    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("service")}
       | ^
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    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_task")}
       | ^
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GNU make is a SystemRequirements.
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Malformed Title field: should not end in a period.
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    14 | \code{$demographic.coord}{
       |                          ^
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    18 | \code{$genetic.coord}{
       |                      ^
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    22 | \code{$demographic.measures}{
       |                             ^
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    26 | \code{$genetic.frequencies}{
       |                            ^
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    70 | {Basic model operations:} \cr
       | ^
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    79 | {Parameter estimation:} \cr
       | ^
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    88 | {Sensitivity and Monte Carlo analyses:} \cr
       | ^
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    98 | {Compare model runs:} \cr
       | ^
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   105 | {Fishery yield analysis:} \cr
       | ^
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   111 | {Visualize model inputs:} \cr
       | ^
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   117 | {Visualize model outputs:} \cr
       | ^
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/streetscape.Rcheck/00install.out' for details.
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.
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installed size is 35.4Mb
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installed size is  9.1Mb
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efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
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    22 | \item{quant}{numeric quantile to calculate {0,1}, default 0.95.}
       |                                            ^
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    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                        ^
checkRd: (-1) cmss.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                            ^
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    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                        ^
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    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                            ^
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    18 |  used for this will be 1.00*10^{-PoissonThreshold}.}
       |                                ^
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    14 | {suggests} aims to make that workflow as minimal and painless as possible,
       | ^
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    30 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{csvdata}
       |                                ^
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    88 | \item{jsondata}{\code{deprecated} use data argument instead; data in nested d3 JSON hierarchy with `{name:...,  children:[];}`}
       |                                                                                                     ^
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    22 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{list}, \code{character},
       |                                ^
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    19 |     \item{\code{Number}:}{code{"numeric"}, number of biclusters in the set}
       |                               ^
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    42 |  \item{color.off}{color code; specifying the color for set(s) which are "{absent}" for an intersection.}
       |                                                                          ^
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     6 | getFittedValues <- function(object) {
       |                                     ^
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    14 | getFittedValues <- function(object) {
       |                                     ^
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checkRd: (-1) tprob.Rd:138: Lost braces in \itemize; meant \describe ?
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    24 | \item{mpl_h0t}{MPL estimates of the baseline hazard for T, i.e. h_{0T}(x_i)}
       |                                                                   ^
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    25 | \item{mpl_h0c}{MPL estimates of the baseline hazard for C, i.e. h_{0C}(x_i)}
       |                                                                   ^
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    26 | \item{mpl_H0t}{MPL estimates of the baseline cumulative hazard for T, i.e. H_{0T}(x_i)}
       |                                                                              ^
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    27 | \item{mpl_H0c}{MPL estimates of the baseline cumulative hazard for C, i.e. H_{0c}(x_i)}
       |                                                                              ^
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    28 | \item{mpl_S0t}{MPL estimates of the baseline survival for T, i.e. S_{0T}(x_i)}
       |                                                                     ^
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    29 | \item{mpl_S0c}{MPL estimates of the baseline survival for C, i.e. S_{0C}(x_i)}
       |                                                                     ^
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    66 | A {data.table} which is stored as an attribute of
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    76 | The estimation procedure here is performed using coxph {survival} and inserting these estimated
       |                                                        ^
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    24 | set, svKomodo loads {svSocket}, starts the socket server listening to the
       |                     ^
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    18 | Komodo and (2) the present {svKomodo} R package that work hand in hand to
       |                            ^
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    28 | Nevertheless, the SciViews-K Komodo addin and the {svKomodo} R package
       |                                                   ^
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    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                          ^
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    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                                         ^
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    37 | Both SciViews-K and {svKomodo} should be considered archived items. I keep
       |                     ^
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    32 | \code{\link[survey:surveysummary]{survey::svymean()}} and related functions from the {survey}
       |                                                                                      ^
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    28 | numeric (scalar or vector): Relative treatment effect upon crossing over from control. Note that this is not the treatment effect (the treatment effect is specified in the call to other functions such as \code{swPwr} or \code{swSim})!  If \code{tx.effect.frac} is set to a scalar with value of 1, the standard SW CRT treatment effect will be presumed. If code{tx.effect.frac} is set to a scalar with a fractional value between 0 and 1, then only the first time point upon crossing over from control will have fractional relative treatment effect; the remaining exposure times will have a relative treatment effect of 1. If a vector of fractional treatment effect is specified, each element of the vector corresponds to the (fractional) treatment effect upon crossing over from control; if the length of the vector is less than total number of exposure times, the remaining time points will have a relative treatment effect value of 1; if the length of the vector is greater than total number of time points after crossing over, not all elements of \code{tx.effect.frac} will be used. The default value is (scalar) 1.
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    18 |   \item{epsilon}{positive convergence tolerance \emph{e}; the iterations converge when |fit - fit_{old}|/|fit| < \emph{e}. Default is \emph{e=1e-04}.}
       |                                                                                                   ^
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    14 | \code{n} x 4 matrix of coordinates consisting of {lat or y, lon or x} pairs for each each site
       |                                                  ^
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    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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       |                                                                                ^
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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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checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                    ^
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                           ^
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                                          ^
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor changes:
checkRd: (-1) single_imputation.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) single_imputation.Rd:23-27: Lost braces in \itemize; meant \describe ?
Error(s) in re-building vignettes:
--- re-building 'creating_prompt_wraps.Rmd' using rmarkdown
--- finished re-building 'creating_prompt_wraps.Rmd'

--- re-building 'getting_started.Rmd' using rmarkdown
File ../man/figures/answer_using_r1-1.png not found in resource path
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'getting_started.Rmd'

--- re-building 'sentiment_analysis.Rmd' using rmarkdown
File ../man/figures/plot_sentiment_analysis-1.png not found in resource path
Error: processing vignette 'sentiment_analysis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'sentiment_analysis.Rmd'

SUMMARY: processing the following files failed:
  'getting_started.Rmd' 'sentiment_analysis.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    libs    21.1Mb
    tiledb   1.3Mb
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) setup_sql_functions.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} System Functions}
       |                ^
checkRd: (-1) setup_sql_functions.Rd:17: Lost braces; missing escapes or markup?
    17 | Installs functions needed to operated {timeseriesdb} in
       |                                       ^
checkRd: (-1) setup_sql_grant_rights.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Grant execute on {timeseriesdb} functions}
       |                         ^
checkRd: (-1) setup_sql_grant_rights.Rd:17: Lost braces; missing escapes or markup?
    17 | Grant execute on {timeseriesdb} functions
       |                  ^
checkRd: (-1) setup_sql_tables.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} System Tables}
       |                ^
checkRd: (-1) setup_sql_tables.Rd:17: Lost braces; missing escapes or markup?
    17 | Installs tables needed to operated {timeseriesdb} in
       |                                    ^
checkRd: (-1) setup_sql_triggers.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} Triggers}
       |                ^
checkRd: (-1) alcohol.Rd:16-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:22-26: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    libs   3.8Mb
Specified C++14: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) partition_undirected_graph.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{cutoff}{Numeric. The value max(0, g_{i,j} - cutoff) so that there are <\code{.num_components}> components in the graph.}
       |                                           ^
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
checkRd: (-1) tierChart.Rd:332: Lost braces
   332 |   If the input argument code{boxes} is \code{F}, the \code{lBox},
       |                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
checkRd: (-1) pmvn.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvn.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvn.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:25: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    examples  12.6Mb
    include    3.6Mb
GNU make is a SystemRequirements.
checkRd: (-1) tv_episode_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the episode_id value found in the change entries.
       |                                                 ^
checkRd: (-1) tv_season_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the season_id value found in the change entries.
       |                                                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) pvalEffectPlot.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:94: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc    9.5Mb
    help   2.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) jsonStr.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Format data as a JSON object (like this: {"x": "120"}).}
       |                                                 ^
checkRd: (-1) jsonStr.Rd:18: Lost braces; missing escapes or markup?
    18 | Format data as a JSON object (like this: {"x": "120"}).
       |                                          ^
checkRd: (-1) fixed_width_no_modeling.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:17: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^
checkRd: (-1) getSegsExtra.Rd:14: Lost braces
    14 | \item{data}{data.table returned from function /code{tdtr}}
       |                                                    ^
checkRd: (-1) ETM.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ETM.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ETM.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ETM.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ETM.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Package suggested but not available for checking: 'gurobi'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is 1113.6Mb
  sub-directories of 1Mb or more:
    R           5.9Mb
    bin         2.7Mb
    help        1.8Mb
    include    59.0Mb
    lib      1019.8Mb
    libs       18.2Mb
    share       5.6Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> 
> ### Name: nn_nll_loss
> ### Title: Nll loss
> ### Aliases: nn_nll_loss
> 
> ### ** Examples
> 
> if (torch_is_installed()) {
+ m <- nn_log_softmax(dim = 2)
+ loss <- nn_nll_loss()
+ # input is of size N x C = 3 x 5
+ input <- torch_randn(3, 5, requires_grad = TRUE)
+ # each element in target has to have 0 <= value < C
+ target <- torch_tensor(c(2, 1, 5), dtype = torch_long())
+ output <- loss(m(input), target)
+ output$backward()
+ 
+ # 2D loss example (used, for example, with image inputs)
+ N <- 5
+ C <- 4
+ loss <- nn_nll_loss()
+ # input is of size N x C x height x width
+ data <- torch_randn(N, 16, 10, 10)
+ conv <- nn_conv2d(16, C, c(3, 3))
+ m <- nn_log_softmax(dim = 1)
+ # each element in target has to have 0 <= value < C
+ target <- torch_empty(N, 8, 8, dtype = torch_long())$random_(1, C)
+ output <- loss(m(conv(data)), target)
+ output$backward()
+ }
======== End of example output (where/before crash/hang up occured ?) ========
Package suggested but not available for checking: 'toscaData'
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) parse_beast_output_files.Rd:23: Lost braces
    23 |     item{\code{estimates}: parameter estimates}
       |         ^
checkRd: (-1) parse_beast_output_files.Rd:24-28: Lost braces
    24 |     item{
       |         ^
checkRd: (-1) parse_beast_output_files.Rd:29-31: Lost braces
    29 |     item{\code{operators}: the BEAST2 MCMC operator
       |         ^
checkRd: (-1) parse_beast_posterior.Rd:28: Lost braces
    28 |     item{\code{estimates}: parameter estimates}
       |         ^
checkRd: (-1) parse_beast_posterior.Rd:29-33: Lost braces
    29 |     item{
       |         ^
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    doc    2.8Mb
checkRd: (-1) Sim-Functions.Rd:99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:100-102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:109-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:111-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:114-116: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) trait_missing.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: 'taxidata'
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs  13.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'fwelnet', 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) trtsel.Rd:69: Lost braces; missing escapes or markup?
    69 | numeric with two values {0,1} and gaussian(link = "identity") otherwise.
       |                         ^
Package suggested but not available for checking: 'TreeDistData'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   1.2Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.1Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data      1.2Mb
    doc       1.3Mb
    extdata  14.8Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   7.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) coef.tridim_transformation.Rd:31: Lost braces
    31 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
checkRd: (-1) coef.tridim_transformation.Rd:32: Lost braces
    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
checkRd: (-1) coef.tridim_transformation.Rd:32: Lost braces; missing escapes or markup?
    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
checkRd: (-1) predict.tridim_transformation.Rd:24: Lost braces
    24 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
checkRd: (-1) predict.tridim_transformation.Rd:25: Lost braces
    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
checkRd: (-1) predict.tridim_transformation.Rd:25: Lost braces; missing escapes or markup?
    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
checkRd: (-1) variable_summary.Rd:18: Lost braces; missing escapes or markup?
    18 | data.frame with "{var_name}" column for the mean and
       |                  ^
checkRd: (-1) variable_summary.Rd:19: Lost braces; missing escapes or markup?
    19 | "{var_name}_{prob}" columns for each probability.
       |  ^
checkRd: (-1) variable_summary.Rd:19: Lost braces; missing escapes or markup?
    19 | "{var_name}_{prob}" columns for each probability.
       |             ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'log2console'
checkRd: (-1) summary.armasubsets.Rd:16: Lost braces
    16 | \item{matrix.logical}{With matrix=TRUE, the matrix is logical TRUE/FALSE or string "*"/code{" "}}
       |                                                                                            ^
checkRd: (-1) tsBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diss.AR.LPC.CEPS.Rd:39: Lost braces; missing escapes or markup?
    39 | If \code{order.x} or {order.y} are \code{NULL}, their respective series will be fitted automatically using a AR model.
       |                      ^
checkRd: (-1) diss.AR.PIC.Rd:31: Lost braces; missing escapes or markup?
    31 | If \code{order.x} or {order.y} are \code{NULL}, their respective series will be fitted automatically using a AR model. If \code{permissive} is \code{TRUE} and no AR order is found automatically, an AR order of 1 will be imposed, if this case fails, then no order can be found and the function produces an error.
       |                      ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) example.database2.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database2.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database3.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database3.Rd:19: Lost braces in \itemize; meant \describe ?
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
'LazyData' is specified without a 'data' directory
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
GNU make is a SystemRequirements.
'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:
    data   4.6Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) repr_dwt.Rd:28: Lost braces; missing escapes or markup?
    28 | The final representation has length equal to floor(n / 2^{level}), where n is a length of original time series.
       |                                                          ^
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) tweedie-internal.Rd:74: Lost braces
    74 |         doi{10.1093/biomet/74.2.221}
       |            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) twosigmag.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |     ^
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |                                  ^
Package which this enhances but not available for checking: 'sl3'
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |  ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |               ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) cambodia.Rd:47: Lost braces
    47 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
checkRd: (-1) microdata.Rd:33: Lost braces
    33 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
checkRd: (-1) u5mr_cohort.Rd:111: Lost braces
   111 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
Problems with news in 'NEWS.md':
No news entries found.
Error(s) in re-building vignettes:
--- re-building 'user_sample_1.Rmd' using rmarkdown
File figure/plot_counter_1-1.png not found in resource path
Error: processing vignette 'user_sample_1.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'user_sample_1.Rmd'

--- re-building 'user_sample_2.Rmd' using rmarkdown
--- finished re-building 'user_sample_2.Rmd'

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SUMMARY: processing the following files failed:
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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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    59 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}
       |                                  ^
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    60 | \item{\code{sim_CI}}: {vector containing the cluster indices for each generated unimodal reference distribution}
       |                       ^
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    61 | \item{\code{pvalue_emp}}: {the empirical p-value:  the proportion of times the cluster index from the reference
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    63 | \item{\code{pvalue_norm}}: {the normalized p-value: the simulated p-value based on comparison to a standard normal distribution }
       |                            ^
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    58 | \item{\code{BestK}}: {A matrix with 1 row and 4 columns named: "Max_CI","Max_CI_wi_1SE","Max_scaled_CI" and "Max_logWCSS_wi_1SE".
       |                      ^
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    63 | \item{\code{full_process}}: {A matrix containing the number of clusters, K, evaluated, the CI from the data, the average CI from the null
       |                             ^
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    66 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}}
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    21 |    \code{train}{The mldr dataset with train examples, that includes all
       |                ^
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       |               ^
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    25 |    \code{validation}{Optionally, only if \code{has.validation = TRUE}.
       |                     ^
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See 'd:/Rcompile/CRANpkg/local/4.4/uuid.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
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    18 | Generate \code{n} random samples from multivariate Gaussian distribution N(0, (L^TL)^{-1})
       |                                                                                      ^
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    97 | \item{ID_level2}{Optional}{variable for unit ID codes. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                           ^
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    99 | \item{dataset}{Optional}{survey data object convertible to \code{data.table}.}
       |                         ^
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   122 | \item{ind_gr}{Optional}{variable by which divided independently X matrix of the auxiliary variables for the calibration. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                        ^
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   124 | \item{use.estVar}{Logical}{value. If value is \code{TRUE}, then \code{R} function \code{estVar} is used for the  estimation of covariance matrix of the residuals. If value is \code{FALSE}, then \code{R} function \code{estVar} is not used for the estimation of covariance matrix of the residuals.}
       |                           ^
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    69 | \item{percentratio}{Positive}{numeric value. All linearized variables are multiplied with \code{percentratio} value, by default - 1.}
       |                              ^
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   121 | \item{month_at_work}{Variable}{for total number of month at work (sum of the number of months spent at full-time work as employee, number of months spent at part-time work as employee, number of months spent at full-time work as self-employed (including family worker), number of months spent at part-time work as self-employed (including family worker)).  One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
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     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Burr distribution due to Parana\'{i}ba et al. (2011) given by
       |                                                                                                                        ^
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     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Fr\'{e}chet distribution due to Barreto-Souza et al. (2011) given by
       |                                                                                           ^
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     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                      ^
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     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                                                      ^
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     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Kumaraswamy Burr XII distribution due to Parana\'{i}ba et al. (2013) given by
       |                                                                                                                                   ^
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    40 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + exp(2*X22)*e
       |                                ^
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    42 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + 6*X22 + e
       |                                ^
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    15 | \item{file.suffix}{Regex expression for end of file name. For example, `file.suffix = '_S\\d{1,2}_.*_R1_.*'` will match R1 files.1 files.}
       |                                                                                             ^
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    23 | The function returns the K-by-K matrices {A_1, ..., A_p} as a list object.
       |                                          ^
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    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                    ^
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    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                                        ^
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    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |      ^
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    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |          ^
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    15 | and dimension information (\code{dim} or code{length}) of each item,
       |                                              ^
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     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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checkRd: (-1) ViSiElse.Rd:114-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:116: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:128-134: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:135-147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:148-157: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:152-153: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:154-155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dim-ViSibook-methods.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dim-ViSibook-methods.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary-ViSigrid-methods.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary-ViSigrid-methods.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       5.4Mb
    extdata   1.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) getTurnType.Rd:38: Lost braces; missing escapes or markup?
    38 | Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
       |               ^
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     22.1Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.5Mb
checkRd: (-1) Data-Examples.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data-Examples.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data-Examples.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aquaporin.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vsts_create_release.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vsts_create_release.Rd:34: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) WACS.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACSreadAgroclim.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) WACSreadAgroclim.Rd:16-17: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'prepr'
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) get_cid.Rd:58-59: Lost braces
    58 | <structure search> is assembled as "{\code{substructure} |
       |                                     ^
checkRd: (-1) get_cid.Rd:59-60: Lost braces
    59 | \code{superstructure} | \code{similarity} | \code{identity}} / {\code{smiles}
       |                                                                ^
checkRd: (-1) get_cid.Rd:70-71: Lost braces
    70 | "{\code{fastidentity} | \code{fastsimilarity_2d} | \code{fastsimilarity_3d} |
       |  ^
checkRd: (-1) get_cid.Rd:71-72: Lost braces
    71 | \code{fastsubstructure} | \code{fastsuperstructure}}/{\code{smiles} |
       |                                                      ^
Running examples in 'webdav-Ex.R' failed
The error most likely occurred in:

> ### Name: webdav_download_file
> ### Title: Download a file from the WebDAV server
> ### Aliases: webdav_download_file
> 
> ### ** Examples
> 
> # Example usage with a public WebDAV server.
> library(magrittr)
> library(httr2)
> test_server <- "https://www.webdavserver.com/" %>%
+   request() %>%
+   req_retry(max_tries = 1, max_seconds = 2, backoff =  ~ 1) %>%
+   req_perform()
Error in `req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.webdavserver.com]: Failed to connect to www.webdavserver.com port 443 after 10005 ms: Timeout was reached
Backtrace:
    ▆
 1. ├─... %>% req_perform()
 2. └─httr2::req_perform(.)
 3.   └─httr2:::handle_resp(req, resp, error_call = error_call)
 4.     └─rlang::cnd_signal(resp)
Execution halted
checkRd: (-1) Session.Rd:146: Lost braces
   146 | sQuote{page load} timeout specifies a time to wait for the page loading
       |       ^
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    client   9.1Mb
    doc      1.0Mb
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) busTrace.Rd:15: Lost braces
    15 | /href{https://crawdad.org/coppe-ufrj/RioBuses/20180319/}
       |      ^
Specified C++11: please drop specification unless essential
checkRd: (-1) WeightedROC.Rd:10: Lost braces; missing escapes or markup?
    10 | integer/numeric with values all in {0=negative,1=positive} or
       |                                    ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       | ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       |                            ^
checkRd: (-1) CLIC.Rd:149: Lost braces
   149 | Composite likelihood {E}{M} algorithm with applications to
       |                         ^
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   3.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_geo_box.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milakes.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:22: Lost braces in \itemize; meant \describe ?
Error(s) in re-building vignettes:
--- re-building 'wiki_utils.Rmd' using rmarkdown

Quitting from wiki_utils.Rmd:151-155 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (r[entity, "count"] > 1) ...`:
! missing value where TRUE/FALSE needed
---
Backtrace:
    ▆
 1. └─wikiTools::w_Wikipedias(entity_list = l, wikilangs = "es|en|fr")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'wiki_utils.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building 'wiki_utils.Rmd'

SUMMARY: processing the following file failed:
  'wiki_utils.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  stop.c:10:6: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/winch.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
checkRd: (-1) secondDerivative.Rd:14: Lost braces
    14 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
checkRd: (-1) windAC.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) windAC.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) windAC.Rd:33: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) word2vec_similarity.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) word2vec_similarity.Rd:31: Lost braces in \itemize; meant \describe ?
Running 'spelling.R' [0s]
  Running 'testthat.R' [36s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > require(testthat)
  Loading required package: testthat
  > test_check("wordmap")
  Loading required package: wordmap
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 115 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-textplot.R:14:5'): textplot_terms works with dictionary ──────
  `print(textplot_terms(wmp1, data_dictionary_LSD2015, max_highlighted = 10))` produced warnings.
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 115 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'wordnetDicts'
checkRd: (-1) wordpiece_cache_dir.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) wordpiece_cache_dir.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) wordpiece_cache_dir.Rd:20-21: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
Package suggested but not available for checking: 'wmtsa'
Malformed Title field: should not end in a period.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    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}}.}
       |                                                                                                                                                                                                     ^
checkRd: (-1) createDemandSite.base.Rd:26: Lost braces
    26 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
checkRd: (-1) createDemandSite.default.Rd:32: Lost braces
    32 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) wtest.Rd:61-64: Lost braces
    61 | {When \code{w.order} =2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
checkRd: (-1) wtest.high.Rd:61-64: Lost braces
    61 | {When \code{w.order} > 2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
checkRd: (-1) batch_modwt_wvar_cpp.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) batch_modwt_wvar_cpp.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) batch_modwt_wvar_cpp.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3_robust.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3_robust.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3_robust.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_wave_variance.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_wave_variance.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_wave_variance.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modwt_wvar_cpp.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modwt_wvar_cpp.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modwt_wvar_cpp.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wvar_cpp.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wvar_cpp.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wvar_cpp.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:67-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateData.Rd:47: Lost braces
    47 | \bold{code{data}} \tab the generated data \cr
       |           ^
checkRd: (-1) generateData.Rd:53: Lost braces
    53 | Refer to \bold{\emph{code{\link{retrieveDataFactory}}}} and to
       |                          ^
checkRd: (-1) qualifyFunctionArguments.Rd:14: Lost braces
    14 | A emph{\code{list}} with following names
       |       ^
checkRd: (-1) qualifyFunctionArguments.Rd:26: Lost braces
    26 | \item{code{arguments}}{a \code{pairList} of argument names and values.
       |           ^
checkRd: (-1) completeManualPage.Rd:12: Lost braces
    12 | See \emph{\bold{code{\link{ProcessingContext}}}}. Only
       |                     ^
checkRd: (-1) produceAllManualPagesFromObject.Rd:14: Lost braces
    14 | See \emph{\bold{\\code{\link{ProcessingContext}}}}.}
       |                       ^
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.5Mb
checkRd: (-1) xshow.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) xshow.Rd:20: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chemnet.Rd:111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chemnet.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:105: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    java  26.5Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
checkRd: (-1) xml_to_df.Rd:144: Lost braces; missing escapes or markup?
   144 | Default {NULL} means the workbook will not be protected with a password}
       |         ^
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  RSDTD.c:134:7: warning: 'xmlSkipBlankChars' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:135:7: warning: 'xmlParseMarkupDecl' is deprecated [-Wdeprecated-declarations]
  RUtils.c:142:5: warning: 'xmlSubstituteEntitiesDefault' is deprecated [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.4/XML.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    libs          2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    2.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) xwfGridsearch.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{iter}{Number of levels in the adaptive grid search. The resolution in b obtained is 2^{-1-iter}.}
       |                                                                                             ^
checkRd: (-1) cat_sim.Rd:110: Lost braces; missing escapes or markup?
   110 | \code{min} and {max} are mandatory for setting limits on the test length. User-defined
       |                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) boot.yhat.Rd:3: Lost braces
     3 | \title{Bootstrap metrics produced from /code{calc.yhat}}
       |                                             ^
checkRd: (-1) boot.yhat.Rd:19: Lost braces
    19 |     Ouput of /code{lm}
       |                   ^
checkRd: (-1) boot.yhat.Rd:22: Lost braces
    22 |     Output of /code{calc.yhat}
       |                    ^
checkRd: (-1) booteval.yhat.rd:3: Lost braces
     3 | \title{Evaluate bootstrap metrics produced from /code{calc.yhat}}
       |                                                      ^
checkRd: (-1) booteval.yhat.rd:5: Lost braces
     5 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
checkRd: (-1) combCI.rd:26: Lost braces
    26 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
checkRd: (-1) commonality.rd:12: Lost braces
    12 |     Output from /code{aps}
       |                      ^
checkRd: (-1) dombin.rd:12: Lost braces
    12 |     Output from /code{dominance}
       |                      ^
checkRd: (-1) dominance.rd:12: Lost braces
    12 |     Output from /code{aps}
       |                      ^
checkRd: (-1) plotCI.yhat.rd:5: Lost braces
     5 |   This function plots CIs that have been produced from /code{booteval.yhat}.
       |                                                             ^
checkRd: (-1) plotCI.yhat.rd:32: Lost braces
    32 |   This function plots CIs that have been produced from /code{booteval.yhat}.   
       |                                                             ^
checkRd: (-1) plotCI.yhat.rd:35: Lost braces
    35 | This returns a plot of CIs that have been produced from /code{booteval.yhat}.
       |                                                              ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) glm.cons.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{method}{the method used in fitting the model. The default method "\code{glm.fit.cons}" uses function {nnnpls} from package nnls instead of \code{lm.fit} to impose the sign of the coefficients. As in \code{glm}, the alternative method "\code{model.frame}" returns the model frame and does no fitting.}
       |                                                                                                            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:74: Escaped LaTeX specials: \_
checkRd: (-1) zid.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:182: Lost braces
   182 |   dQuote{tab-delimited text file} when you have done and close the spreadsheet
       |         ^
checkRd: (-1) in.zoom.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_ztable.Rd:75: Lost braces; missing escapes or markup?
    75 | must be NULL or contain only elements of {"h","t","b","p","!","H"}.}
       |                                          ^
checkRd: (-1) ztable_sub.Rd:78: Lost braces; missing escapes or markup?
    78 | must be NULL or contain only elements of {"h","t","b","p","!","H"}.
       |                                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory