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    14 | \code{n} x 4 matrix of coordinates consisting of {lat or y, lon or x} pairs for each each site
       |                                                  ^
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    28 | before plotting {ex: \code{trans = c(s = "exp", d = "exp")}}/}
       |                 ^
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.csv’
'LazyData' is specified without a 'data' directory
File ‘systemfonts/libs/systemfonts.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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    32 | inside of curly brackets, i.e., { } . For instance, if estimate = 1.23
       |                                 ^
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    33 | and error = 0.45, then \code{form} = "{estimate} ({error})" will return
       |                                       ^
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    33 | and error = 0.45, then \code{form} = "{estimate} ({error})" will return
       |                                                   ^
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    68 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
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    67 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
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'LazyData' is specified without a 'data' directory
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    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |   ^
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    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |                      ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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   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.
       |                                                                                   ^
Specified C++11: please drop specification unless essential
File ‘tardis/libs/tardis.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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
Package suggested but not available for checking: ‘tashudata’
'LazyData' is specified without a 'data' directory
File ‘tau/libs/tau.so’:
  Found non-API call to R: ‘SET_S4_OBJECT’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
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    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
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    35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
       |                                                                                                                                                                                                                                                                                                                                                  ^
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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    32 | link{squaredError}
       |     ^
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'LazyData' is specified without a 'data' directory
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   427 |       \item  Changes to \code{simulate.stergm} parameters: addition of \code{duration.dependent} parameter: {Logical: Whether the model terms in formula or model are duration dependent. E.g., if a duration-dependent term  is used in estimation/simulation model, the probability of forming or dissolving a tie may dependent on the age the dyad status. If TRUE, the matrix of tie ages will be allocated.}
       |                                                                                                             ^
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    18 | code{\link[ergm:blocks-ergmConstraint]{blocks}} constraints and
       |     ^
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     9 | code{discordance_fraction} of proposed toggles being made on the set of discordant dyads,
       |     ^
Specified C++11: please drop specification unless essential
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    19 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
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    23 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
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    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
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    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
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    10 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
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    16 | \item{\code{func}}{prepared for objective functions like SYS_LSF$func <- function(x){return(x[1] + x[2])}}
       |                                                                                     ^
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'LazyData' is specified without a 'data' directory
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    37 |  {The 2 in the first row means there are two cycles;}
       |  ^
checkRd: (-1) permucycle.Rd:38: Lost braces; missing escapes or markup?
    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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    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |               ^
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    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |                                  ^
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    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |                                                ^
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    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |                                                    ^
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    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |                                                       ^
Packages which this enhances but not available for checking:
  'mhurdle', 'mnlogit', 'Zelig'
Unknown package ‘mhurdle’ in Rd xrefs
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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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No news entries found.
File ‘textrecipes/libs/textrecipes.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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    20 |  \\tabular{rrrrr}{
       |           ^
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    20 |  \\tabular{rrrrr}{
       |                  ^
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File ‘textshaping/libs/textshaping.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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    63 | NOTE: Currently only n in {2, 3, 4, 5} are supported. For n=5 some numerical
       |                           ^
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    31 | The teigen family. Stat Comput 22:1021{1029. <doi.org/10.1007/
       |                                       ^
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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File ‘tgstat/libs/tgstat.so’:
  Found non-API call to R: ‘R_curErrorBuf’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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File ‘this.path/libs/this.path.so’:
  Found non-API calls to R: ‘IS_SCALAR’, ‘R_PromiseExpr’, ‘SETLENGTH’,
    ‘SET_ENVFLAGS’, ‘SET_PRCODE’, ‘SET_PRENV’, ‘SET_PRVALUE’,
    ‘SET_S4_OBJECT’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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GNU make is a SystemRequirements.
File ‘tibble/libs/tibble.so’:
  Found non-API call to R: ‘SET_S4_OBJECT’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tibblify/libs/tibblify.so’:
  Found non-API calls to R: ‘R_PromiseExpr’, ‘SETLENGTH’,
    ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
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    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
File ‘tidygraph/libs/tidygraph.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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    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 ?
checkRd: (-1) separate_genes.Rd:14: Lost braces
    14 | microbial genes like AbcD, default [A-Za-z][a-z]{2}[A-Z0-9]+}
       |                                                 ^
File ‘tidyr/libs/tidyr.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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
checkRd: (-1) get_tidysq_options.Rd:37: Lost braces
    37 | \item tidysq_pillar_max_width [code{integer(1)}]\cr
       |                                    ^
checkRd: (-1) read_fasta.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_fasta.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
generate_control.html:87:1 (generate_control.Rd:36): Warning: trimming empty <li>
generate_control.html:86:1 (generate_control.Rd:36): Warning: trimming empty <ol>
generate_weights.html:220:1 (generate_weights.Rd:102): Warning: trimming empty <li>
generate_weights.html:219:1 (generate_weights.Rd:102): Warning: trimming empty <ol>
Package suggested but not available for checking: ‘rrelaxiv’
File ‘timechange/libs/timechange.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘timeless/libs/timeless.so’:
  Found non-API calls to R: ‘SET_ENCLOS’, ‘SET_ENVFLAGS’, ‘SET_PRCODE’,
    ‘SET_PRENV’, ‘SET_PRVALUE’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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) POSIXst-class.Rd:247: Lost braces
   247 |   do any conversion on the POSIX{l,c}t objects).
       |                                 ^
checkRd: (-1) alcohol.Rd:16-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:22-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) add_md.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{body}{an XML object generated via {tinkr}}
       |                                         ^
checkRd: (-1) md_ns.Rd:13: Lost braces; missing escapes or markup?
    13 | The {commonmark} package is used to translate markdown to XML, but it does
       |     ^
checkRd: (-1) md_ns.Rd:14: Lost braces; missing escapes or markup?
    14 | not assign a namespace prefix, which means that {xml2} will auto-assign a
       |                                                 ^
checkRd: (-1) stylesheet.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{The {tinkr} stylesheet}
       |            ^
checkRd: (-1) stylesheet.Rd:14: Lost braces; missing escapes or markup?
    14 | This function returns the path to the {tinkr} stylesheet
       |                                       ^
checkRd: (-1) stylesheet.Rd:11: Lost braces; missing escapes or markup?
    11 | stylesheet used by {tinkr}.
       |                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'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.}
       |                                           ^
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
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
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
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘tok/libs/tok.so’:
  Found non-API calls to R: ‘SET_ENCLOS’, ‘SET_ENVFLAGS’, ‘SET_PRCODE’,
    ‘SET_PRENV’, ‘SET_PRVALUE’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
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’
'LazyData' is specified without a 'data' directory
File ‘transformr/libs/transformr.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) Blavet.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) trans.Rd:46: Lost braces; missing escapes or markup?
    46 | "Found {trans("file", .n = n_files)} in {trans("directory", .n = n_dirs)}".
       |        ^
checkRd: (-1) trans.Rd:46: Lost braces; missing escapes or markup?
    46 | "Found {trans("file", .n = n_files)} in {trans("directory", .n = n_dirs)}".
       |                                         ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘WSGeometry’
Package which this enhances but not available for checking: ‘fwelnet’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'CohortGenerator', 'Capr'
checkRd: (-1) trtsel.Rd:69: Lost braces; missing escapes or markup?
    69 | numeric with two values {0,1} and gaussian(link = "identity") otherwise.
       |                         ^
Package suggested but not available for checking: ‘TreeDistData’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘triangulr/libs/triangulr.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
File ‘triptych/libs/triptych.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘TRMF-package.Rmd’ using rmarkdown
Error: processing vignette 'TRMF-package.Rmd' failed with diagnostics:
The closing fence on line 45 ("```") in TRMF-package.Rmd does not match the opening fence "  ```" on line 43. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info.
--- failed re-building ‘TRMF-package.Rmd’

SUMMARY: processing the following file failed:
  ‘TRMF-package.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ypr_sel.html:113:1 (ypr_sel.Rd:31): Warning: trimming empty <li>
ypr_sel.html:112:1 (ypr_sel.Rd:31): Warning: trimming empty <ul>
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
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{" "}}
       |                                                                                            ^
Fortran STOP
IEEE arithmetic exceptions signaled: INEXACT
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 ?
checkRd: (-1) binary_transform.Rd:16: Lost braces; missing escapes or markup?
    16 | Converts any variable with two possible values to a {0,1} binary
       |                                                     ^
checkRd: (-1) binary_transform.Rd:13: Lost braces; missing escapes or markup?
    13 | A vector with values in {0,1}.
       |                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) repr_dwt.Rd:28: Lost braces; missing escapes or markup?
    28 | The final representation has length equal to floor(n / 2^{level}), where n is a length of original time series.
       |                                                          ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'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}
       |            ^
File ‘tweenr/libs/tweenr.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) fit_stm.Rd:25: Lost braces
    25 | \item{xcov}{Either a \[stats]{formula} with an empty left-hand side specifying external covariates
       |                              ^
'LazyData' is specified without a 'data' directory
'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
File ‘tzdb/libs/tzdb.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
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.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) alt_gsmar.Rd:50: Lost braces; missing escapes or markup?
    50 |   In addition to the S3 methods listed under the topic "Methods (by generic)", the \code{predict} and {simulate} methods
       |                                                                                                       ^
'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:
    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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
File ‘unigd/libs/unigd.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) reg_1d.Rd:42: Lost braces; missing escapes or markup?
    42 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
checkRd: (-1) reg_2d.Rd:33: Lost braces; missing escapes or markup?
    33 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simRedCard.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simRedCard.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) mllogitnorm.Rd:45: Lost braces
    45 | link[dlogitnorm]{dlogitnorm}for the normal density.
       |                 ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) UNPaC_Copula.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}
       |                                  ^
checkRd: (-1) UNPaC_Copula.Rd:60: Lost braces; missing escapes or markup?
    60 | \item{\code{sim_CI}}: {vector containing the cluster indices for each generated unimodal reference distribution}
       |                       ^
checkRd: (-1) UNPaC_Copula.Rd:61-62: Lost braces
    61 | \item{\code{pvalue_emp}}: {the empirical p-value:  the proportion of times the cluster index from the reference
       |                           ^
checkRd: (-1) UNPaC_Copula.Rd:63: Lost braces; missing escapes or markup?
    63 | \item{\code{pvalue_norm}}: {the normalized p-value: the simulated p-value based on comparison to a standard normal distribution }
       |                            ^
checkRd: (-1) UNPaC_num_clust.Rd:58-62: Lost braces
    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".
       |                      ^
checkRd: (-1) UNPaC_num_clust.Rd:63-65: Lost braces
    63 | \item{\code{full_process}}: {A matrix containing the number of clusters, K, evaluated, the CI from the data, the average CI from the null
       |                             ^
checkRd: (-1) UNPaC_num_clust.Rd:66: Lost braces; missing escapes or markup?
    66 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}}
       |                                  ^
'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) encoder.Rd:32-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) encoder.Rd:38-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) encoder.Rd:45-48: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘USA.state.boundaries.data’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) arctic.oscillations.Rd:19: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) arctic.oscillations.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) babies.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:43: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) exec.pay.Rd:5: Escaped LaTeX specials: \$
checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) sp500.excess.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
checkRd: (-1) partition_fold.Rd:21-22: Lost braces
    21 |    \code{train}{The mldr dataset with train examples, that includes all
       |                ^
checkRd: (-1) partition_fold.Rd:23-24: Lost braces
    23 |    \code{test}{The mldr dataset with test examples, defined by the
       |               ^
checkRd: (-1) partition_fold.Rd:25-26: Lost braces
    25 |    \code{validation}{Optionally, only if \code{has.validation = TRUE}.
       |                     ^
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
checkRd: (-1) sendTasks.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sendTasks.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Running examples in ‘vapour-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gdal_raster_data
> ### Title: General raster read and convert
> ### Aliases: gdal_raster_data gdal_raster_dsn gdal_raster_image
> 
> ### ** Examples
> 
> dsn <- system.file("extdata/sst.tif", package = "vapour")
> par(mfrow = c(2, 2))
> ## do nothing, get native
> X <- gdal_raster_data(dsn)

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: warp_general_cpp(dsn, target_crs, as.numeric(target_ext), as.integer(target_dim),     as.numeric(target_res), bands = as.integer(bands), resample = resample,     silent = FALSE, band_output_type = band_output_type, options = options,     dsn_outname = "")
 2: gdal_raster_data(dsn)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
checkRd: (-1) sample_gen.Rd:18: Lost braces; missing escapes or markup?
    18 | Generate \code{n} random samples from multivariate Gaussian distribution N(0, (L^TL)^{-1})
       |                                                                                      ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) vardannual.Rd:97: Lost braces
    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.}
       |                           ^
checkRd: (-1) vardannual.Rd:99: Lost braces
    99 | \item{dataset}{Optional}{survey data object convertible to \code{data.table}.}
       |                         ^
checkRd: (-1) vardcrospoor.Rd:122: Lost braces
   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.}
       |                        ^
checkRd: (-1) vardcrospoor.Rd:124: Lost braces
   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.}
       |                           ^
checkRd: (-1) vardom_othstr.Rd:69: Lost braces
    69 | \item{percentratio}{Positive}{numeric value. All linearized variables are multiplied with \code{percentratio} value, by default - 1.}
       |                              ^
checkRd: (-1) varpoord.Rd:121: Lost braces
   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.}
       |                               ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) betaburr.Rd:7: Lost braces
     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
       |                                                                                                                        ^
checkRd: (-1) betafrechet.Rd:7: Lost braces
     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
       |                                                                                           ^
checkRd: (-1) frechet.Rd:7: Lost braces
     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
       |                                                                                      ^
checkRd: (-1) frechet.Rd:7: Lost braces
     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
       |                                                                                                                      ^
checkRd: (-1) kumburr7.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Kumaraswamy Burr XII distribution due to Parana\'{i}ba et al. (2013) given by
       |                                                                                                                                   ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateDCSIS.Rd:40: Lost braces
    40 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + exp(2*X22)*e
       |                                ^
checkRd: (-1) simulateDCSIS.Rd:42: Lost braces
    42 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + 6*X22 + e
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get.miniseq.sample.files.Rd:15: Lost braces
    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.}
       |                                                                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) Acoef_sh.Rd:23: Lost braces; missing escapes or markup?
    23 | The function returns the K-by-K matrices {A_1, ..., A_p} as a list object.
       |                                          ^
checkRd: (-1) VARshrink.Rd:58: Lost braces; missing escapes or markup?
    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                    ^
checkRd: (-1) VARshrink.Rd:58: Lost braces; missing escapes or markup?
    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) decomposition.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |      ^
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |          ^
checkRd: (-1) moving.estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) datasets.Rd:15: Lost braces
    15 | and dimension information (\code{dim} or code{length}) of each item,
       |                                              ^
GNU make is a SystemRequirements.
File ‘vctrs/libs/vctrs.so’:
  Found non-API calls to R: ‘R_PromiseExpr’, ‘SETLENGTH’, ‘SET_ENCLOS’,
    ‘SET_S4_OBJECT’, ‘SET_TRUELENGTH’, ‘STDVEC_DATAPTR’,
    ‘UNSET_S4_OBJECT’

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
Specified C++11: please drop specification unless essential
File ‘vdiffr/libs/vdiffr.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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
checkRd: (-1) additiveBeta.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:33: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) predcomp.test.Rd:51: Lost braces; missing escapes or markup?
    51 | S = dbar/sqrt(2*pi*se_{d}(0)/N),
       |                       ^
checkRd: (-1) predcomp.test.Rd:53: Lost braces; missing escapes or markup?
    53 | where d is the loss differential, d = e1 - e2 (e1 = loss(x, xhat1) and e2 = loss(x, xhat2)), dbar is its sample mean, and se_{d}(0) is the standard error for d, which must be estimated, and N is the length of the series investigated.  Let V = 2*pi*se_{d}(0), then V is estimated by
       |                                                                                                                              ^
checkRd: (-1) predcomp.test.Rd:53: Lost braces; missing escapes or markup?
    53 | where d is the loss differential, d = e1 - e2 (e1 = loss(x, xhat1) and e2 = loss(x, xhat2)), dbar is its sample mean, and se_{d}(0) is the standard error for d, which must be estimated, and N is the length of the series investigated.  Let V = 2*pi*se_{d}(0), then V is estimated by
       |                                                                                                                                                                                                                                                            ^
checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex125.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
File ‘vetr/libs/vetr.so’:
  Found non-API call to R: ‘SETLENGTH’

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
checkRd: (-1) fit.vfp.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LinRegChol.Rd:21: Lost braces; missing escapes or markup?
    21 | Do linear regression of form (X^T O X + P)^{-1} X^T y where O is omega, P is
       |                                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) VirtualArray-single-bracket-method.Rd:6: Lost braces
     6 | \title{Indexing to extract subsets of a 'code{\link[via:XArray-class]{VirtualArray}}'-class object}
       |                                              ^
checkRd: (-1) subset.Rd:20: Lost braces
    20 | \item{drop}{\code{logical} in case the result of subsetting is a single element, should the \\code{\link[via:XArray-class]{VirtualArray}} wrapper be dropped?}
       |                                                                                                   ^
checkRd: (-1) vic_param.Rd:311: Lost braces
   311 | albedo must be supplied in code{forcing_veg}. Default = 1.}
       |                                ^
checkRd: (-1) vic_param.Rd:323: Lost braces
   323 | supplied in code{forcing_veg}. Default = 1.}
       |                 ^
checkRd: (-1) vic_param.Rd:341: Lost braces
   341 | be supplied in code{forcing_veg} Default = 0.}
       |                    ^
checkRd: (-1) show_query.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) show_query.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) show_query.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:16: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) RVineMatrix.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RVineMatrix.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RVineMatrix.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
Found the following HTML validation problems:
RVineClarkeTest.html:56:32 (RVineClarkeTest.Rd:31): Warning: trimming empty <code>
RVineClarkeTest.html:68:32 (RVineClarkeTest.Rd:41): Warning: trimming empty <code>
'LazyData' is specified without a 'data' directory
checkRd: (-1) viridis.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:24-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:31-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePopulation.Rd:75: Lost braces; missing escapes or markup?
    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.
       |                                                                                                                                                                                                                                                                                                                                                    ^
checkRd: (-1) NSpec.DB.Rd:16: Lost braces; missing escapes or markup?
    16 |   ...{currently not used}
       |      ^
checkRd: (-1) wavelength-methods.Rd:32: Lost braces; missing escapes or markup?
    32 | A call to {new} returns a newly allocated object from the class identified by the first argument.
       |           ^
checkRd: (-1) phasePortrait.Rd:350: Lost braces; missing escapes or markup?
   350 |   \code{vMod = xMod^(1/lambda)} and {vArg = xArg^(1/lambda)}\cr\cr
       |                                     ^
checkRd: (-1) compdesc.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) ViSiElse.Rd:101-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:105-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:108-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:112-113: Lost braces in \itemize; meant \describe ?
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) aminoAcidFun.Rd:37: Lost braces
    37 | \item{ownVLFreduced}{ownVLFMatrix}{A matrix containing only those specimen that have VLFs as well as the amino acids at the positions that contain VLFs and NAs in all other positions of the sequence.  Only appears if own is not NULL.}
       |                                   ^
checkRd: (-1) vlfFun.Rd:36: Lost braces
    36 | \item{ownVLFreduced}{ownVLFMatrix}{A matrix containing only those specimen that have VLFs as well as the nucleotides at the positions that contain VLFs and NAs in all other positions of the sequence.  Only appears if own is not NULL.}
       |                                   ^
Specified C++11: please drop specification unless essential
checkRd: (-1) getTurnType.Rd:38: Lost braces; missing escapes or markup?
    38 | Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
       |               ^
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘vroom/libs/vroom.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’,
    ‘STDVEC_DATAPTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
Found the following HTML validation problems:
get_logger.html:57:1 (get_logger.Rd:21): Warning: trimming empty <dt>
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) anchor_points_grey.Rd:9: Lost braces
     9 | Zeeden et al., (2013) and anchored to the code{\link{astrosignal_example}} \cr
       |                                               ^
checkRd: (-1) retrack_wt_MC.Rd:206: Lost braces
   206 | be off in certain intervals. the link[WaverideR]{retrack_wt_MC} mitigates
       |                                                 ^
checkRd: (-1) retrack_wt_MC.Rd:40: Lost braces
    40 | link[WaverideR]{analyze_wavelet} wavelet function
       |                ^
checkRd: (-1) retrack_wt_MC.Rd:41: Lost braces
    41 | To create a list use the link[base]{list} function}
       |                                    ^
checkRd: (-1) retrack_wt_MC.Rd:44: Lost braces
    44 | To create the matrix use the link[base]{cbind} function and only add the
       |                                        ^
Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
Specified C++11: please drop specification unless essential
checkRd: (-1) accessC.wst.rd:24: Lost braces
    24 | Note that coefficients returned by this function are in emph{packet order}. They can be used \emph{as is} but for many applications it might be more useful to deal with the coefficients in packets: see the function \code{\link{getpacket.wst}} for further details. 
       |                                                             ^
checkRd: (-1) griddata.rd:18: Lost braces
    18 | \code{G}{Codes the value of the linear interpolant matrix for the corresponding entry in \code{gridt}. The value at each point corresponds to the proportion of the original data point pointed to by \code{Gindex} that contributes to the new value at the corresponding \code{gridt} value. See Kovac, (1997), page 81 for further information.}
       |         ^
checkRd: (-1) makegrid.rd:13: Lost braces; missing escapes or markup?
    13 | \item{gridn}{The number of grid points in the dyadic grid that the (x,y) gets interpolated to. By default this is the next power of two larger than the length of {x}.}
       |                                                                                                                                                                   ^
checkRd: (-1) makewpstDO.rd:29: Lost braces
    29 | /bold{12}, 45-56.
       |      ^
checkRd: (-1) wd.object.rd:47: Lost braces
    47 | The wd class of objects has methods for the following generic functions: \code{\link{plot}}, \code{\link{threshold}}, \code{\link{summary}}, \code{\link{print}}, code{\link{draw}}.
       |                                                                                                                                                                       ^
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’
checkRd: (-1) wdpa_clean.Rd:23: Lost braces
    23 | \item{crs}{\code{character} or code{integer} object representing a
       |                                    ^
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} |
       |                                                      ^
checkRd: (-1) Session.Rd:146: Lost braces
   146 | sQuote{page load} timeout specifies a time to wait for the page loading
       |       ^
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
checkRd: (-1) predict.SDMfit.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.SDMfit.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
File ‘websocket/libs/websocket.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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
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
'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 ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) secondDerivative.Rd:14: Lost braces
    14 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
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 ?
checkRd: (-1) Hoover.Rd:21: Lost braces; missing escapes or markup?
    21 | Let x_{i} be the income of the i-th person and \eqn{\overline{x}} be the mean income. Then the Hoover index H is:
       |       ^
checkRd: (-1) RicciSchutz.Rd:21: Lost braces; missing escapes or markup?
    21 | In the case of an empirical distribution with n elements where y_{i} denotes the wealth of household i and \eqn{\overline{y}} the sample average, the Ricci and Schutz coefficient can be expressed as:
       |                                                                  ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘winfapReader.Rmd’ using rmarkdown

Quitting from lines 163-176 [unnamed-chunk-4] (winfapReader.Rmd)
Error: processing vignette 'winfapReader.Rmd' failed with diagnostics:
Can't subset columns that don't exist.
✖ Column `feh-pooling` doesn't exist.
--- failed re-building ‘winfapReader.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following HTML validation problems:
benefits.html:96:1 (benefits.Rd:39): Warning: trimming empty <h3>
beveridge.html:66:1 (beveridge.Rd:29): Warning: trimming empty <h3>
happiness.html:141:1 (happiness.Rd:54): Warning: trimming empty <h3>
hprice3.html:99:1 (hprice3.Rd:40): Warning: trimming empty <h3>
checkRd: (-1) word2vec_similarity.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) word2vec_similarity.Rd:31: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘wordnetDicts’
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.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) item.side.Rd:35: Lost braces
    35 |         code{TRUE}. If any other value, the axis is not drawn.}
       |             ^
Malformed Title field: should not end in a period.
checkRd: (-1) createDemandSite.Rd:26: Lost braces
    26 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
checkRd: (-1) createDemandSite.base.Rd:26: Lost braces
    26 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
checkRd: (-1) createDemandSite.default.Rd:32: Lost braces
    32 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) wtest.Rd:61-64: Lost braces
    61 | {When \code{w.order} =2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
checkRd: (-1) wtest.high.Rd:61-64: Lost braces
    61 | {When \code{w.order} > 2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
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}}}}.}
       |                       ^
checkRd: (-1) xbrlSECdev01.Rd:20: Lost braces in \itemize; meant \describe ?
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
Found the following files/directories:
  ‘xgb.txt’
GNU make is a SystemRequirements.
checkRd: (-1) XMLGetters-methods.Rd:165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:168-169: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:171: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:172: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:179-182: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:191: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) xml_to_df.Rd:144: Lost braces; missing escapes or markup?
   144 | Default {NULL} means the workbook will not be protected with a password}
       |         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rbokeh’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
checkRd: (-1) xwfGridsearch.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{iter}{Number of levels in the adaptive grid search. The resolution in b obtained is 2^{-1-iter}.}
       |                                                                                             ^
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
'LazyData' is specified without a 'data' directory
'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
File ‘ymd/libs/ymd.so’:
  Found non-API calls to R: ‘SET_ENCLOS’, ‘SET_ENVFLAGS’, ‘SET_PRCODE’,
    ‘SET_PRENV’, ‘SET_PRVALUE’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
File ‘yyjsonr/libs/yyjsonr.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'RNRCS', 'metScanR', 'rnoaa'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) glm.cons.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{method}{the method used in fitting the model. The default method "\code{glm.fit.cons}" uses function {nnnpls} from package nnls instead of \code{lm.fit} to impose the sign of the coefficients. As in \code{glm}, the alternative method "\code{model.frame}" returns the model frame and does no fitting.}
       |                                                                                                            ^
checkRd: (-1) label_kansuji.Rd:48: Lost braces; missing escapes or markup?
    48 | but if TRUE and installed '{scales}` package, 1.10 will be displayed.}
       |                            ^
Found the following HTML validation problems:
kana.html:65:1 (kana.Rd:33): Warning: trimming empty <dt>
'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
checkRd: (-1) inside2trans.Rd:124: Lost braces
   124 | \bold{Linking number --- {Wikipedia}{,} The Free Encyclopedia}.
       |                                     ^
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
       |         ^
File ‘zoomerjoin/libs/zoomerjoin.so’:
  Found non-API calls to R: ‘SET_ENCLOS’, ‘SET_ENVFLAGS’, ‘SET_PRCODE’,
    ‘SET_PRENV’, ‘SET_PRVALUE’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) abclass.Rd:133: Lost braces; missing escapes or markup?
   133 |     \code{abclass.control()} returns an object of class {abclass.control}
       |                                                         ^
checkRd: (-1) supclass.Rd:109: Lost braces; missing escapes or markup?
   109 | to solve the equivalent linear programming problem via the package {Rglpk}.
       |                                                                    ^
checkRd: (-1) supclass.Rd:110: Lost braces; missing escapes or markup?
   110 | It is recommended to use a recent version of {GLPK}.
       |                                              ^
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'readr', 'stringr'

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘mosaic’

Packages suggested but not available for checking:
  'car', 'ggplot2', 'HH', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) abess.Rd:260: Lost braces in \itemize; meant \describe ?
checkRd: (-1) abess.Rd:261: Lost braces in \itemize; meant \describe ?
checkRd: (-1) abess.Rd:262: Lost braces in \itemize; meant \describe ?
checkRd: (-1) abess.Rd:263: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coef.abesspca.Rd:16: Lost braces; missing escapes or markup?
    16 | This parameter is omitted if {sparse.type = "kpc"}.}
       |                              ^
checkRd: (-1) coef.abesspca.Rd:22: Lost braces; missing escapes or markup?
    22 | This parameter is omitted if {sparse.type = "fpc"}.}
       |                              ^
checkRd: (-1) generate.data.Rd:51: Lost braces
    51 | code{cortype = 3} denotes the constant structure,
       |     ^
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'googledrive', 'swfscMisc', 'kableExtra', 'gtsummary', 'ggplot2',
  'purrr', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lme4’

Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'INLA', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'sparsegl', 'fda', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'colourpicker', 'emojifont'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'od', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'dplyr', 'tmap', 'pct'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'usethis', 'tibble', 'tidyr', 'tidyselect',
  'purrr'

Packages suggested but not available for checking:
  'devtools', 'testthat', 'httptest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'reldist'

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'purrr', 'scattermore'

Packages suggested but not available for checking: 'cowplot', 'testthat'

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

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'huxtable', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'RSQLite', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lubridate', 'dplyr', 'ggplot2', 'purrr'

Packages suggested but not available for checking:
  'patchwork', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'stringr', 'readxl', 'readr', 'tibble'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Package suggested but not available for checking: ‘optimx’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) overstallwoods.Rd:184-185: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:186-187: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:188-189: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:190-191: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'DatabaseConnector', 'dplyr', 'readr', 'lubridate'

Packages suggested but not available for checking: 'tidyr', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'purrr', 'readr', 'stringr'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘effects’
Running examples in ‘acss-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: exp2
> ### Title: Data from Experiment 2 in Gauvrit, Singmann, Soler-Toscano &
> ###   Zenil
> ### Aliases: exp2
> ### Keywords: dataset
> 
> ### ** Examples
> 
> 
> # load data
> data(exp2)
> 
> exp2$K <- acss(exp2$string, 6)[,"K.6"]
> 
> m_log <- glm(response ~ K, exp2, family = binomial)
> summary(m_log)

Call:
glm(formula = response ~ K, family = binomial, data = exp2)

Coefficients:
            Estimate Std. Error z value Pr(>|z|)    
(Intercept) -69.8169     9.9890  -6.989 2.76e-12 ***
K             1.9004     0.2709   7.015 2.30e-12 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for binomial family taken to be 1)

    Null deviance: 276.94  on 199  degrees of freedom
Residual deviance: 183.37  on 198  degrees of freedom
AIC: 187.37

Number of Fisher Scoring iterations: 5

> 
> # odds ratio of K:
> exp(coef(m_log)[2])
       K 
6.688694 
> 
> # calculate threshold of 0.5
> (threshold <- -coef(m_log)[1]/coef(m_log)[2])
(Intercept) 
   36.73763 
> 
> require(effects)
Loading required package: effects
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘effects’
> require(lattice)
Loading required package: lattice
> plot(Effect("K", m_log), rescale.axis = FALSE, ylim = c(0, 1))
Error in Effect("K", m_log) : could not find function "Effect"
Calls: plot
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
      user system elapsed
acss 7.855  0.643  13.929
checkRd: (-1) Ehrenfest.Rd:19: Lost braces
    19 | In this experiment there are i balls in Urn I, and remaining 2n-i balls in Urn II. Then at any instance, the probability of selecting a ball from Urn I and placing it in Urn II is i/2n, and the other way of placing a ball from Urn II to Urn I is (2n-i)/2n. At each instant we let the number i of balls in the Urn I to be the state of the system. Thus, the state space is S = { 0, 1, 2, \ldots, 2n }. Then we can pass from state i only to either of the states i-1 or i+1.
       |                                                                                                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) Ehrenfest.Rd:20: Lost braces
    20 | Here, S = {0, 1, \ldots, 2n}. 
       |           ^
Package required but not available: ‘GDINA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cosinor', 'cosinor2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DiagrammeR', 'ggplot2', 'readr', 'reshape2', 'stringr'

Packages suggested but not available for checking: 'gdistance', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'accelerometry', 'dplyr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dbplyr', 'dplyr', 'forcats', 'ggplot2', 'hms', 'lubridate',
  'modelr', 'patchwork', 'RSQLite', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'tidyselect', 'tibble', 'shinytest2', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggmap', 'lubridate', 'tibble', 'slider'

Packages suggested but not available for checking:
  'ggplot2', 'mockery', 'roxygen2', 'styler', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running examples in ‘ActivityIndex-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Sigma0
> ### Title: \bar{sigma}_i computing using raw accelerometry data
> ### Aliases: Sigma0
> 
> ### ** Examples
> 
> filename = system.file("extdata","sample_GT3X+.csv.gz",package="ActivityIndex")
> res = ReadGT3XPlus(filename)
> hertz = res$Hertz
> x = res$Raw[ 1:1000, c("Time", "X", "Y", "Z")]
> res = Sigma0(x, hertz = hertz)
> testthat::expect_equal(res, c(SD = 0.184321637135534))
Error in loadNamespace(x) : there is no package called ‘testthat’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'tidyr', 'lubridate', 'devtools'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking: 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'readr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'progress'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cplm', 'lme4', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lubridate', 'dplyr', 'purrr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lubridate', 'dplyr', 'ggplot2', 'tibble', 'purrr', 'gt',
  'paletteer', 'recipes', 'readr', 'tidyr', 'vctrs'

Packages suggested but not available for checking: 'testthat', 'thematic'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘forecast’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'caret', 'tidyr', 'dplyr', 'ConsRank'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available:
  'Anthropometry', 'tolerance', 'univOutl'

Package suggested but not available for checking: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'optimx', 'ROI.plugin.optimx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'purrr'

Packages suggested but not available for checking: 'devtools', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'DataVisualizations', 'plotly'

Packages suggested but not available for checking: 'reshape2', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'phyloseq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'dplyr'
checkRd: (-1) adapt.Rd:46: Lost braces
    46 | \item{qvals}{a vector of values in [0, 1]U{Inf}. Q-values. See Details}
       |                                           ^
checkRd: (-1) corr_lfdr.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ctgm_lfdr.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ctgm_lfdr.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot_2d.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{plot_2d_lfdr} gives the contour plot of local FDR estimates when all p-values are equal to \code{targetp}. It is recommended to run \code{plot_2d_lfdr} for multiple \code{targetp}'s ranging from {0.001, 0.005, 0.01, 0.05}.
       |                                                                                                                                                                                                          ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'vdiffr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Advanced-example.Rmd’ using rmarkdown

Quitting from lines 216-217 [prior_posterior_20] (Advanced-example.Rmd)
Error: processing vignette 'Advanced-example.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘Advanced-example.Rmd’

--- re-building ‘Basic-examples.Rmd’ using rmarkdown
--- finished re-building ‘Basic-examples.Rmd’

--- re-building ‘Overview.Rmd’ using rmarkdown

Quitting from lines 249-254 [unnamed-chunk-10] (Overview.Rmd)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
The following required package was unavailable: ggplot2. 
Consider installing with the following command: install.packages("ggplot2")
--- failed re-building ‘Overview.Rmd’

SUMMARY: processing the following files failed:
  ‘Advanced-example.Rmd’ ‘Overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'DeconRNASeq', 'WGCNA'
checkRd: (-1) SVMDECON.Rd:23: Lost braces; missing escapes or markup?
    23 | and the best result from three values of v = {0.25, 0.5, 0.75}
       |                                              ^
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Licensed to the Apache Software Foundation (ASF) under one
  > # or more contributor license agreements.  See the NOTICE file
  > # distributed with this work for additional information
  > # regarding copyright ownership.  The ASF licenses this file
  > # to you under the Apache License, Version 2.0 (the
  > # "License"); you may not use this file except in compliance
  > # with the License.  You may obtain a copy of the License at
  > #
  > #   http://www.apache.org/licenses/LICENSE-2.0
  > #
  > # Unless required by applicable law or agreed to in writing,
  > # software distributed under the License is distributed on an
  > # "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
  > # KIND, either express or implied.  See the License for the
  > # specific language governing permissions and limitations
  > # under the License.
  > 
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Licensed to the Apache Software Foundation (ASF) under one
  > # or more contributor license agreements.  See the NOTICE file
  > # distributed with this work for additional information
  > # regarding copyright ownership.  The ASF licenses this file
  > # to you under the Apache License, Version 2.0 (the
  > # "License"); you may not use this file except in compliance
  > # with the License.  You may obtain a copy of the License at
  > #
  > #   http://www.apache.org/licenses/LICENSE-2.0
  > #
  > # Unless required by applicable law or agreed to in writing,
  > # software distributed under the License is distributed on an
  > # "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
  > # KIND, either express or implied.  See the License for the
  > # specific language governing permissions and limitations
  > # under the License.
  > 
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Licensed to the Apache Software Foundation (ASF) under one
  > # or more contributor license agreements.  See the NOTICE file
  > # distributed with this work for additional information
  > # regarding copyright ownership.  The ASF licenses this file
  > # to you under the Apache License, Version 2.0 (the
  > # "License"); you may not use this file except in compliance
  > # with the License.  You may obtain a copy of the License at
  > #
  > #   http://www.apache.org/licenses/LICENSE-2.0
  > #
  > # Unless required by applicable law or agreed to in writing,
  > # software distributed under the License is distributed on an
  > # "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
  > # KIND, either express or implied.  See the License for the
  > # specific language governing permissions and limitations
  > # under the License.
  > 
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'DBItest', 'arrow'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘gsDesign’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr', 'purrr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shinyFiles', 'stringr', 'dplyr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'parsnip', 'dplyr', 'purrr', 'tibble'

Packages suggested but not available for checking:
  'devtools', 'recipes', 'roxygen2', 'testthat', 'workflows'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'adephylo', 'progress'
checkRd: (-1) varipart.Rd:19: Lost braces
    19 | \item{type}{a character specifying the algorithm which should be used to adjust R-squared (either \code{"simulated"} or \ code{"parametric"}).}
       |                                                                                                                               ^
Running examples in ‘ade4-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: loocv.between
> ### Title: Leave-one-out cross-validation for a 'bca'
> ### Aliases: loocv.between plot.bcaloocv print.bcaloocv
> ### Keywords: dplot multivariate
> 
> ### ** Examples
> 
> # Data = meaudret
> data(meaudret)
> pca1 <- dudi.pca(meaudret$env, scannf = FALSE, nf = 3)
> bca1 <- bca(pca1, meaudret$design$site, scannf = FALSE, nf = 3)
> pst1 <- paste0("Meaudret BGA randtest: p=",
+ randtest(bca1)$pvalue, " ratio=", round(bca1$ratio, 2))
> xbca1 <- loocv(bca1, progress = TRUE)
Error in loadNamespace(x) : there is no package called ‘progress’
Calls: loocv ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
fourthcorner 4.56      0   6.556
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'igraph', 'ggplot2', 'reshape2', 'dplyr'

Packages suggested but not available for checking:
  'adespatial', 'hierfstat', 'poppr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
checkRd: (-1) adeoptions.Rd:21-23: Lost braces
    21 |   \code{epsilon}{  the smallest significant distance between two points
       |                 ^
checkRd: (-1) adeoptions.Rd:25-27: Lost braces
    25 |   \code{shortprint}{  logical.  Defines whether special \code{show}
       |                    ^
Packages required but not available: 'phylobase', 'adegenet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forcats', 'dplyr', 'readr', 'tidyr', 'haven'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'dvmisc'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'lubridate', 'reshape2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggpubr', 'latex2exp', 'forcats'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'tidyr', 'dplyr', 'purrr', 'lubridate'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘AdhereRViz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'AdhereR', 'colourpicker', 'RMariaDB', 'RSQLite'

Packages suggested but not available for checking:
  'readODS', 'readxl', 'haven'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'phylobase', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dendextend'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'yardstick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lubridate', 'dplyr', 'rvest'

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

Packages suggested but not available for checking:
  'WeightIt', 'eventglm', 'geepack', 'ggplot2', 'mice', 'pammtools',
  'pec', 'riskRegression', 'testthat', 'tidyr', 'ggpp', 'vdiffr',
  'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
'LazyData' is specified without a 'data' directory
Running examples in ‘adklakedata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adk_lake_shapes
> ### Title: Return path to Lake Polygons Shapefile
> ### Aliases: adk_lake_shapes
> 
> ### ** Examples
> 
> library(sf)
Linking to GEOS 3.12.1, GDAL 3.9.0, PROJ 9.4.1; sf_use_s2() is TRUE
> bl = read_sf(adklakedata::adk_shape())
Error in process_cpl_read_ogr(x, quiet, check_ring_dir = check_ring_dir,  : 
  package tibble not available: install first?
Calls: read_sf ... st_read -> st_read.character -> process_cpl_read_ogr
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) Amatdual.Rd:15: Lost braces
    15 |   \item{removelist}{a vector of indices into env{X} of the lifted coefficients during the transform (in the order of removal). }
       |                                                 ^
checkRd: (-1) fwtnp.Rd:30: Lost braces
    30 | Given \eqn{n} points on a line, \env{input}, each with a corresponding env{f} value this algorithm computes a lifting transform of the (\env{input},\env{f}) data. If lengths are inputted (\env{inputtype="lengths"}), then the gridpoints are taken to be the left endpoints of the intervals defined by the lengths inputted. 
       |                                                                           ^
Packages suggested but not available for checking: 'tidyverse', 'SynthETIC'
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'stringr', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'diffdf', 'pkgdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'admiral', 'admiraldev', 'dplyr', 'lubridate', 'tidyselect'

Packages suggested but not available for checking:
  'devtools', 'diffdf', 'pkgdown', 'testthat', 'roxygen2', 'stringr',
  'tibble', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'admiral', 'admiraldev', 'dplyr', 'lubridate', 'purrr', 'stringr',
  'hms', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'devtools', 'diffdf', 'pkgdown', 'testthat', 'roxygen2', 'tibble',
  'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'admiraldev', 'dplyr', 'hms', 'lubridate', 'purrr', 'stringr',
  'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'diffdf', 'readxl', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'pkgdown', 'testthat', 'roxygen2', 'usethis'
Packages required but not available:
  'admiral', 'admiraldev', 'dplyr', 'hms', 'lubridate', 'metatools',
  'purrr', 'stringr', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'devtools', 'diffdf', 'pkgdown', 'roxygen2', 'styler', 'testthat',
  'tibble', 'usethis'

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'flexsurv', 'reshape2', 'testthat'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'readr', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages required but not available: 'ggplot2', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'rstan', 'ggplot2'

Packages suggested but not available for checking: 'shinystan', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'stringr', 'purrr', 'tidyr', 'lubridate', 'ggplot2',
  'vctrs', 'progress'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'dplyr', 'ggplot2', 'tidyr'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'qgraph'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'BayesFactor', 'dplyr', 'car', 'effects', 'forcats', 'GGally',
  'ggplot2', 'Hmisc', 'readr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggplot2’
Running examples in ‘adw-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adw
> ### Title: Angular Distance Weighting Interpolation.
> ### Aliases: adw
> 
> ### ** Examples
> 
> set.seed(2)
> dd <- data.frame(lon = runif(100, min = 110, max = 117),
+                  lat = runif(100, min = 31, max = 37),
+                  value = runif(100, min = -10, max = 10))
> head(dd)
       lon      lat     value
1 111.2942 32.20561  7.173832
2 114.9166 33.56583  2.903207
3 114.0133 36.88360  2.055973
4 111.1764 35.97353  9.439614
5 116.6069 32.72184 -2.466855
6 116.6043 34.57550  6.382290
> 
> # example 1
> grd <- adw(dd, extent = c(110, 117, 31, 37), gridsize = 0.5, cdd = 500)
> head(grd)
     lon   lat       value
1 110.25 31.25  0.09027313
2 110.75 31.25  1.00411953
3 111.25 31.25 -0.35292188
4 111.75 31.25 -0.47570806
5 112.25 31.25 -1.57521787
6 112.75 31.25 -1.10541492
> 
> # example 2
> hmap <- cnmap::getMap(code = "410000") |> sf::st_make_valid() # return a 'sf' object.
Error in process_cpl_read_ogr(x, quiet, check_ring_dir = check_ring_dir,  : 
  package tibble not available: install first?
Calls: <Anonymous> ... st_read -> st_read.character -> process_cpl_read_ogr
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown

Quitting from lines 48-74 [unnamed-chunk-3] (Introduction.Rmd)
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ggplot2', 'dplyr', 'purrr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'purrr', 'tibble'

Packages suggested but not available for checking:
  'ISOweek', 'kableExtra', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'qvalue', 'tidyr', 'modelr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) fitaep.Rd:14: Lost braces
    14 | \item A sequence of goodness-of-fit measures consist of Akaike Information Criterion (\code{AIC}), Consistent Akaike Information Criterion (\code{CAIC}), Bayesian Information Criterion (\code{BIC}), Hannan-Quinn information criterion (\code{HQIC}), Anderson-Darling (\code{AD}), Cram\'{e}er-von Misses (\code{CVM}), Kolmogorov-Smirnov (\code{KS}), and log-likelihood (\code{log-likelihood}) statistics.
       |                                                                                                                                                                                                                                                                                              ^
Packages required but not available:
  'dplyr', 'ggvis', 'lubridate', 'plotly', 'ggplot2', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'tidyr', 'ggplot2', 'ggthemes', 'stringr',
  'tidyselect'

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

Packages suggested but not available for checking:
  'dynlm', 'effects', 'forecast', 'mlogit', 'rugarch',
  'sampleSelection', 'systemfit'

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

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'DescTools', 'kableExtra', 'ggmcmc', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'pbkrtest', 'lmerTest', 'car', 'reshape2'

Packages suggested but not available for checking:
  'optimx', 'nloptr', 'testthat', 'mlmRev', 'dplyr', 'tidyr',
  'ggplot2', 'MEMSS', 'effects', 'ggbeeswarm', 'cowplot', 'jtools',
  'ggpubr', 'ggpol', 'glmmTMB', 'brms', 'rstanarm', 'see', 'ez',
  'ggResidpanel', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'ggplot2', 'ggrepel'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) gini.w.Rd:20: Lost braces; missing escapes or markup?
    20 | where \eqn{x_i,x_j} are incomes of individuals \eqn{i} and {j}, respectively, \eqn{n} is the number of individuals, \eqn{\mu_w} is the mean income. The Gini coefficient ranges between 1 (perfect equality) and 1 (perfect inequality).
       |                                                            ^
Packages required but not available: 'reshape2', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'ggplot2', 'igraph', 'mixtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'car', 'forecast', 'olsrr', 'ggplot2'

Package suggested but not available for checking: ‘roxygen2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'photobiology', 'R2jags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'aftgee', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lubridate', 'GGIR', 'dplyr', 'stringr', 'ggplot2', 'RSQLite'

Packages suggested but not available for checking:
  'devtools', 'testthat', 'shinytest2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘roxygen2’
Package required but not available: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'broom', 'car', 'caret', 'stringr'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'faraway'
Running examples in ‘aglm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aglm
> ### Title: Fit an AGLM model with no cross-validation
> ### Aliases: aglm
> 
> ### ** Examples
> 
> 
> #################### Gaussian case ####################
> 
> library(MASS) # For Boston
> library(aglm)
> 
> ## Read data
> xy <- Boston # xy is a data.frame to be processed.
> colnames(xy)[ncol(xy)] <- "y" # Let medv be the objective variable, y.
> 
> ## Split data into train and test
> n <- nrow(xy) # Sample size.
> set.seed(2018) # For reproducibility.
> test.id <- sample(n, round(n/4)) # ID numbders for test data.
> test <- xy[test.id,] # test is the data.frame for testing.
> train <- xy[-test.id,] # train is the data.frame for training.
> x <- train[-ncol(xy)]
> y <- train$y
> newx <- test[-ncol(xy)]
> y_true <- test$y
> 
> ## Fit the model
> model <- aglm(x, y)  # alpha=1 (the default value)
> 
> ## Predict for various alpha and lambda
> lambda <- 0.1
> y_pred <- predict(model, newx=newx, s=lambda)
> rmse <- sqrt(mean((y_true - y_pred)^2))
> cat(sprintf("RMSE for lambda=%.2f: %.5f \n\n", lambda, rmse))
RMSE for lambda=0.10: 4.73502 

> 
> lambda <- 1.0
> y_pred <- predict(model, newx=newx, s=lambda)
> rmse <- sqrt(mean((y_true - y_pred)^2))
> cat(sprintf("RMSE for lambda=%.2f: %.5f \n\n", lambda, rmse))
RMSE for lambda=1.00: 5.70778 

> 
> alpha <- 0
> model <- aglm(x, y, alpha=alpha)
> 
> lambda <- 0.1
> y_pred <- predict(model, newx=newx, s=lambda)
> rmse <- sqrt(mean((y_true - y_pred)^2))
> cat(sprintf("RMSE for alpha=%.2f and lambda=%.2f: %.5f \n\n", alpha, lambda, rmse))
RMSE for alpha=0.00 and lambda=0.10: 5.15538 

> 
> #################### Binomial case ####################
> 
> library(aglm)
> library(faraway)
Error in library(faraway) : there is no package called ‘faraway’
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘igraph’
Package suggested but not available for checking: ‘INLA’
Packages suggested but not available for checking: 'testthat', 'lme4'
Running examples in ‘AgreementInterval-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ai
> ### Title: ai
> ### Aliases: ai
> 
> ### ** Examples
> 
> ai(x=1:4, y=c(1, 1, 2, 4))
Error in loadNamespace(x) : there is no package called ‘lme4’
Calls: ai ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'miscF', 'lme4', 'R2jags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'FielDHub', 'tibble', 'dplyr', 'tidyr', 'stplanr',
  'ggspatial'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AER', 'broom', 'car', 'desplot', 'dplyr', 'effects', 'equivalence',
  'FrF2', 'gge', 'ggplot2', 'HH', 'lme4', 'nullabor', 'pbkrtest',
  'reshape2', 'qicharts', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lmerTest', 'pbkrtest', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'lme4', 'ggpubr', 'lmerTest', 'ggrepel',
  'tibble', 'statgenSTA'

Package which this enhances but not available for checking: ‘asreml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'drc', 'ggplot2', 'dplyr', 'rcompanion', 'broom', 'egg', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'lme4', 'ggrepel', 'cowplot', 'drc'

Package suggested but not available for checking: ‘roxygen2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'readxl', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'parsnip', 'dials', 'dplyr', 'ggplot2', 'hardhat', 'purrr',
  'rsample', 'tibble', 'tidyr', 'tune', 'vctrs', 'workflows'

Packages suggested but not available for checking:
  'modeldata', 'recipes', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'grantham', 'purrr', 'stringr', 'tibble', 'tidyr', 'vctrs'

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'dplyr', 'tibble', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘AhoCorasickTrieTests.R’ [5s/9s]
  Running ‘benchmark.R’ [5s/8s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'tidyr', 'dplyr', 'randomNames'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'readxl', 'tidyr', 'ggplot2', 'igraph', 'tibble'

Packages suggested but not available for checking: 'kableExtra', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > testthat::test_check("ahw")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package required but not available: ‘unmarked’

Packages suggested but not available for checking:
  'glmmTMB', 'lme4', 'R2jags', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'car', 'dplyr', 'furrr', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘run-all.R’ [0s/1s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘meta’

Packages suggested but not available for checking: 'DiagrammeR', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'meta', 'stringr'

Package suggested but not available for checking: ‘onewaytests’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'iotarelr', 'reshape2', 'smotefamily', 'stringr'

Packages suggested but not available for checking:
  'tidytext', 'testthat', 'ggplot2', 'shinyFiles', 'readtext', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'ggplot2', 'dplyr', 'tidyr', 'metR', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

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

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tinysnapshot’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'progress', 'readr', 'readxl', 'rvest',
  'stringr', 'tidyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) CreateInputsPert.Rd:65: Lost braces
    65 | \emph{InputsPert}{[list] object of class \emph{InputsModel} containing the ensembles of perturbed model inputs required to perform data assimilation:}
       |                  ^
Packages required but not available: 'DiagrammeR', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggmcmc', 'GGally', 'ggplot2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘V01_get_started.Rmd’ using rmarkdown
--- finished re-building ‘V01_get_started.Rmd’

--- re-building ‘V02.1_param_optim.Rmd’ using rmarkdown

Quitting from lines 14-25 [setup] (V02.1_param_optim.Rmd)
Error: processing vignette 'V02.1_param_optim.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘V02.1_param_optim.Rmd’

--- re-building ‘V02.2_param_mcmc.Rmd’ using rmarkdown

Quitting from lines 14-20 [unnamed-chunk-1] (V02.2_param_mcmc.Rmd)
Error: processing vignette 'V02.2_param_mcmc.Rmd' failed with diagnostics:
there is no package called 'ggmcmc'
--- failed re-building ‘V02.2_param_mcmc.Rmd’

--- re-building ‘V03_param_sets_GR4J.Rmd’ using rmarkdown
--- finished re-building ‘V03_param_sets_GR4J.Rmd’

--- re-building ‘V04_cemaneige_hysteresis.Rmd’ using rmarkdown
--- finished re-building ‘V04_cemaneige_hysteresis.Rmd’

--- re-building ‘V05_sd_model.Rmd’ using rmarkdown
--- finished re-building ‘V05_sd_model.Rmd’

SUMMARY: processing the following files failed:
  ‘V02.1_param_optim.Rmd’ ‘V02.2_param_mcmc.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'testthat', 'tibble'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'reshape2', 'tibble'

Packages suggested but not available for checking: 'testthat', 'httptest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'MazamaCoreUtils', 'MazamaTimeSeries', 'readr',
  'stringr', 'tidyselect'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'httr2', 'tibble'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘readr’

Packages suggested but not available for checking: 'tibble', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘stuve.pdf’
Packages required but not available:
  'tidyr', 'EstCRM', 'dplyr', 'tibble', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'igraph', 'dplyr', 'ggplot2', 'stringr', 'ggraph', 'tidygraph',
  'ggforce', 'textstem', 'tibble', 'tidytext', 'ggwordcloud', 'tidyfst'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot.dke.fun.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item{las}{ Numeric in {0,1,2,3}; the style of axis labels. 
       |                          ^
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) interpp.Rd:119: Lost braces
   119 |   If \code{linear} is \\code{TRUE}, linear
       |                             ^
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggplot2', 'airr', 'dplyr', 'igraph', 'progress', 'readr', 'tibble',
  'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'readr', 'stringr', 'dataverse', 'censable', 'geomander',
  'tidyselect', 'redist', 'redistmetrics'

Packages suggested but not available for checking: 'rmapshaper', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking: 'eemR', 'EEM'
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'kableExtra', 'testthat', 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'dplyr', 'furrr', 'ggplot2', 'ggpubr', 'purrr', 'stringr',
  'tidyr', 'univariateML'

Packages suggested but not available for checking:
  'patchwork', 'readr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyselect', 'tidyr', 'tibble', 'lubridate'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

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

Packages suggested but not available for checking:
  'devtools', 'httptest', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lubridate', 'taxize', 'ritis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'org.Hs.eg.db', 'AnnotationDbi', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'HelpersMG', 'tidyr'

Packages suggested but not available for checking:
  'purrr', 'rstan', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gh', 'httr2'

Packages suggested but not available for checking: 'httptest2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BiodiversityR', 'adegenet'

Packages suggested but not available for checking:
  'poppr', 'dplyr', 'ggplot2', 'GGally', 'ggforce', 'ggrepel', 'ggsci',
  'gggibbous', 'gganimate', 'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) ASBT.Rd:36-37: Lost braces
    36 | \item{method}{Method for aggregating across categories: {"none", "max",
       |                                                         ^
checkRd: (-1) Aggregator.Rd:26: Lost braces; missing escapes or markup?
    26 | {"none", "max", "sum"}. Default: "none".}
       | ^
checkRd: (-1) DGP.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DGP.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DGP.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DGP.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OLS.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OLS.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OLS.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OLS.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'broom', 'ggplot2', 'tidyr', 'stringr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'htmlTable', 'readxl', 'reshape2', 'rio',
  'stringr', 'survminer', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyr', 'dplyr', 'bigrquery', 'purrr', 'dbplyr', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'kableExtra', 'googlesheets4', 'tibble', 'forcats', 'gh'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'testthat', 'reshape2', 'dplyr'
Running ‘testall.R’ [0s/1s]
Running the tests in ‘tests/testall.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘alluvial.Rmd’ using rmarkdown

Quitting from lines 17-25 [setup] (alluvial.Rmd)
Error: processing vignette 'alluvial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘alluvial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'lubridate', 'vctrs'

Packages suggested but not available for checking: 'slider', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'forcats'
Running examples in ‘alone-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: episodes
> ### Title: Episodes
> ### Aliases: episodes
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Packages required but not available:
  'ggplot2', 'dlookr', 'dplyr', 'ggmosaic', 'purrr', 'tibble', 'tidyr',
  'tidyselect'

Package suggested but not available for checking: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘car’
Specified C++11: please drop specification unless essential
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'dplyr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'ggridges'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘alphahull’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'purrr', 'readr', 'stringr', 'tibble', 'tidyr', 'timetk'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available: 'car', 'effects'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Packages suggested but not available for checking: 'testthat', 'roxygen2'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘repr’

Packages suggested but not available for checking:
  'purrr', 'readr', 'tibble', 'testthat', 'pryr', 'stringr', 'tidyr',
  'dplyr', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'usethis'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'purrr', 'lubridate', 'dplyr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) altopt.ic.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggmap', 'reshape2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'kableExtra', 'readr', 'readxl',
  'tibble', 'tidyr', 'tidyverse', 'webchem'

Packages suggested but not available for checking:
  'metaboliteIDmapping', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sjmisc', 'furrr'

Packages suggested but not available for checking: 'stringr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'stringr'

Packages suggested but not available for checking: 'ggplot2', 'RefManageR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
File ‘ambient/libs/ambient.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'ggplot2', 'latex2exp', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Note: skipping ‘vignette1_simulation.Rmd’ due to unavailable dependencies:
  'ggplot2'
Note: skipping ‘vignette2_trawlfct_estimation.Rmd’ due to unavailable dependencies:
  'ggplot2', 'latex2exp'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘broom’
Running examples in ‘Amelia-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mi.combine
> ### Title: Combine results from analyses on imputed data sets
> ### Aliases: mi.combine
> 
> ### ** Examples
> 
> data(africa)
> a.out <- amelia(x = africa, cs = "country", ts = "year", logs =
+ "gdp_pc")
-- Imputation 1 --

  1  2  3

-- Imputation 2 --

  1  2  3

-- Imputation 3 --

  1  2  3

-- Imputation 4 --

  1  2

-- Imputation 5 --

  1  2  3

> 
> imp.mods <- with(a.out, lm(gdp_pc ~ infl + trade))
> 
> mi.combine(imp.mods, conf.int = TRUE)
Error in `mi.combine()`:
! {broom} package required for mi.combine
Backtrace:
    ▆
 1. └─Amelia::mi.combine(imp.mods, conf.int = TRUE)
 2.   └─rlang::abort("{broom} package required for mi.combine")
Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘network’
Packages required but not available: 'heatmaply', 'readxl'

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'bayesplot', 'Hmisc'

Package suggested but not available for checking: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggcorrplot', 'ggplot2', 'reshape2'

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

Package suggested but not available for checking: ‘AICcmodavg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'MplusAutomation', 'reshape2', 'stringr', 'devtools',
  'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'AHSurv', 'flexsurv'

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

Package suggested but not available for checking: ‘ggplot2’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'progress', 'readxl', 'rvest'

Packages which this enhances but not available for checking:
  'cleaner', 'ggplot2', 'janitor', 'skimr', 'tibble', 'tidyselect',
  'tsibble'
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'broom', 'ggplot2', 'ggraph', 'moveHMM', 'suncalc', 'tidygraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'kableExtra', 'progress', 'purrr', 'reshape2',
  'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Hmisc', 'testthat'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'DESeq2', 'ggplot2', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'fda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'arrow'
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > ## Test `analogue` using the `testthat` package
  > 
  > ## Setup
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Hmisc', 'ggplot2', 'plotly', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggpubr', 'patchwork', 'purrr', 'Seurat',
  'stringr'

Packages suggested but not available for checking: 'Signac', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'mockery', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'RSQLite', 'dbplyr', 'tidyselect', 'pillar', 'hms'

Packages suggested but not available for checking:
  'testthat', 'stringr', 'tibble', 'arrow'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'ggplot2', 'cowplot'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'weights'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pryr’
checkRd: (-1) animate.Rd:625-627: Lost braces
   625 | group = function(...) {
       |                       ^
Package required but not available: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'gganimate', 'ggplot2', 'plotly', 'purrr', 'tibble',
  'tidyr', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Packages suggested but not available for checking:
  'gh', 'gistr', 'testthat', 'devtools', 'Hmisc', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tensorflow', 'dplyr', 'keras', 'tfdatasets', 'exifr', 'imager'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'animation', 'crawl', 'ggmap', 'dplyr', 'ggplot2', 'igraph',
  'lubridate', 'stringr', 'tidyr', 'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'igraph', 'lubridate', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'reshape2', 'ggplot2', 'testthat'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) concat.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                     ^
checkRd: (-1) concat.Rd:35: Lost braces
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                               ^
checkRd: (-1) concat.Rd:35: Lost braces
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                                             ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'ggpubr'

Package suggested but not available for checking: ‘GEOquery’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'purrr', 'tibble', 'dplyr', 'readr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'stringr', 'colourpicker'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'mc2d', 'EnvStats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘igraph’
Packages required but not available: 'superb', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'timetk', 'sweep', 'tibbletime', 'purrr', 'tibble', 'tidyr',
  'ggplot2'

Packages suggested but not available for checking:
  'tidyverse', 'tidyquant', 'stringr', 'testthat', 'devtools',
  'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2', 'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'superb', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'car', 'ggplot2', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'DescTools', 'HH'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'DescTools', 'HH'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'gganimate', 'ggplot2', 'testthat'
Running examples in ‘anscombiser-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anscombise_gif
> ### Title: Animation of several Anscombised datasets
> ### Aliases: anscombise_gif
> 
> ### ** Examples
> 
> # Animate some Anscombe-like datasets produced using input1 to input8
> x <- list(input1, input2, input3, input4, input5, input6, input7, input8)
> idem <- c(FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE)
> anim <- anscombise_gif(x, idempotent = idem)
Error in anscombise_gif(x, idempotent = idem) : 
  Package ''ggplot2'' is required. Please install it.
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘caret’

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lubridate', 'stringr', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'antaresRead', 'antaresProcessing', 'plotly', 'lubridate',
  'geojsonio'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'smacof'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘DescTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'competitiontoolbox'
checkRd: (-1) PS-methods.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:65-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Sim-Functions.Rd:126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:127-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:138-140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:141-143: Lost braces in \itemize; meant \describe ?
Packages required but not available: 'GGally', 'bayesplot'

Packages suggested but not available for checking:
  'dendextend', 'ggdendro', 'ggplot2'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'readr', 'lubridate', 'vroom', 'purrr', 'stringr',
  'usethis', 'roxygen2', 'progress'

Packages suggested but not available for checking:
  'testthat', 'nycflights13'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘lme4’
Running examples in ‘aod-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: iccbin
> ### Title: Intra-Cluster Correlation for Binomial Data
> ### Aliases: iccbin show,iccbin-method
> ### Keywords: htest
> 
> ### ** Examples
> 
> 
> data(rats)
> tmp <- rats[rats$group == "TREAT", ]
> # A: glmm (model linearization)
> iccbin(n, y, data = tmp, method = "A")
Error in loadNamespace(x) : there is no package called ‘lme4’
Calls: iccbin ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package suggested but not available for checking: ‘lme4’
checkRd: (-1) gof.Rd:32: Lost braces
    32 | Assuming that the data length is \eqn{N} and the number of the parameters in the model is \eqn{p}, eqn{D} and eqn{X^2} are compared to a chi-squared distribution with \eqn{N-p} degrees of freedom.
       |                                                                                                       ^
checkRd: (-1) gof.Rd:32: Lost braces
    32 | Assuming that the data length is \eqn{N} and the number of the parameters in the model is \eqn{p}, eqn{D} and eqn{X^2} are compared to a chi-squared distribution with \eqn{N-p} degrees of freedom.
       |                                                                                                                  ^
checkRd: (-1) iccbin.Rd:23: Lost braces
    23 |   \item{m}{A vector of the numbers of successes (proportions are eqn{y = m / n}).}
       |                                                                     ^
checkRd: (-1) varbin.Rd:22: Lost braces
    22 |   \item{m}{A vector of the numbers of successes (proportions are eqn{y = m / n}).}
       |                                                                     ^
Running examples in ‘aods3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: iccbin
> ### Title: Intra-Cluster Correlation for Clustered Binomial data
> ### Aliases: iccbin print.iccbin
> ### Keywords: datagen
> 
> ### ** Examples
> 
> data(rats)
> z <- rats[rats$group == "TREAT", ]
> # A: glmm (model linearization)
> iccbin(z$n, z$m, method = "A")
Error in loadNamespace(x) : there is no package called ‘lme4’
Calls: iccbin ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘roxygen2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat'
Error(s) in re-building vignettes:
  ...
--- re-building ‘access_inequality.Rmd’ using rmarkdown

Quitting from lines 25-31 [unnamed-chunk-2] (access_inequality.Rmd)
Error: processing vignette 'access_inequality.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘access_inequality.Rmd’

--- re-building ‘access_maps.Rmd’ using rmarkdown

Quitting from lines 28-33 [unnamed-chunk-2] (access_maps.Rmd)
Error: processing vignette 'access_maps.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘access_maps.Rmd’

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

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

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

--- re-building ‘landuse_maps.Rmd’ using rmarkdown

Quitting from lines 25-31 [unnamed-chunk-2] (landuse_maps.Rmd)
Error: processing vignette 'landuse_maps.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘landuse_maps.Rmd’

--- re-building ‘population_maps.Rmd’ using rmarkdown

Quitting from lines 25-32 [unnamed-chunk-2] (population_maps.Rmd)
Error: processing vignette 'population_maps.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘population_maps.Rmd’

SUMMARY: processing the following files failed:
  ‘access_inequality.Rmd’ ‘access_maps.Rmd’ ‘landuse_maps.Rmd’
  ‘population_maps.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'optimizeR', 'oeli'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'lubridate', 'tidyr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'SurvMetrics', 'testthat', 'tibble'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'cellranger', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rstan', 'dplyr', 'tibble', 'BayesFactor', 'broom', 'car',
  'highcharter', 'purrr', 'stringr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sparklyr', 'dbplyr'

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggforce', 'ggplot2', 'Seurat'

Packages suggested but not available for checking:
  'cowplot', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'MBESS', 'purrr', 'stringr', 'tibble'

Packages suggested but not available for checking: 'afex', 'ez', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'broom', 'dplyr', 'tibble', 'MBESS'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘apaTables’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readr', 'purrr', 'dplyr', 'stringr', 'arrow'

Packages suggested but not available for checking:
  'janitor', 'tidyr', 'kableExtra', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available:
  'dplyr', 'ggplot2', 'ggpubr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'randomcoloR', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'AER', 'ggplot2', 'ChainLadder'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggpubr', 'ggplot2', 'dplyr', 'tidyr', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available:
  'dplyr', 'igraph', 'reshape2', 'tibble', 'ggplot2', 'ggrepel',
  'ggforce'

Packages suggested but not available for checking:
  'Spectrum', 'clusterProfiler', 'gprofiler2', 'DOSE', 'org.Hs.eg.db',
  'testthat', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'igraph', 'phangorn'
Error(s) in re-building vignettes:
  ...
--- re-building ‘DrawingPhylogenies.Rnw’ using Sweave
--- finished re-building ‘DrawingPhylogenies.Rnw’

--- re-building ‘MoranI.Rnw’ using Sweave
--- finished re-building ‘MoranI.Rnw’

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

Error: processing vignette 'RandomTopologies.Rnw' failed with diagnostics:
 chunk 10 
Error in library(phangorn) : there is no package called ‘phangorn’

--- failed re-building ‘RandomTopologies.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'phangorn', 'adegenet'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) aphylo-class.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
checkRd: (-1) raphylo.Rd:33: Lost braces; missing escapes or markup?
    33 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
checkRd: (-1) sim_fun_on_tree.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
Found the following HTML validation problems:
mislabel.html:25:1 (mislabel.Rd:20): Warning: trimming empty <p>
raphylo.html:25:1 (raphylo.Rd:57): Warning: trimming empty <p>
sim_fun_on_tree.html:25:1 (sim_fun_on_tree.Rd:50): Warning: trimming empty <p>
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'vdiffr'
checkRd: (-1) predict_adjust.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'episensr', 'ggraph', 'igraph'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'ggplot2', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘vcdExtra’
Error(s) in re-building vignettes:
  ...
--- re-building ‘aplore3-examples.Rnw’ using knitr
\chapter{\texttt{glow} datasets}

\section{\texttt{glow500}}










Quitting from lines 5-6 [unnamed-chunk-15] (./ch/glow.Rnw)

Quitting from lines 28-50 (aplore3-examples.Rnw)
Error: processing vignette 'aplore3-examples.Rnw' failed with diagnostics:
there is no package called 'vcdExtra'
--- failed re-building ‘aplore3-examples.Rnw’

SUMMARY: processing the following file failed:
  ‘aplore3-examples.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'aplot', 'dplyr', 'forcats', 'ggfun', 'ggplot2', 'purrr', 'tibble',
  'tidyr', 'ggstar'

Package suggested but not available for checking: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggfun', 'ggplot2', 'ggplotify', 'patchwork'

Package suggested but not available for checking: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) iconplot.Rd:172: Lost braces
   172 |     the height of the area containing the panels and a margin of size code{100 * 0.1} 
       |                                                                           ^
Packages required but not available:
  'dplyr', 'tidyr', 'purrr', 'this.path', 'tidyselect'

Packages suggested but not available for checking: 'testthat', 'tibble'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'stringr'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2', 'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘rvest’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'hardhat', 'purrr', 'tibble', 'tidyr',
  'tidyselect'

Packages suggested but not available for checking:
  'modeldata', 'recipes', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘optmatch’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'httr2', 'purrr', 'tibble'

Package suggested but not available for checking: ‘testthat’

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

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

Packages suggested but not available for checking:
  'BayesianTools', 'daymetr', 'FedData', 'ggplot2', 'metrica',
  'nasapower', 'nloptr', 'sensitivity', 'soilDB'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘APBinary_PPV.csv’ ‘APBinary_TPF.csv’
  ‘APBinary_ap_summary(method=perturbation,B=1500).csv’
  ‘APBinary_auc_summary(method=perturbation,B=1500).csv’
  ‘APSurv_PPV.csv’ ‘APSurv_TPF.csv’
  ‘APSurv_ap_summary(method=bootstrap,B=500).csv’
  ‘APSurv_auc_summary(method=bootstrap,B=500).csv’
  ‘CompareAP_Binary_dap_summary(method=none).csv’
  ‘CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv’
Packages required but not available: 'erer', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'tidyselect', 'forcats', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'srvyr', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'openair', 'dplyr', 'loa', 'ggplot2', 'tidyr', 'lubridate', 'purrr',
  'ggtext'

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

Packages suggested but not available for checking:
  'soilDB', 'sharpshootR', 'markovchain', 'testthat', 'Hmisc', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'lubridate'

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

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readr', 'broom', 'dplyr', 'tidyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tibble', 'dplyr', 'stringr', 'lubridate', 'readr'

Packages suggested but not available for checking: 'testthat', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'phytools', 'rgbif'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                              ^
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                                            ^
Packages required but not available: 'ggplot2', 'qqplotr'

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

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'tibble', 'tidygeocoder'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arcgisutils', 'httr2'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arcgisutils', 'httr2'

Packages suggested but not available for checking:
  'dbplyr', 'dplyr', 'testthat', 'tidyselect', 'vctrs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arcgisutils', 'httr2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arcgislayers', 'arcgisutils', 'httr2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dbplyr', 'httr2'

Packages suggested but not available for checking:
  'arcgisbinding', 'vctrs', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'plotly', 'reshape2'

Packages suggested but not available for checking: 'SEAHORS', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyverse', 'skimr', 'stringr', 'snakecase', 'testthat', 'feather',
  'readr'

Packages suggested but not available for checking:
  'broom', 'caret', 'gtsummary', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Package suggested but not available for checking: ‘TDA’
Package required but not available: ‘tibble’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'rvest', 'stringr', 'tibble',
  'tidyr'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lubridate', 'RSQLite'

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'ggplot2', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) estimate_t0.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_t0.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_t0.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:75: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking: 'dplyr', 'httr2'
File ‘arcpbf/libs/arcpbf.so’:
  Found non-API calls to R: ‘SET_ENCLOS’, ‘SET_ENVFLAGS’, ‘SET_PRCODE’,
    ‘SET_PRENV’, ‘SET_PRVALUE’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'rvest', 'stringr', 'cowplot', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'tibble', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘lubridate’

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'nardl', 'car', 'stringr', 'purrr', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'dynlm', 'ggplot2', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'tibble', 'testthat'
Running examples in ‘ards-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_ards
> ### Title: Adds data to an Analysis Results Dataset
> ### Aliases: add_ards
> 
> ### ** Examples
> 
> library(ards)
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'readr', 'stringr', 'tibble', 'tidyr', 'tidyselect',
  'tabshiftr', 'ontologics', 'purrr', 'rmapshaper', 'progress'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
File ‘area/libs/area.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'tidyr', 'dplyr', 'purrr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ingredients', 'iBreakDown', 'gistr', 'auditor', 'DALEX',
  'fairmodels'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'tibble', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown

Quitting from lines 24-34 [arf] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'colourpicker', 'lubridate', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'tidyverse', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘run-all.R’ [0s/1s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'DescribeDF', 'dplyr', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'text2speech', 'purrr', 'rvest', 'progress', 'hms'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'arrow', 'progress', 'readr', 'dplyr', 'dbplyr', 'nycflights13',
  'testthat', 'RSQLite', 'vroom'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘arkdb.Rmd’ using rmarkdown

Quitting from lines 45-52 [unnamed-chunk-1] (arkdb.Rmd)
Error: processing vignette 'arkdb.Rmd' failed with diagnostics:
there is no package called 'dbplyr'
--- failed re-building ‘arkdb.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'rugarch', 'tensorflow', 'keras'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Running examples in ‘ar.matrix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Q.AR1
> ### Title: Precision matrix for an AR1 process
> ### Aliases: Q.AR1 r.AR1
> 
> ### ** Examples
> 
> require("ggplot2")
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> # simulate AR1 GMRF
> obs <- r.AR1(100, M=30, sigma=1, rho=.98)
> # resulting matrix is n x M
> dim(obs)
[1] 100  30
> # subtract off the first time point to more easily observe correlation
> obs_adj <- obs - obs[,1]
> # move objects to a data frame
> ar1_df <- data.frame(obs=c(t(obs_adj)), realization=rep(1:100, each=30),
+                      time=rep(1:30, 100))
> # plot each realization
> ggplot(data=ar1_df, aes(time, obs, group=realization, color=realization)) +
+     geom_line()
Error in ggplot(data = ar1_df, aes(time, obs, group = realization, color = realization)) : 
  could not find function "ggplot"
Execution halted
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'oligo', 'oligoClasses', 'pdInfoBuilder'
Packages unavailable to check Rd xrefs: ‘oligo’, ‘oligoClasses’
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyselect', 'dplyr', 'lubridate', 'readr', 'stringr', 'tidyr',
  'purrr', 'eurostat', 'ggplot2', 'tibble', 'archive'

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'reshape2', 'dplyr', 'ggplot2', 'viridis', 'testthat'
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘purrr’

Packages suggested but not available for checking: 'ggarrow', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'blob', 'dbplyr', 'decor', 'dplyr', 'hms', 'lubridate', 'pillar',
  'stringr', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'broom', 'testthat', 'geepack'
Running examples in ‘arsenal-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: modelsum
> ### Title: Fit models over each of a set of independent variables with a
> ###   response variable
> ### Aliases: modelsum
> 
> ### ** Examples
> 
> 
> data(mockstudy)
> 
> tab1 <- modelsum(bmi ~ sex + age, data = mockstudy)
Error in check_pkg("broom") : 
  Package 'broom' is required for this functionality, but is not installed.
Calls: modelsum -> modelsum_guts -> check_pkg
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'dplyr'
Running examples in ‘arthistory-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: artists
> ### Title: Artists by edition of Gardner or Janson's art history textbook
> ### Aliases: artists
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lme4', 'car', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tidyr', 'lmerTest', 'phia', 'DescTools',
  'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'stringr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'kknn'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'pmml', 'arulesViz', 'testthat'
Running examples in ‘arules-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pmml
> ### Title: Read and Write PMML
> ### Aliases: pmml write.PMML read.PMML
> ### Keywords: interface
> 
> ### ** Examples
> 
> data("Groceries")
> 
> rules <- apriori(Groceries, parameter = list(support = 0.001))
Apriori

Parameter specification:
 confidence minval smax arem  aval originalSupport maxtime support minlen
        0.8    0.1    1 none FALSE            TRUE       5   0.001      1
 maxlen target  ext
     10  rules TRUE

Algorithmic control:
 filter tree heap memopt load sort verbose
    0.1 TRUE TRUE  FALSE TRUE    2    TRUE

Absolute minimum support count: 9 

set item appearances ...[0 item(s)] done [0.00s].
set transactions ...[169 item(s), 9835 transaction(s)] done [0.01s].
sorting and recoding items ... [157 item(s)] done [0.00s].
creating transaction tree ... done [0.00s].
checking subsets of size 1 2 3 4 5 6 done [0.02s].
writing ... [410 rule(s)] done [0.00s].
creating S4 object  ... done [0.00s].
> rules <- head(rules, by = "lift")
> rules
set of 6 rules 
> 
> ### save rules as PMML
> write.PMML(rules, file = "rules.xml")
Error in as.vector(x, "character") : 
  cannot coerce type 'closure' to vector of type 'character'
Calls: write.PMML -> check_installed
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'igraph', 'ggplot2', 'ggraph', 'tibble', 'tidyr', 'dplyr', 'plotly'

Packages suggested but not available for checking: 'tidygraph', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'hms', 'lubridate', 'lutz', 'purrr', 'readr', 'spsurvey',
  'stringr', 'suncalc', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'patchwork', 'readxl', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'magick', 'tibble'

Packages suggested but not available for checking:
  'decor', 'mockery', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Hmisc’
Package required but not available: ‘stringr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'haven', 'readr', 'vroom', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lubridate', 'lutz', 'purrr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'alphahull', 'TDA', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘adaptive_shrinkage.Rmd’ using rmarkdown

Quitting from lines 28-30 [load_packages] (adaptive_shrinkage.Rmd)
Error: processing vignette 'adaptive_shrinkage.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘adaptive_shrinkage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'exact2x2', 'exactci', 'bpcp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'httr2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'batchtools', 'ggplot2', 'llama', 'mlr', 'reshape2', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sna’
Running examples in ‘asnipe-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: network_permutation
> ### Title: Perform Permutation
> ### Aliases: network_permutation
> 
> ### ** Examples
> 
> 
> ### USING TIMES, ETC.
> 
> data("group_by_individual")
> data("times")
> 
> # subset GBI (to reduce run time of the example)
> gbi <- gbi[,1:80]
> 
> ## define to 2 x N x N network to hold two association matrices
> networks <- array(0, c(2, ncol(gbi), ncol(gbi)))
> 
> ## calculate network for first half of the time
> networks[1,,] <- get_network(gbi, data_format="GBI", 
+ 	association_index="SRI", times=times, start_time=0, 
+ 	end_time=max(times)/2)
Generating  80  x  80  matrix
> networks[2,,] <- get_network(gbi, data_format="GBI",
+ 	association_index="SRI", times=times, 
+ 	start_time=max(times)/2, end_time=max(times))
Generating  80  x  80  matrix
> 
> ## calculate the weighted degree
> library(sna)
Error in library(sna) : there is no package called ‘sna’
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
get_network 4.407  0.016   6.863
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sem’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dae', 'devtools', 'dplyr', 'ggplot2', 'nloptr', 'qqplotr',
  'reshape2', 'stringr'

Packages suggested but not available for checking:
  'lmerTest', 'pbkrtest', 'testthat'

Package which this enhances but not available for checking: ‘asreml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cowplot', 'factoextra', 'ggplot2', 'scattermore', 'superheat'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                    ^
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                                                                                                                 ^
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                                                                                                                          ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘dplyr’

Packages suggested but not available for checking: 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'AER', 'faraway', 'testthat'
Running examples in ‘assessor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: resid_semiconti
> ### Title: Residuals for regression models with semicontinuous outcomes
> ### Aliases: resid_semiconti
> 
> ### ** Examples
> 
> ## Tweedie model
> library(tweedie)
> library(statmod)
> n <- 500
> x11 <- rnorm(n)
> x12 <- rnorm(n)
> beta0 <- 5
> beta1 <- 1
> beta2 <- 1
> lambda1 <- exp(beta0 + beta1 * x11 + beta2 * x12)
> y1 <- rtweedie(n, mu = lambda1, xi = 1.6, phi = 10)
> # Choose parameter p
> # True model
> model1 <-
+   glm(y1 ~ x11 + x12,
+     family = tweedie(var.power = 1.6, link.power = 0)
+   )
> resid.tweedie <- resid_semiconti(model1)
> 
> ## Tobit regression model
> library(VGAM)
Loading required package: stats4
Loading required package: splines
> beta13 <- 1
> beta14 <- -3
> beta15 <- 3
> 
> set.seed(1234)
> x11 <- runif(n)
> x12 <- runif(n)
> lambda1 <- beta13 + beta14 * x11 + beta15 * x12
> sd0 <- 0.3
> yun <- rnorm(n, mean = lambda1, sd = sd0)
> y <- ifelse(yun >= 0, yun, 0)
> 
> # Using VGAM package
> # True model
> fit1 <- vglm(formula = y ~ x11 + x12, tobit(Upper = Inf, Lower = 0, lmu = "identitylink"))
> # Missing covariate
> fit1miss <- vglm(formula = y ~ x11, tobit(Upper = Inf, Lower = 0, lmu = "identitylink"))
> 
> resid.tobit1 <- resid_semiconti(fit1, plot = TRUE)
> resid.tobit2 <- resid_semiconti(fit1miss, plot = TRUE)
> 
> # Using AER package
> library(AER)
Error in library(AER) : there is no package called ‘AER’
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
resid_quasi 7.786  0.157  12.203
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'RiskPortfolios', 'riskParityPortfolio'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot.AssetPricing.Rd:199-200: Lost braces
   199 |   yakka. (Note that \code{flap} stands for dQuote{function list
       |                                                  ^
Packages required but not available:
  'caret', 'ggplot2', 'reshape2', 'stringr'

Packages suggested but not available for checking: 'klaR', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'dfdr'

Packages suggested but not available for checking: 'kableExtra', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'asteRiskData', 'plotly', 'dplyr', 'ggmap'
Specified C++11: please drop specification unless essential
checkRd: (-1) readOEM.Rd:34: Lost braces
    34 |   always, the identifier has the format YYYY-NNNP{PP}, where YYYY is the year
       |                                                  ^
checkRd: (-1) readOEM.Rd:36: Lost braces
    36 |   during year YYYY and P{PP} is a part specifier comprising 1 to 3 capital letters
       |                         ^
checkRd: (-1) readOEM.Rd:74-75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readOEM.Rd:76-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readOEM.Rd:80-86: Lost braces in \itemize; \value handles \item{}{} directly
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘haplo.stats’
Running examples in ‘asymLD-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compute.ALD
> ### Title: Compute ALD.
> ### Aliases: compute.ALD
> 
> ### ** Examples
> 
> library(asymLD)
> 
> # An example using haplotype frequencies from Wilson(2010)
> data(hla.freqs)
> hla.a_b <- hla.freqs[hla.freqs$locus1=="A" & hla.freqs$locus2=="B",]
> compute.ALD(hla.a_b)
   ALD.x.y is asymmetric LD for locus x conditioned on locus y

  locus1 locus2       F.1    F.1.2        F.2     F.2.1   ALD.1.2   ALD.2.1
1      A      B 0.1021811 0.340332 0.04876543 0.1903394 0.5150291 0.3857872
> hla.freqs$locus <- paste(hla.freqs$locus1, hla.freqs$locus2, sep="-")
> compute.ALD(hla.freqs[hla.freqs$locus=="C-B",])
   ALD.x.y is asymmetric LD for locus x conditioned on locus y

  locus1 locus2        F.1     F.1.2        F.2     F.2.1   ALD.1.2   ALD.2.1
1      C      B 0.08637241 0.7350216 0.05040254 0.4520268 0.8425979 0.6503396
> # Note: additonal columns on the input dataframe (e.g., "locus" above) are allowed, but
> # ignored by the function.
> 
> # An example using genotype data from the haplo.stats package
> require(haplo.stats)
Loading required package: haplo.stats
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘haplo.stats’
> data(hla.demo)
Warning in data(hla.demo) : data set ‘hla.demo’ not found
> geno <- hla.demo[,5:8]  #DPB-DPA
Error: object 'hla.demo' not found
Execution halted
Package required but not available: ‘smacof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
Loading required package: dplyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'dplyr'

Quitting from lines 59-69 [example_fig] (example.Rmd)
Error: processing vignette 'example.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'testthat', 'stringr'

Packages suggested but not available for checking:
  'dplyr', 'profvis', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'doBy', 'reshape2', 'Hmisc', 'DescTools'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'stR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ataCoKriging.Rd:52: Lost braces; missing escapes or markup?
    52 | only one contrained condition for all points and all variables, \\sum_{i=1}^n\\lambda_i +\\sum_{j=1}^m\\beta_j =1, assuming expected means of variables known and constant with the study area.
       |                                                                       ^
checkRd: (-1) ataCoKriging.Rd:52: Lost braces; missing escapes or markup?
    52 | only one contrained condition for all points and all variables, \\sum_{i=1}^n\\lambda_i +\\sum_{j=1}^m\\beta_j =1, assuming expected means of variables known and constant with the study area.
       |                                                                                                ^
Packages suggested but not available for checking: 'testthat', 'ggplot2'
checkRd: (-1) simulation_dgp.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{x_discrete}{TRUE if the distribution of the covariate is uniform on {-3.0, -2.9, ..., 3.0} and
       |                                                                           ^
checkRd: (-1) simulation_dgp.Rd:23: Lost braces
    23 | \item{att_oracle}{the sample analog of E[D{Y(1) - Y(0)}|D=1]}
       |                                           ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ATbounds_vignette.Rmd’ using rmarkdown

Quitting from lines 344-357 [unnamed-chunk-27] (ATbounds_vignette.Rmd)
Error: processing vignette 'ATbounds_vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘ATbounds_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘bench’

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'readr', 'dplyr', 'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'openair', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'readr', 'rdflib'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggridges'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘trtf’
Packages required but not available:
  'httr2', 'purrr', 'stringr', 'snakecase', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'forcats', 'ggplot2', 'ggraph', 'igraph', 'magick',
  'testthat', 'tidygraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'roxygen2', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'lubridate', 'lme4', 'arm', 'tibble', 'stringr', 'ggplot2',
  'progress'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'ggbeeswarm', 'ggthemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) audioSample.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) audioSample.Rd:21: Lost braces in \itemize; meant \describe ?
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages required but not available: 'DALEX', 'ggplot2', 'ggrepel'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'ggplot2', 'readr', 'stringr', 'lubridate', 'narray',
  'imputeTS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'readr'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'unmarked'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'penaltyLearning', 'atime', 'ggrepel'
Running examples in ‘aum-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aum_line_search
> ### Title: aum line search
> ### Aliases: aum_line_search
> 
> ### ** Examples
> 
> 
> if(require("data.table"))setDTthreads(1L)#for CRAN check.
Loading required package: data.table
> 
> ## Example 1: two binary data.
> (bin.diffs <- aum::aum_diffs_binary(c(0,1)))
Key: <example, pred>
   example  pred fp_diff fn_diff
     <int> <num>   <num>   <num>
1:       0     0       1       0
2:       1     0       0      -1
> if(requireNamespace("ggplot2"))plot(bin.diffs)
Loading required namespace: ggplot2
Failed with error:  ‘there is no package called ‘ggplot2’’
> bin.line.search <- aum::aum_line_search(bin.diffs, pred.vec=c(10,-10))
> if(requireNamespace("ggplot2"))plot(bin.line.search)
Loading required namespace: ggplot2
Failed with error:  ‘there is no package called ‘ggplot2’’
> 
> ## Example 2: two changepoint examples, one with three breakpoints.
> data(neuroblastomaProcessed, package="penaltyLearning", envir=environment())
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘penaltyLearning’
Calls: data -> find.package
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘speed-comparison.Rmd’ using knitr

Quitting from lines 22-44 [unnamed-chunk-1] (speed-comparison.Rmd)
Error: processing vignette 'speed-comparison.Rmd' failed with diagnostics:
there is no package called 'penaltyLearning'
--- failed re-building ‘speed-comparison.Rmd’

SUMMARY: processing the following file failed:
  ‘speed-comparison.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'igraph', 'reshape2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'stringr', 'progress'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'purrr', 'tibble'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'ggplot2'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Packages required but not available:
  'dplyr', 'broom', 'ggplot2', 'tibble', 'progress'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'SimDesign', 'thurstonianIRT', 'MplusAutomation', 'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readr', 'dplyr', 'enrichR', 'DESeq2', 'ggplot2', 'ggrepel', 'GSVA',
  'purrr', 'reshape2', 'stringr', 'tidyr', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'stringr', 'tidyr', 'tibble', 'pryr', 'igraph'

Packages suggested but not available for checking:
  'readxl', 'rvest', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'ggplot2', 'lubridate'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'gear', 'broom'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'lme4', 'tibble', 'EBMAforecast', 'ggplot2', 'tidyr',
  'purrr', 'forcats', 'vglmer', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'annotate', 'fgsea', 'org.Hs.eg.db', 'clusterProfiler', 'msigdbr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'plotly', 'ggfortify'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Autoplotprotein-package.Rd:27: Lost braces
    27 | code{\link{help}}
       |     ^
checkRd: (-1) Autoplotprotein.Rd:25: Lost braces
    25 | code{\link{help}}
       |     ^
checkRd: (-1) data.Rd:22: Lost braces
    22 | code{\link{help}}
       |     ^
checkRd: (-1) domain_data.Rd:29: Lost braces
    29 | code{\link{help}}
       |     ^
checkRd: (-1) length_data.Rd:32: Lost braces
    32 | code{\link{help}}
       |     ^
checkRd: (-1) plotdomain.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotmutagensis.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotsite.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) site_data.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
Packages required but not available: 'dplyr', 'echarts4r', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'moonBook', 'dplyr', 'stringr', 'tidyr', 'purrr', 'mice',
  'patchwork', 'ggplot2', 'broom', 'tidycmprsk', 'pammtools'

Packages suggested but not available for checking:
  'finalfit', 'lme4', 'survminer', 'PairedData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tableone', 'ggplot2', 'Hmisc', 'car', 'coxed', 'dplyr', 'tidyr',
  'plotly', 'randomForestSRC', 'survAUC', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘roxygen2’
Packages required but not available:
  'dplyr', 'stringr', 'tidyselect', 'purrr', 'janitor', 'tibble',
  'broom', 'ggeasy', 'ggplot2', 'jtools', 'ggthemes', 'patchwork',
  'tidyr', 'parsnip', 'recipes', 'rsample', 'tune', 'workflows',
  'framecleaner', 'presenter', 'yardstick', 'dials', 'broom.mixed',
  'igraph'

Packages suggested but not available for checking:
  'forcats', 'hardhat', 'ggstance', 'readr', 'lubridate'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forecast', 'lubridate', 'ggplot2', 'ggrepel', 'progress'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ijtiff', 'purrr', 'strex', 'stringr'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'styler', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘matlab2r’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'prophet', 'dplyr', 'lubridate', 'tidyr', 'forecast', 'ggplot2',
  'plotly'

Package suggested but not available for checking: ‘stringr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidytext', 'tibble'

Packages suggested but not available for checking: 'usethis', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'tidyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readxl', 'ggplot2', 'stringr', 'tidyr', 'ggthemes', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
Error(s) in re-building vignettes:
  ...
--- re-building ‘full-example.Rmd’ using rmarkdown

Quitting from lines 222-243 [unnamed-chunk-7] (full-example.Rmd)
Error: processing vignette 'full-example.Rmd' failed with diagnostics:
there is no package called 'caret'
--- failed re-building ‘full-example.Rmd’

SUMMARY: processing the following file failed:
  ‘full-example.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'purrr', 'ggplot2', 'janitor', 'lubridate', 'tidyr',
  'ggrepel'
Error(s) in re-building vignettes:
  ...
--- re-building ‘a_intro.Rmd’ using rmarkdown

Quitting from lines 121-124 [unnamed-chunk-2] (a_intro.Rmd)
Error: processing vignette 'a_intro.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘a_intro.Rmd’

--- re-building ‘b_analyze-hass-cntry.Rmd’ using rmarkdown

Quitting from lines 22-29 [setup] (b_analyze-hass-cntry.Rmd)
Error: processing vignette 'b_analyze-hass-cntry.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘b_analyze-hass-cntry.Rmd’

--- re-building ‘b_analyze-hass-region.Rmd’ using rmarkdown

Quitting from lines 24-31 [setup] (b_analyze-hass-region.Rmd)
Error: processing vignette 'b_analyze-hass-region.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘b_analyze-hass-region.Rmd’

--- re-building ‘b_analyze-hass.Rmd’ using rmarkdown

Quitting from lines 24-31 [setup] (b_analyze-hass.Rmd)
Error: processing vignette 'b_analyze-hass.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘b_analyze-hass.Rmd’

SUMMARY: processing the following files failed:
  ‘a_intro.Rmd’ ‘b_analyze-hass-cntry.Rmd’ ‘b_analyze-hass-region.Rmd’
  ‘b_analyze-hass.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'phytools', 'stringr', 'tidytree'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'gapminder'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'roxygen2'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'viridis', 'haven', 'readxl', 'readODS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lubridate', 'dplyr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'mockery', 'pkgdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘lubridate’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘vctrs’

Packages suggested but not available for checking:
  'AzureTableStor', 'odbc', 'dplyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'vctrs', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'AzureStor', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'tibble', 'dplyr', 'tidyr', 'tidyselect'

Packages suggested but not available for checking: 'testthat', 'AzureStor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'dplyr'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'AzureStor'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘vctrs’

Packages suggested but not available for checking: 'readr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'AzureStor', 'vctrs'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘blob’

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'nlmixr2', 'nlmixr2est', 'nonmem2rx', 'rxode2'

Packages suggested but not available for checking:
  'testthat', 'lixoftConnectors', 'PKNCA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'dynutils', 'purrr'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking: 'testthat', 'dplyr'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'igraph', 'reshape2', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'pcalg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bacon.Rmd’ using rmarkdown

Quitting from lines 54-60 [plot] (bacon.Rmd)
Error: processing vignette 'bacon.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘bacon.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dlstats', 'usethis'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.r’ [0s/0s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'readr'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rstan', 'bayesplot', 'ggplot2', 'ggplotify', 'ggrepel', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'parsnip', 'butcher', 'C50', 'dials', 'dplyr', 'furrr', 'hardhat',
  'purrr', 'rsample', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'AmesHousing', 'modeldata', 'recipes', 'testthat', 'yardstick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'lubridate', 'testthat', 'tibble', 'tidyr'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bagyo.Rmd’ using rmarkdown
--- finished re-building ‘bagyo.Rmd’

--- re-building ‘visualisation.Rmd’ using rmarkdown

Quitting from lines 20-25 [setup] (visualisation.Rmd)
Error: processing vignette 'visualisation.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘visualisation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > rm(list=ls())
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'purrr', 'readr', 'readxl', 'rematch2', 'stringr', 'tibble',
  'tidyr', 'vctrs'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'tibble'
Error in get(f, envir = code_env) : 
  cannot return a promise (PROMSXP) object
Calls: <Anonymous> -> Filter -> unlist -> lapply -> FUN -> get
Execution halted
Error in get0(al, envir = code_env, mode = "list", inherits = FALSE) : 
  cannot return a promise (PROMSXP) object
Calls: <Anonymous> -> get0
Execution halted
Running examples in ‘bakeoff-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bakers
> ### Title: Bakers
> ### Aliases: bakers
> ### Keywords: datasets
> 
> ### ** Examples
> 
> if (require('tibble')) {
+   bakers
+  }
Loading required package: tibble
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘tibble’
> head(bakers)
Error in head(bakers) : cannot return a promise (PROMSXP) object
Execution halted
Packages required but not available:
  'R2jags', 'lubridate', 'robCompositions', 'ggplot2', 'ggpubr',
  'reshape2', 'shinyFiles'

Packages suggested but not available for checking:
  'testthat', 'knitcitations'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'rstan', 'dplyr', 'tidyr', 'Hmisc', 'ggplot2'

Package suggested but not available for checking: ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'rstan', 'stringr', 'tidyr', 'multidplyr',
  'ggplot2', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'igraph', 'networkD3', 'testthat', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
Packages required but not available: 'loo', 'bridgesampling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'tibble', 'tidyr', 'lubridate', 'janitor',
  'stringr'

Packages suggested but not available for checking: 'httptest', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R2jags', 'ggplot2', 'ggExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘distributions3’

Packages suggested but not available for checking: 'keras', 'tensorflow'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'igraph', 'animation', 'furrr'

Packages suggested but not available for checking: 'plotly', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BFpack', 'sna'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘ggplot2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘kmediods.Rmd’ using rmarkdown

Quitting from lines 19-21 [setup] (kmediods.Rmd)
Error: processing vignette 'kmediods.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘kmediods.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘fdpbandsdata’
Packages required but not available:
  'dplyr', 'stringr', 'lubridate', 'tidyr', 'fabR', 'madshapR'

Package suggested but not available for checking: ‘usethis’

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

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'viridis'

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

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dplyr’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'rfPermute', 'swfscMisc', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rvest', 'stringr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'sva'

Package suggested but not available for checking: ‘ArrayExpress’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
Packages suggested but not available for checking: 'shinytest', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) barcoding.spe.identify2.Rd:27: Lost braces; missing escapes or markup?
    27 | read.dna() from package {ape} was used to obtain DNAbin object for unaligned non-coding barcodes.
       |                         ^
Packages suggested but not available for checking: 'roxygen2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'lme4'
Packages required but not available: 'ggcharts', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'ggiraph', 'ggnewscale', 'ggplot2', 'ggraph',
  'igraph', 'patchwork', 'purrr', 'tidybayes', 'tidygraph', 'tidyr',
  'tidytreatment', 'tibble'

Packages suggested but not available for checking:
  'ggridges', 'ggforce', 'lvplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘base64enc/libs/base64enc.so’:
  Found non-API call to R: ‘SETLENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'janitor', 'lubridate', 'purrr', 'rvest',
  'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'furrr', 'ggrepel', 'reshape2', 'RSQLite', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'mice', 'Hmisc', 'purrr', 'sae'

Packages suggested but not available for checking: 'testthat', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'dplyr', 'tibble', 'readr', 'stringr', 'bigrquery',
  'dbplyr', 'typed'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'slippymath', 'magick'

Packages suggested but not available for checking:
  'ggplot2', 'mapedit', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
Running examples in ‘basemodels-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dummyClassifier
> ### Title: a method used for the train function in caret
> ### Aliases: dummyClassifier
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # Split the data into training and testing sets
> set.seed(2023)
> index <- sample(1:nrow(iris), nrow(iris) * 0.8)
> train_data <- iris[index,]
> test_data <- iris[-index,]
> 
> ctrl1 <- caret::trainControl(method = "none")
Error in loadNamespace(x) : there is no package called ‘caret’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_to_basemodels.Rmd’ using rmarkdown

Quitting from lines 39-53 [unnamed-chunk-3] (intro_to_basemodels.Rmd)
Error: processing vignette 'intro_to_basemodels.Rmd' failed with diagnostics:
there is no package called 'caret'
--- failed re-building ‘intro_to_basemodels.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'rms', 'do'

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

Packages suggested but not available for checking:
  'forcats', 'ggplot2', 'GO.db', 'GSEABase', 'org.Hs.eg.db',
  'reactome.db', 'testthat'

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

Packages suggested but not available for checking: 'testthat', 'vdiffr'

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

Packages suggested but not available for checking: 'lubridate', 'testthat'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'rmcfs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'ggrepel', 'ggplotify', 'network',
  'sna', 'dendextend', 'stringr', 'GGally', 'ggnetwork', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'tibble', 'tidyr', 'dplyr', 'igraph', 'tidygraph',
  'ggraph'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'GGally', 'roxygen2', 'dplyr', 'testthat', 'faraway'
File ‘BAS/libs/BAS.so’:
  Found non-API call to R: ‘SETLENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lubridate', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BatchJobs', 'RSQLite'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rvest', 'dplyr', 'stringr', 'tidyr', 'lubridate', 'furrr', 'purrr',
  'tibble'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'broom', 'dplyr', 'geepack', 'ggplot2', 'purrr', 'stringr', 'tibble',
  'tidyr'

Package suggested but not available for checking: ‘tidyverse’

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

Packages suggested but not available for checking:
  'future.batchtools', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'concaveman', 'dplyr', 'tidyselect', 'purrr', 'latex2exp',
  'vtable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'hypervolume', 'phytools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Anthropometry', 'dplyr', 'ggplot2', 'lubridate', 'purrr', 'readr',
  'reshape2', 'rvest', 'stringr', 'tibble', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'loo', 'rstan'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'egg', 'ggplot2', 'igraph'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'reshape2', 'cowplot', 'ggExtra'

Packages suggested but not available for checking: 'testthat', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'ggplot2', 'rstan', 'mcmcse'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lme4', 'tibble', 'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'plotly', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) coupledMetropolis.Rd:83-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:86-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:89-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:92-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:95-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:98-100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:101-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:104-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:110-112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:113-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:116-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:119-121: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:122-124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:125-127: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bayesDP', 'dplyr', 'purrr'

Packages suggested but not available for checking:
  'testthat', 'pkgdown', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) bayesDccGarch.Rd:91: Lost braces; missing escapes or markup?
    91 | \item{$H_n1 }{ Bayesian prediction of volatilities and co-volatilities for y_{n+1}.}
       |                                                                              ^
checkRd: (-1) bayesDccGarch.Rd:92: Lost braces; missing escapes or markup?
    92 | \item{$R_n1 }{ Bayesian prediction of coditional correlation for y_{n+1}.}
       |                                                                    ^
Packages required but not available:
  'dplyr', 'ggplot2', 'loo', 'reshape2', 'rstan'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Running examples in ‘BayesDissolution-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bmn
> ### Title: Bayesian Multivariate Normal Model for Dissolution Profile
> ###   Modeling
> ### Aliases: bmn
> 
> ### ** Examples
> 
> ### dis_data comes loaded with the package
> ### We set B = 1000 to obtain 1000 posterior samples
> B <- 1000
> post <- bmn(dis_data, B = B)
> 
> ### We can check how well the posterior samples of the means are mixing by
> ### plotting the individual chains by time point
> burnin <- B * 0.1     # A 10% burn-in
> post$mu_R <- post$muR[,-(1:burnin)]
> post$mu_T <- post$muT[,-(1:burnin)]
> 
> N <- B - burnin      # Number of posterior samples after burn-in
> chains <- data.frame(samples = rep(c(1:N, 1:N), each = ncol(dis_data) - 1),
+                      group = rep(c("muR", "muT"), each = (ncol(dis_data) - 1) * N),
+                      timepoint = paste("Time Point", rep(1:(ncol(dis_data) - 1), 2 * N)),
+                      values = c(c(post$mu_R), c(post$mu_T)))
> 
> g <- ggplot2::ggplot(chains, ggplot2::aes(samples, values)) +
+                      ggplot2::geom_line() +
+                      ggplot2::labs(x = "Iterations", y = "Posterior Sample Values") +
+                      ggplot2::facet_wrap(group ~ timepoint) +
+                      ggplot2::theme(text = ggplot2::element_text(size = 16))
Error in loadNamespace(x) : there is no package called ‘ggplot2’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) GroupSingleVoxelFETS.Rd:53: Lost braces
    53 | online trajectories related to the state parameter, the simulated BOLD responses, \mjseqn{\hat{Y}}{ascii}.
       |                                                                                                   ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'tibble', 'tidyr', 'tmap'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'testthat', 'arm', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Packages suggested but not available for checking:
  'tibble', 'readxl', 'testthat', 'ggfortify'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

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

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'INLA', 'purrr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bayesplot', 'ggplot2', 'forecast', 'loo', 'rstan', 'bridgesampling',
  'lubridate', 'prophet'

Package suggested but not available for checking: ‘ggfortify’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bayesplot', 'ggplot2', 'loo', 'rstan'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) gMLE.bb.Rd:18: Lost braces
    18 |   \item{optim.method}{optimization method in \code{optim()}{stats}.}
       |                                                            ^
Packages required but not available:
  'AquaticLifeHistory', 'bayesplot', 'dplyr', 'ggplot2', 'loo',
  'rstan', 'tibble', 'tidybayes'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available: 'reshape2', 'ggplot2', 'nse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'purrr', 'tidyr'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DoseFinding', 'ggplot2', 'nloptr', 'RBesT'

Packages suggested but not available for checking:
  'clinDR', 'dplyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R2jags', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'heatmaply', 'networkD3', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rstan', 'ggplot2', 'ggpubr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'brms', 'parsnip', 'dplyr', 'purrr', 'tibble'

Packages suggested but not available for checking:
  'devtools', 'recipes', 'roxygen2', 'rstan', 'testthat', 'workflows'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggforce', 'ggplot2', 'ggtext', 'gt', 'reshape2', 'tibble',
  'tidyr'

Packages suggested but not available for checking:
  'patchwork', 'purrr', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DHARMa', 'gap', 'bridgesampling'

Packages suggested but not available for checking:
  'sensitivity', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'mcmcse', 'PottsUtils', 'rstan'
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.bayeslm.fit.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{X         }{ If call \code{bayeslm} with matrices input \code{x} and {y} but not formula, pass new matrix to predict here. See example for details.}
       |                                                                              ^
GNU make is a SystemRequirements.
Packages required but not available: 'optimx', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Packages required but not available: 'ggplot2', 'testthat'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘posterior’

Packages suggested but not available for checking: 'rstanarm', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot-traj.Rd:71: Lost braces; missing escapes or markup?
    71 | the plots are saved into directory {sim.dir}/predictions/migTrajectories.}
       |                                    ^
Packages required but not available: 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'progress', 'tidyr', 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'furrr', 'ggplot2', 'lubridate', 'progress', 'purrr',
  'tidyr'

Packages suggested but not available for checking:
  'testthat', 'ggforce', 'datamods', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bayesplot', 'dplyr', 'ggplot2', 'ggpubr', 'posterior', 'stringr',
  'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available:
  'brms', 'ggplot2', 'loo', 'dplyr', 'tidyr', 'purrr', 'tibble',
  'tidyselect'

Packages suggested but not available for checking: 'rstan', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'doBy'

Package suggested but not available for checking: ‘qtlnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nimble', 'StatMatch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gsDesign', 'ggplot2', 'R2jags'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'ggplot2', 'patrick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggridges', 'posterior', 'reshape2', 'tibble',
  'tidyselect'

Packages suggested but not available for checking:
  'ggfortify', 'loo', 'rstan', 'rstanarm', 'shinystan', 'testthat',
  'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bayesLife', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'bayesplot', 'ggplot2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘bayesPO.Rmd’ using rmarkdown

Quitting from lines 18-32 [setup] (bayesPO.Rmd)
Error: processing vignette 'bayesPO.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘bayesPO.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'ggridges', 'reshape2', 'tidyr', 'R2jags',
  'rstanarm', 'brms'

Packages suggested but not available for checking: 'rstan', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'kableExtra'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bayesppd-vignette.Rmd’ using rmarkdown

Quitting from lines 34-40 [unnamed-chunk-2] (bayesppd-vignette.Rmd)
Error: processing vignette 'bayesppd-vignette.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘bayesppd-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'forecast', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘roxygen2’
Package suggested but not available for checking: ‘roxygen2’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'colourpicker', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'janitor', 'dplyr', 'purrr', 'rstanarm', 'groupdata2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘TeachingSampling’
Packages required but not available: 'rstan', 'dplyr', 'ggplot2', 'lme4'

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

Package suggested but not available for checking: ‘BDgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'GGally', 'riskRegression'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BayesFactor', 'bayesplot', 'blavaan', 'bridgesampling', 'brms',
  'gamm4', 'ggdist', 'ggplot2', 'glmmTMB', 'lme4', 'mediation',
  'patchwork', 'posterior', 'rstan', 'rstanarm', 'see', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘ggplot2’
Packages required but not available: 'bridgesampling', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'rstan', 'BayesFactor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) BayesTreePrior.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:41: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘faraway’
Packages required but not available:
  'rstan', 'ggplot2', 'bayesplot', 'viridis', 'reshape2', 'dplyr'

Package suggested but not available for checking: ‘loo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'BDgraph', 'ess'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Packages required but not available: 'rstan', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'progress', 'ggplot2', 'ggpubr'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggfortify', 'lme4', 'reshape2', 'tibble',
  'tidyr', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dataRetrieval', 'dplyr', 'lubridate', 'readxl'

Packages suggested but not available for checking:
  'devtools', 'imputeTS', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Seurat', 'tidytable'

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘httr2’

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) getOperatingSystem.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:30: Lost braces in \itemize; meant \describe ?
Running ‘run-all.R’ [0s/0s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rms', 'ggplot2', 'AICcmodavg', 'Hmisc', 'optimx', 'testthat'
Note: skipping ‘mle2.Rnw’ due to unavailable dependencies: 'Hmisc'
Note: skipping ‘quasi.Rnw’ due to unavailable dependencies: 'AICcmodavg'
Packages required but not available: 'dplyr', 'ggplot2', 'igraph', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'nloptr', 'testthat'
Package suggested but not available for checking: ‘Hmisc’
Note: skipping ‘BBvignetteJSS.Stex’ due to unavailable dependencies:
  'Hmisc'
Package required but not available: ‘greybox’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'c3net', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'lme4', 'mixAK'

Packages suggested but not available for checking:
  'cowplot', 'joineRML', 'survminer', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) goftype1.Rd:4: Lost braces
     4 | \description{The goodness-of-fit (GOF) measures consist of Anderson-Darling (\code{AD}) and Cram\'{e}er-von Misses (\code{CVM}) statistics for progressive type-I interval censoring scheme are given, respectively, by
       |                                                                                                   ^
Package required but not available: ‘gRbase’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dbplyr', 'dplyr', 'tibble', 'leaflet.extras', 'purrr', 'readr',
  'readxl', 'tidyselect'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘biclust’
Running examples in ‘BcDiag-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anomedOnlybic
> ### Title: The anomedOnlybic function
> ### Aliases: anomedOnlybic
> ### Keywords: anomedOnlybic
> 
> ### ** Examples
> 
> data(breastc)
> library(biclust)
Error in library(biclust) : there is no package called ‘biclust’
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'MCMCvis', 'purrr', 'reshape2', 'rstan'

Packages suggested but not available for checking:
  'plotly', 'testthat', 'vdiffr', 'voi'

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

Packages suggested but not available for checking:
  'testthat', 'latex2exp', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nimble', 'igraph'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'ggridges', 'purrr', 'ggforce', 'dplyr', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bcdata', 'progress'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘lubridate’
checkRd: (-1) WindowSweep.Rd:32: Lost braces
    32 | `code{\link{GetVT}}`.   Otherwise, any column (e.g. \code{"Depth"}) in the 
       |      ^
checkRd: (-1) WindowSweep.Rd:36: Lost braces
    36 | \code{T.mid}  from the output of the `code{\link{GetVT}}`.}
       |                                           ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘UnivariateBCPA.Rmd’ using rmarkdown

Quitting from lines 43-59 [unnamed-chunk-3] (UnivariateBCPA.Rmd)
Error: processing vignette 'UnivariateBCPA.Rmd' failed with diagnostics:
could not find function "dhours"
--- failed re-building ‘UnivariateBCPA.Rmd’

--- re-building ‘bcpa.rnw’ using knitr
--- finished re-building ‘bcpa.rnw’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘blob’
Running ‘a-init-db.R’ [0s/1s]
  Running ‘b-import-db.R’ [0s/1s]
  Running ‘c-export-db.R’ [0s/1s]
  Running ‘d-types.R’ [0s/1s]
Running the tests in ‘tests/d-types.R’ failed.
Complete output:
  > library(bcputility)
  > # test map data types
  > testTypeMapping <- function() {
  +   mapDataTypes(data.frame(
  +     int = 1:5L,
  +     numeric = seq(0, 1, length.out = 5),
  +     character = LETTERS[1:5],
  +     factor = paste(LETTERS[1:5], LETTERS[1:5], sep = ''),
  +     logical = c(TRUE, FALSE, TRUE, FALSE, TRUE),
  +     date = seq(Sys.Date() - 4, Sys.Date(), 1L),
  +     datetime = seq(Sys.time() - 5, Sys.time(), length.out = 5)
  +   )
  +   ) |>
  +     identical(
  +       c(int = "TINYINT", numeric = "FLOAT", character = "VARCHAR(1)",
  +         factor = "VARCHAR(2)", logical = "BIT", date = "DATE",
  +         datetime = "DATETIME")) |>
  +     stopifnot()
  +   # test varChar
  +   (varChar(paste(rep('A', 1), collapse = '')) == 'VARCHAR(1)') |>
  +     stopifnot()
  +   (varChar(paste(rep('A', 8001), collapse = '')) == 'VARCHAR(MAX)') |>
  +     stopifnot()
  +   (varChar(NA_character_) == 'VARCHAR(1)') |>
  +     stopifnot()
  +   # test varBinary
  +   (varBinary(blob::as_blob(raw(length = 1))) == 'VARBINARY(1)') |>
  +     stopifnot()
  +   (varBinary(blob::as_blob(raw(length = 8001))) == 'VARBINARY(MAX)') |>
  +     stopifnot()
  +   (varBinary(blob::as_blob(NA)) == 'VARBINARY(0)') |>
  +     stopifnot()
  +   (int(2) == 'TINYINT') |>
  +     stopifnot()
  +   (int(2^8) == 'SMALLINT') |>
  +     stopifnot()
  +   (int(2^15) == 'INTEGER') |>
  +     stopifnot()
  +   (int(2^31) == 'BIGINT') |>
  +     stopifnot()
  + }
  > testTypeMapping()
  Error in loadNamespace(x) : there is no package called 'blob'
  Calls: testTypeMapping ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'stringr', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CoordinateCleaner', 'dplyr', 'ggplot2', 'purrr', 'readr',
  'rgnparser', 'stringr', 'taxadb', 'tibble', 'tidyselect'

Packages suggested but not available for checking:
  'cowplot', 'rvest', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'ggplot2'

Packages suggested but not available for checking:
  'ssgraph', 'huge', 'skimr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tibble', 'dplyr', 'tidyr', 'ggplot2', 'ggpubr', 'randomcoloR',
  'purrr', 'tmap', 'progress'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'stringr', 'testthat', 'tuber'
Running ‘test_all.R’ [0s/1s]
Running the tests in ‘tests/test_all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘dump.txt’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'cvCovEst', 'testthat'
Running examples in ‘bdsvd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: detect.blocks
> ### Title: Block Detection
> ### Aliases: detect.blocks
> 
> ### ** Examples
> 
> #In the first example, we replicate the simulation study for the ad hoc procedure
> #Est_0.1 from Bauer (202Xa). In the second example, we manually compute the first step
> #of BD-SVD, which can be done using the bdsvd() and/or single.bdsvd(), for constructed
> #sparse loadings
> 
> #Example 1: Replicate the simulation study (a) from Bauer (202Xa) for the ad hoc
> #procedure Est_0.1.
> 
> p <- 500 #Number of variables
> n <- 125 #Number of observations
> b <- 500 #Number of blocks
> design <- "a"
> 
> #Simulate data matrix X
> set.seed(1)
> Sigma <- bdsvd.cov.sim(p = p, b = b, design = design)
> X <- mvtnorm::rmvnorm(n, mean=rep(0, p), sigma=Sigma)
> colnames(X) <- 1:p
> 
> #Perform the ad hoc procedure
> detect.blocks(cvCovEst::scadEst(dat = X, lambda = 0.2), threshold = 0)
Error in loadNamespace(x) : there is no package called ‘cvCovEst’
Calls: detect.blocks ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
bdsvd           7.294  0.039   9.683
bdsvd.structure 6.004  0.102   8.474
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'sqldf', 'taxize', 'treemap', 'ggplot2'

Package suggested but not available for checking: ‘rinat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'haven', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'drc', 'ggplot2', 'purrr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'stringr', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'loo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'beautier', 'phangorn', 'readr', 'stringr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following files/directories:
  ‘beast_plot_toy.pdf’
Packages required but not available: 'purrr', 'stringr'

Packages suggested but not available for checking: 'readr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'stringr', 'tibble', 'tidyr', 'yodel'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'stringr'

Packages suggested but not available for checking: 'biomaRt', 'GEOquery'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CoordinateCleaner', 'cowplot', 'dplyr', 'forcats', 'ggplot2',
  'ggspatial', 'igraph', 'lubridate', 'paletteer', 'readr', 'stringr',
  'tidyselect'

Packages suggested but not available for checking:
  'bdc', 'devtools', 'galah', 'janitor', 'pkgdown', 'plotly', 'purrr',
  'rgnparser', 'rvest', 'taxadb', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rstan', 'tidyr', 'ggplot2', 'cowplot', 'dplyr', 'odeGUTS'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2', 'optimx'

Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr', 'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DiagrammeR', 'ggplot2', 'googlesheets4', 'ufs', 'viridis'

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'reshape2', 'ggplot2', 'ggfortify', 'lubridate'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘belg1.Rmd’ using rmarkdown

Quitting from lines 13-32 [setup] (belg1.Rmd)
Error: processing vignette 'belg1.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘belg1.Rmd’

--- re-building ‘belg2.Rmd’ using rmarkdown
--- finished re-building ‘belg2.Rmd’

SUMMARY: processing the following file failed:
  ‘belg1.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'LambertW', 'loo', 'purrr', 'rstan'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'benchmarkme', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'benchmarkmeData', 'dplyr', 'stringr', 'tibble'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pillar', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'forcats', 'ggbeeswarm', 'ggplot2', 'ggridges', 'testthat',
  'tidyr', 'vctrs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
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: ‘testthat’
Running ‘run-all.R’ [0s/1s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'benthos', 'readr', 'purrr', 'dplyr', 'tidyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'rstan', 'tidybayes', 'tidyr'

Packages suggested but not available for checking:
  'bayesplot', 'posterior', 'stringr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) sockeye.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sockeye.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:14: Lost braces in \itemize; meant \describe ?
Packages required but not available: 'dplyr', 'readr'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ergm', 'network'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'rstan'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘leaflet.extras’
Packages required but not available: 'tibble', 'landscapemetrics'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘caret’
Packages required but not available:
  'dplyr', 'ggplot2', 'ggridges', 'patchwork', 'stringr', 'tibble'

Package suggested but not available for checking: ‘readr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'LambertW', 'dplyr', 'recipes', 'tibble', 'butcher', 'purrr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
checkRd: (-1) gen.data.Rd:42: Lost braces
    42 | code{cortype = 2} denotes the constant structure, where the \eqn{(i,j)} entry of covariance
       |     ^
Packages required but not available:
  'tidyr', 'dplyr', 'readxl', 'ggplot2', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'DALEX', 'ggplot2', 'ggthemes'
Running examples in ‘BetaBit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: food
> ### Title: The food data from Rijksinstituut voor Volksgezondheid en Milieu
> ### Aliases: food food_max food_mini food_all food_pl food_max_pl
> ###   food_mini_pl food_all_pl
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library("ggplot2")
Error in library("ggplot2") : there is no package called ‘ggplot2’
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'mice'
Running examples in ‘betaMC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MCMI
> ### Title: Generate the Sampling Distribution of Regression Parameters
> ###   Using the Monte Carlo Method for Data with Missing Values
> ### Aliases: MCMI
> ### Keywords: betaMC mc
> 
> ### ** Examples
> 
> # Data ---------------------------------------------------------------------
> data("nas1982", package = "betaMC")
> nas1982_missing <- mice::ampute(nas1982)$amp # data set with missing values
Error in loadNamespace(x) : there is no package called ‘mice’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
Note: skipping ‘betareg.Rnw’ due to unavailable dependencies: 'car'
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Malformed Title field: should not end in a period.
Packages required but not available:
  'ggplot2', 'plotly', 'forecast', 'stringr', 'rvest', 'lubridate',
  'dplyr', 'sqldf'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'ergm', 'Bergm'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'doBy', 'Hmisc'
Packages suggested but not available for checking:
  'testthat', 'tibble', 'dplyr'
Running examples in ‘bfsl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: augment.bfsl
> ### Title: Augment Data with Information from a bfsl Object
> ### Aliases: augment.bfsl
> 
> ### ** Examples
> 
> fit = bfsl(pearson_york_data)
> 
> augment(fit)
Error in loadNamespace(x) : there is no package called ‘dplyr’
Calls: augment ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘DescTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'httr2', 'rvest', 'tibble', 'janitor', 'tidyRSS', 'purrr', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'lme4', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘EnvStats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pryr', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'BFpack', 'GGally', 'ggplot2', 'ggridges', 'network', 'sna'

Packages suggested but not available for checking:
  'networktools', 'mice', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'testthat', 'dplyr', 'tidyr'
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bggum.Rmd’ using rmarkdown

Quitting from lines 125-142 [reshape_data] (bggum.Rmd)
Error: processing vignette 'bggum.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘bggum.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘igraph’

Packages suggested but not available for checking: 'dplyr', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'qgraph', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'ggthemes', 'progress', 'purrr', 'readr',
  'stringr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) sp_bgsmtr.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{c.star}{The threshold for computing posterior tail probabilities p_{ij} for Bayesian FDR as defined in Section 3.2 of  Song, Ge et al.(2019). If not specified the default is to set this threshold as the minimum posterior standard deviation, where the minimum is taken over all regression coefficients in the model.}
       |                                                                          ^
Package required but not available: ‘readxl’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘prevtoinc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘FrF2’
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Package required but not available: ‘R2jags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) fmridata.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fmridata.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fmridata.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fmridata.Rd:21: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Package required but not available: ‘rBiasCorrection’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'viridis', 'dendextend', 'randomcoloR', 'biclust'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bibliometrix’
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'ggrepel', 'igraph', 'plotly',
  'openalexR', 'readr', 'readxl', 'rscopus', 'tidyr', 'tidytext'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rcrossref', 'stringr'

Packages suggested but not available for checking: 'devtools', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggVennDiagram', 'UpSetR'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘igraph’
Error(s) in re-building vignettes:
  ...
--- re-building ‘BiCausality_demo.Rmd’ using knitr

Quitting from lines 49-52 [unnamed-chunk-4] (BiCausality_demo.Rmd)
Error: processing vignette 'BiCausality_demo.Rmd' failed with diagnostics:
there is no package called 'igraph'
--- failed re-building ‘BiCausality_demo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'tidyr', 'biclust', 'dplyr', 'nycflights13'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'ggplot2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'crypto2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bidask.Rmd’ using rmarkdown

Quitting from lines 46-51 [unnamed-chunk-2] (bidask.Rmd)
Error: processing vignette 'bidask.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘bidask.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2'
checkRd: (-1) BiDimRegression.Rd:29: Lost braces; missing escapes or markup?
    29 | \item \code{euclidean.df1, affine.df1} -  degrees of freedom of the nominator used for the F-statistics propagated by Nakaya (1997); df1 = p-2, with p is the number of elements  needed to calculate the referring model: p=4 for the Euclidean and p=6 for the affine geometry {Nakaya, 1997, Table 1}.
       |                                                                                                                                                                                                                                                                                  ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘calibration.Rmd’ using rmarkdown

Quitting from lines 25-34 [raw-data] (calibration.Rmd)
Error: processing vignette 'calibration.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘calibration.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #Tests for BIEN package
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'tidyr', 'MplusAutomation'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Package required but not available: ‘miceadds’

Packages which this enhances but not available for checking:
  'Hmisc', 'intsvy', 'LSAmitR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘igraph’
Running examples in ‘bifurcatingr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bfa_tree_plot
> ### Title: Plotting Bifurcating Autoregressive Trees
> ### Aliases: bfa_tree_plot
> 
> ### ** Examples
> 
> z <- bfa_tree_gen(31, 1, 1, 1, 0.5, 0.5, 0, 10, c(0.7))
> bfa_tree_plot(z)
Error in loadNamespace(x) : there is no package called ‘igraph’
Calls: bfa_tree_plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
bfa_ls_bc_ci     6.248  0.000   8.882
bfa_ls_bc        5.625  0.008   8.078
bfa_boot2fast_ls 4.896  0.016   7.129
bfa_boot1_ls     3.478  0.031   5.423
Error(s) in re-building vignettes:
  ...
--- re-building ‘bifurcatingr.Rmd’ using rmarkdown

Quitting from lines 44-45 [unnamed-chunk-5] (bifurcatingr.Rmd)
Error: processing vignette 'bifurcatingr.Rmd' failed with diagnostics:
there is no package called 'igraph'
--- failed re-building ‘bifurcatingr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'ffbase', 'RSQLite'
Package required but not available: ‘haplo.stats’

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

Packages suggested but not available for checking:
  'INLA', 'testthat', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ergm', 'network', 'tidyr', 'stringr', 'intergraph', 'igraph',
  'purrr', 'dplyr', 'readr', 'ergm.multi'

Packages suggested but not available for checking:
  'testthat', 'sna', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘solartime’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSQLite’
Found the following calls to data() loading into the global environment:
File ‘biglm/R/bigglm.R’:
  data(reset = TRUE)
  data(reset = FALSE)
See section ‘Good practice’ in ‘?data’.
Packages required but not available: 'ggplot2', 'progress', 'plotly'

Package suggested but not available for checking: ‘testthat’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check
> ### Title: Check SMDs of the matched data set.
> ### Aliases: check
> 
> ### ** Examples
> 
> # To run this example, you must load the optmatch package.
> 
> # Caliper of .2 on the propensity score, near fine balance of
> # education, a robust Mahalanobis distrance for X.
> data(nh0506)
> attach(nh0506)
> X<-cbind(female,age,black,hispanic,education,povertyr,bmi)
> m<-nfmatch(z=z,p=propens,fine=education,X=X,caliper=.2,dat=nh0506,rank=FALSE)
Error in nearfine(z, fine, dist, dat, ncontrol, penalty, max.cost, nearexPenalty,  : 
  Error: package optmatch (>= 0.9-1) not loaded.  To run rcbalance command, you must install optmatch first and agree to the terms of its license.
Calls: nfmatch -> nearfine
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘vctrs’

Packages suggested but not available for checking: 'pillar', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) pQF.Rd:30: Lost braces; missing escapes or markup?
    30 | When \code{M} is not square, a randomised estimator for the trace of \code{crossprod(M)^2} is used. This is the sample size. When \code{M} is of \code{"matrixfree"} and does not include the trace of {crossprod(M)} as a component, this sample size will also be used to compute that. See Hutchinson reference. }
       |                                                                                                                                                                                                        ^
Packages suggested but not available for checking: 'testthat', 'RSQLite'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'clock', 'tibble'

Packages suggested but not available for checking:
  'blob', 'dbplyr', 'dplyr', 'hms', 'readr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arrow', 'bigrquery', 'tibble'

Packages suggested but not available for checking: 'testthat', 'hms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'bigstatsr', 'ggplot2', 'vctrs'

Packages suggested but not available for checking:
  'dbplyr', 'dplyr', 'Hmisc', 'pcadapt', 'RSQLite', 'testthat',
  'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'cowplot', 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'plotly', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) VARXFit.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXLagCons.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXLagCons.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘dplyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘nloptr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following files/directories:
  ‘ccf_ccf_ID31_ID32_res.jpg’ ‘ccf_ccf_ID31_ID32_res.pdf’
  ‘output_ENSO_NHSST.tmp’ ‘plot_plot_ts_RAW_BIN_enso_sst.pdf’
  ‘plot_plot_ts_RAW_BIN_enso_sst01.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst02.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst03.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst04.png’ ‘plot_ts_ACER_ABRUPT.pdf’
  ‘plot_ts_ACER_ABRUPT01.png’ ‘plot_ts_ACER_ABRUPT02.png’
  ‘plot_ts_ACER_ABRUPT03.png’ ‘plot_ts_ACER_ABRUPT04.png’
  ‘salida_ACER_ABRUPT.tmp’ ‘scaterplot_scatterplot_ENSO_SST.jpg’
  ‘scaterplot_scatterplot_ENSO_SST.pdf’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘dplyr’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘network’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggpubr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
checkRd: (-1) binom.confint.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:32-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:45: Lost braces in \itemize; meant \describe ?
Running examples in ‘binom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: binom.bayes
> ### Title: Binomial confidence intervals using Bayesian inference
> ### Aliases: binom.bayes binom.bayes.densityplot
> ### Keywords: univar htest models
> 
> ### ** Examples
> 
> # Example using highest probability density.
> hpd <- binom.bayes(
+   x = 0:10, n = 10, type = "highest", conf.level = 0.8, tol = 1e-9)
> print(hpd)
   method  x  n shape1 shape2       mean       lower     upper sig
1   bayes  0 10    0.5   10.5 0.04545455 0.000000000 0.0769566 0.2
2   bayes  1 10    1.5    9.5 0.13636364 0.003771457 0.2145408 0.2
3   bayes  2 10    2.5    8.5 0.22727273 0.053633312 0.3494770 0.2
4   bayes  3 10    3.5    7.5 0.31818182 0.127646004 0.4728042 0.2
5   bayes  4 10    4.5    6.5 0.40909091 0.214091147 0.5858428 0.2
6   bayes  5 10    5.5    5.5 0.50000000 0.309892028 0.6901080 0.2
7   bayes  6 10    6.5    4.5 0.59090909 0.414157185 0.7859089 0.2
8   bayes  7 10    7.5    3.5 0.68181818 0.527195809 0.8723540 0.2
9   bayes  8 10    8.5    2.5 0.77272727 0.650522982 0.9463667 0.2
10  bayes  9 10    9.5    1.5 0.86363636 0.785459228 0.9962285 0.2
11  bayes 10 10   10.5    0.5 0.95454545 0.923043403 1.0000000 0.2
> binom.bayes.densityplot(hpd)
Loading required namespace: ggplot2
Failed with error:  ‘there is no package called ‘ggplot2’’
Error in binom.bayes.densityplot(hpd) : 
  requireNamespace("ggplot2") is not TRUE
Calls: binom.bayes.densityplot -> stopifnot
Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'hedgehog'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'penaltyLearning', 'ggplot2', 'testthat'
Running examples in ‘binsegRcpp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: random_set_vec
> ### Title: random set vec
> ### Aliases: random_set_vec
> 
> ### ** Examples
> 
> 
> library(data.table)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘comparisons.Rmd’ using knitr

Quitting from lines 94-95 [unnamed-chunk-8] (comparisons.Rmd)
Error: processing vignette 'comparisons.Rmd' failed with diagnostics:
there is no package called 'penaltyLearning'
--- failed re-building ‘comparisons.Rmd’

--- re-building ‘cross-validation.Rmd’ using knitr
--- finished re-building ‘cross-validation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'rstan', 'dplyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'igraph', 'testthat'
Specified C++11: please drop specification unless essential
checkRd: (-1) aa.index.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:15: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:16: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:17: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:18: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:20-23: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) example.data.Rd:33-37: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) example.data.Rd:38-39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) example.data.Rd:40-41: Lost braces in \enumerate; meant \describe ?
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat'
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Rcmdr', 'ggplot2'

Packages suggested but not available for checking:
  'car', 'effects', 'ENMeval', 'red', 'igraph', 'readxl', 'dplyr',
  'concaveman'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bsplus', 'dplyr', 'ggplot2', 'mixtools', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'kableExtra'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘biogas_quick_start.Rnw’ using knitr

Quitting from lines 263-268 [unnamed-chunk-7] (biogas_quick_start.Rnw)
Error: processing vignette 'biogas_quick_start.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘biogas_quick_start.Rnw’

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

Quitting from lines 180-187 [unnamed-chunk-6] (calcBgMan_function.Rnw)
Error: processing vignette 'calcBgMan_function.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘calcBgMan_function.Rnw’

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

Quitting from lines 145-152 [unnamed-chunk-5] (calcBgVol_function.Rnw)
Error: processing vignette 'calcBgVol_function.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘calcBgVol_function.Rnw’

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

SUMMARY: processing the following files failed:
  ‘biogas_quick_start.Rnw’ ‘calcBgMan_function.Rnw’
  ‘calcBgVol_function.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'ggplot2', 'testthat'
checkRd: (-1) calc_ed.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_pi.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_si.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) cluster_reg_exp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
Running examples in ‘biogram-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.criterion_distribution
> ### Title: Plot criterion distribution
> ### Aliases: plot.criterion_distribution
> 
> ### ** Examples
> 
> target_feature <- create_feature_target(10, 375, 15, 600) 
> example_result <- distr_crit(target = target_feature[,1], 
+                              feature = target_feature[,2])
> plot(example_result)
> 
> # a ggplot2 plot
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
biogram-package 7.528  0.058   10.43
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'tibble', 'dplyr', 'purrr', 'ggplot2', 'cowplot', 'tidyr'

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'biomaRt'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'igraph'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'WGCNA', 'ggsci', 'caret', 'ggplot2', 'ggpubr', 'viridis',
  'ggthemes', 'ggstatsplot', 'mlr3verse', 'ggforce', 'igraph',
  'ggnetwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ROC.Rd:55: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:56: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:57: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:58: Lost braces in \enumerate; \value handles \item{}{} directly
Packages required but not available:
  'biomaRt', 'tibble', 'dplyr', 'readr', 'stringr', 'purrr'

Packages suggested but not available for checking: 'devtools', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'httr2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'cowplot', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

Packages which this enhances but not available for checking:
  'asreml', 'ARTool', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'ggplot2', 'dplyr'

Packages suggested but not available for checking:
  'Hmisc', 'car', 'caret', 'ENMeval', 'ggpubr', 'testthat',
  'tidyterra', 'ggtext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'imager', 'magick'

Package suggested but not available for checking: ‘imagerExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) simulation.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:60-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:65: Lost braces in \itemize; meant \describe ?
Packages required but not available:
  'ggplot2', 'survminer', 'onewaytests', 'car'

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'frictionless', 'ggplot2', 'lubridate', 'lutz', 'readr',
  'tidyr', 'viridis'

Packages suggested but not available for checking:
  'ggspatial', 'rosm', 'testthat', 'tidyselect', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bipartite', 'ggplot2', 'igraph', 'tidyr'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) mmds.2D.multi.Rd:118: Lost braces
   118 |   a numeric value in inches indicating the height of graph outfile. Default differs by outfile.type. The resolution for tiff and png figures is 150 dpi. See \code{pdf}, code{tiff}, \code{png}, \code{postscript}.
       |                                                                                                                                                                              ^
checkRd: (-1) mmds.2D.plot.Rd:134: Lost braces
   134 |   a numeric value in inches indicating the height of graph outfile. Default differs by outfile.type. The resolution for tiff and png figures is 150 dpi. See \code{pdf}, code{tiff}, \code{png}, \code{postscript}.
       |                                                                                                                                                                              ^
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'vctrs', 'tibble', 'dplyr', 'pillar', 'stringr', 'readr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'plsRcox', 'survAUC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'car', 'bshazard', 'Epi', 'dplyr'
Running examples in ‘biostat3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lincom
> ### Title: Linear combination of regression parameters.
> ### Aliases: lincom
> 
> ### ** Examples
> 
>   fit <- glm(chd ~ hieng*job + offset(log(y)), data=diet, family=poisson)
>   lincom(fit, c("hienghigh+hienghigh:jobconductor",
+                 "hienghigh+hienghigh:jobbank"),
+          eform=TRUE)
Loading required namespace: car
Failed with error:  ‘there is no package called ‘car’’
Error in lincom(fit, c("hienghigh+hienghigh:jobconductor", "hienghigh+hienghigh:jobbank"),  : 
  Install the 'car' package to use the lincom function
Execution halted
Packages suggested but not available for checking: 'ggplot2', 'car'
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'afex', 'cowplot', 'dplyr', 'forcats', 'ggh4x', 'ggplot2', 'purrr',
  'reportRmd', 'rstatix', 'stringr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
Package required but not available: ‘biomaRt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'dplyr', 'tidyr', 'stringr', 'tibble'

Package suggested but not available for checking: ‘bipartite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'sna', 'igraph'

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

Packages suggested but not available for checking:
  'dclone', 'mice', 'micemd', 'miceadds'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'vctrs', 'dplyr', 'stringr'

Packages suggested but not available for checking:
  'easycensus', 'wru', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'reshape2', 'tibble', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'cowplot', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'AnnotationDbi', 'GO.db', 'org.Hs.eg.db', 'GOSemSim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'Seurat', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Packages required but not available:
  'loo', 'rstan', 'dplyr', 'tibble', 'purrr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) keypos.rd:27: Lost braces
    27 |   an integer vector of the same length as code{x} containing positions relativ to code{sort(unique(x), na.last=FALSE)}
       |                                               ^
checkRd: (-1) keypos.rd:27: Lost braces
    27 |   an integer vector of the same length as code{x} containing positions relativ to code{sort(unique(x), na.last=FALSE)}
       |                                                                                       ^
Package required but not available: ‘phytools’

Package suggested but not available for checking: ‘mvMORPH’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'progress', 'purrr', 'stringr'

Packages suggested but not available for checking:
  'ggplot2', 'httptest', 'testthat', 'tidyquant'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'roxygen2'
File ‘bit/libs/bit.so’:
  Found non-API call to R: ‘SETLENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘BoolNet’
Packages suggested but not available for checking: 'testthat', 'vdiffr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'stringr', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mrfDepth’
Packages suggested but not available for checking: 'testthat', 'devtools'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘DHARMa’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bkmr', 'rstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R6P', 'ggplot2', 'ggmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spaMM', 'nloptr'

Packages suggested but not available for checking: 'testthat', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readr', 'dplyr', 'purrr', 'lubridate', 'tidyr', 'stringr'

Packages suggested but not available for checking:
  'ggplot2', 'tidyterra', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'stringr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'ggExtra'
Packages required but not available: 'ggplot2', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'stringr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'loo', 'rstan', 'bayesplot'

Package suggested but not available for checking: ‘cmdstanr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) RLdata500.Rd:8: Lost braces
     8 | A data frame with five variables: \code{fname_c1},\code{lname_c1},  \code{by}, code{bm}, \code{bd}.
       |                                                                                    ^
checkRd: (-1) identity.RLdata500.Rd:15: Lost braces
    15 | format A vector that contains the code{id}
       |                                       ^
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arm', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘vctrs’

Packages suggested but not available for checking: 'pillar', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Packages required but not available: 'dplyr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'cowplot', 'automap', 'tmap', 'biomod2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial_1.Rmd’ using rmarkdown

Quitting from lines 71-81 [unnamed-chunk-3] (tutorial_1.Rmd)
Error: processing vignette 'tutorial_1.Rmd' failed with diagnostics:
there is no package called 'tmap'
--- failed re-building ‘tutorial_1.Rmd’

--- re-building ‘tutorial_2.Rmd’ using rmarkdown

Quitting from lines 40-50 [unnamed-chunk-2] (tutorial_2.Rmd)
Error: processing vignette 'tutorial_2.Rmd' failed with diagnostics:
there is no package called 'tmap'
--- failed re-building ‘tutorial_2.Rmd’

SUMMARY: processing the following files failed:
  ‘tutorial_1.Rmd’ ‘tutorial_2.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘pryr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'intergraph', 'network'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sna’
checkRd: (-1) durban.Rd:16: Lost braces; missing escapes or markup?
    16 | This data set was obtained from the durban.rowcol {agridat} example in package 'agridat' 
       |                                                   ^
checkRd: (-1) fraction.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fraction.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fraction.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'nbpMatching', 'RItools', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'devtools', 'questionr', 'reldist', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘stringr’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'car', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'caret', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'caret', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'tibble', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'readr', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'janitor', 'lubridate', 'readr', 'stringr', 'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘sem’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'ggplot2', 'loo', 'rstan'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rstan', 'edstan', 'ggplot2', 'GGUM', 'loo'

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

Packages suggested but not available for checking: 'testthat', 'tibble'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'rstan'

Packages suggested but not available for checking:
  'qgraph', 'reshape2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'brms', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'cmdstanr', 'cowplot', 'ggplot2', 'ggthemes', 'mixtur', 'stringr',
  'testthat', 'tidybayes', 'usethis', 'waldo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘rvest’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'ggplot2', 'bayesplot', 'loo'

Packages suggested but not available for checking:
  'reshape2', 'bridgesampling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'rstan', 'CARBayes', 'CARBayesST', 'inlabru', 'ggpubr'

Packages suggested but not available for checking:
  'INLA', 'loo', 'cowplot', 'ggrepel', 'testthat', 'ggspatial',
  'tidyr', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'igraph', 'gRain', 'gRbase', 'mlr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘methods.Rmd’ using rmarkdown
--- finished re-building ‘methods.Rmd’

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

--- re-building ‘usage.rmd’ using rmarkdown

Quitting from lines 121-122 [unnamed-chunk-5] (usage.rmd)
Error: processing vignette 'usage.rmd' failed with diagnostics:
Package graph needed 
--- failed re-building ‘usage.rmd’

SUMMARY: processing the following file failed:
  ‘usage.rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'janitor', 'lubridate', 'readr', 'readxl', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'factormodel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'igraph', 'gRbase', 'gRain'
Packages required but not available: 'ggplot2', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'gRain', 'gRbase', 'purrr', 'qgraph', 'reshape2',
  'tidyr'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fastDummies', 'semPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr', 'viridis'

Packages suggested but not available for checking: 'testthat', 'BNPmix'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'threejs'

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

Packages suggested but not available for checking: 'qgraph', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |               ^
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |                                             ^
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ggplot2', 'cytofan', 'dplyr', 'reshape2'
checkRd: (-1) refAnnots.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) refAnnots.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:13-14: Lost braces in \itemize; meant \describe ?
Error(s) in re-building vignettes:
  ...
--- re-building ‘bodenmiller.Rmd’ using rmarkdown

Quitting from lines 13-24 [setup] (bodenmiller.Rmd)
Error: processing vignette 'bodenmiller.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘bodenmiller.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'purrr', 'tibble'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Extractor.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:19: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'Hmisc', 'lubridate', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'readr', 'tidyr', 'tidyselect', 'rvest'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'sangerseqR', 'testthat', 'tibble'
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'rvest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following HTML validation problems:
bayes.lin.reg.html:27:32 (bayes.lin.reg.Rd:77): Warning: trimming empty <code>
bayes.lin.reg.html:32:32 (bayes.lin.reg.Rd:79): Warning: trimming empty <code>
Packages suggested but not available for checking: 'testthat', 'bnstruct'
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'imager', 'HelpersMG'

Package suggested but not available for checking: ‘ijtiff’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'parsnip', 'dials', 'dplyr', 'purrr', 'tibble'

Packages suggested but not available for checking:
  'modeldata', 'rsample', 'testthat', 'tune'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
Packages suggested but not available for checking:
  'downlit', 'tibble', 'testthat'
Running ‘test-all.R’ [1s/1s]
  Running ‘test-rmd.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘BoolNet’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'testthat', 'igraph'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'igraph', 'ggplot2', 'intergraph', 'GGally', 'network',
  'sna'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ARDL', 'dplyr', 'stringr', 'usethis'

Packages suggested but not available for checking: 'reshape2', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'readxl'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'pkgdown', 'devtools', 'mockery'
Packages suggested but not available for checking: 'roxygen2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘mice’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'igraph', 'IsingFit', 'qgraph', 'dplyr', 'tidyr',
  'IsingSampler', 'mgm', 'NetworkToolbox', 'networktools', 'tibble',
  'tidyselect'

Packages suggested but not available for checking:
  'GGMncv', 'BDgraph', 'graphicalVAR', 'huge'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plsRglm', 'bipartite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'lme4', 'rms', 'gt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'qvalue', 'testthat'
Package unavailable to check Rd xrefs: ‘qvalue’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) bootSVD.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{Y}{initial data sample, which can be either a matrix or a \code{\link{ff}} matrix. \code{Y} can be either tall (\eqn{p} by \eqn{n}) or wide (\eqn{n} by \eqn{p}). If \code{Y} is entered and \code{V}, \code{d} and \code{U} (see definitions below) are not entered, then \code{bootSVD} will also compute the SVD of \code{Y}. In this case where the SVD is computed, \code{bootSVD} will assume that the larger dimension of \code{Y} is \eqn{p}, and the smaller dimension of code {Y} is \eqn{n} (i.e. \code{bootSVD} assumes that (\eqn{p>n}). This assumption can be overriden by manually entering \code{V}, \code{U} and \code{d}.\cr
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               ^
Packages suggested but not available for checking: 'testthat', 'ggplot2'
GNU make is a SystemRequirements.
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'npboottprm'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R2jags', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘borrowr-package.Rmd’ using rmarkdown

Quitting from lines 36-42 [unnamed-chunk-2] (borrowr-package.Rmd)
Error: processing vignette 'borrowr-package.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘borrowr-package.Rmd’

SUMMARY: processing the following file failed:
  ‘borrowr-package.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'cplexAPI', 'testthat', 'ggplot2', 'ggpubr', 'dplyr', 'kableExtra',
  'devtools', 'bestsubset'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘BOSO.Rmd’ using rmarkdown

Quitting from lines 21-29 [LoadFunctions] (BOSO.Rmd)
Error: processing vignette 'BOSO.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘BOSO.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'RSQLite', 'phangorn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'kableExtra'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘BOSSreg.Rmd’ using rmarkdown

Quitting from lines 308-333 [unnamed-chunk-21] (BOSSreg.Rmd)
Error: processing vignette 'BOSSreg.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘BOSSreg.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'ggplot2', 'tibble', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘imager’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test_plotting_functions.R’ [2s/3s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘qicharts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

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

Packages suggested but not available for checking:
  'dplyr', 'rhino', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'plotly'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'stringr', 'testthat'
File ‘box/libs/box.so’:
  Found non-API call to R: ‘SET_ENVFLAGS’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Needed for subshells openend in tests, and does no harm otherwise.
  > # See <https://github.com/hadley/testthat/issues/144> for details.
  > Sys.setenv(R_TESTS = '')
  > testthat::test_check('box')
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available:
  'dplyr', 'purrr', 'rio', 'stringr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'tidyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mcmcse', 'fabMix'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DiagrammeR', 'dplyr', 'purrr', 'rvest', 'tidyr', 'huxtable',
  'stringr', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘haven’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'lubridate', 'ggplot2', 'cowplot', 'tibble',
  'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'furrr', 'purrr', 'rstan', 'stringr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'NPflow', 'progress'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geojsonio', 'rgbif'

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'fbst', 'progress'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'devtools', 'dplyr', 'ggplot2', 'tidyr'

Packages suggested but not available for checking:
  'broom', 'ggfortify', 'installr', 'rstatix', 'tidyverse'

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

Packages suggested but not available for checking:
  'Hmisc', 'car', 'ggplot2', 'ggrepel', 'mediation'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'readxl', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'GJRM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘tidyverse’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'ggpubr', 'purrr', 'readr', 'stringr',
  'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'lme4', 'phyloseq', 'tibble'

Packages suggested but not available for checking:
  'devtools', 'testthat', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'caret', 'DALEX', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'ggfittext', 'ggplot2', 'broom', 'purrr', 'readr', 'readxl',
  'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'breathteststan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'rstan', 'stringr', 'tidyr', 'breathtestcore'

Packages suggested but not available for checking:
  'ggplot2', 'shinystan', 'igraph', 'bayesplot', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) brglm.Rd:173: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:174: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:175-176: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:177-178: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:179-180: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:181-182: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:183-184: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:58: Lost braces in \itemize; meant \describe ?
Packages required but not available: 'dplyr', 'piggyback'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'reshape2', 'ggplot2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘the_bridgedist_basics.Rmd’ using rmarkdown

Quitting from lines 33-45 [unnamed-chunk-3] (the_bridgedist_basics.Rmd)
Error: processing vignette 'the_bridgedist_basics.Rmd' failed with diagnostics:
there is no package called 'reshape2'
--- failed re-building ‘the_bridgedist_basics.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following HTML validation problems:
Bridge.html:80:32 (Bridge.Rd:63): Warning: trimming empty <code>
Bridge.html:85:32 (Bridge.Rd:65): Warning: trimming empty <code>
Packages required but not available: 'ggplot2', 'plotly'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'patchwork', 'tibble', 'tidyr', 'ggplot2',
  'ggedit', 'kableExtra', 'stringr'

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

Packages suggested but not available for checking:
  'testthat', 'R2jags', 'BayesFactor', 'rstan', 'rstanarm', 'nimble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'Hmisc'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'lubridate', 'tibble', 'forcats', 'GGally', 'patchwork'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking: 'httptest', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'purrr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'brms', 'posterior'

Packages suggested but not available for checking: 'testthat', 'margins'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'brms', 'dplyr', 'ggplot2', 'ggridges', 'posterior', 'purrr',
  'tibble', 'tidyr', 'tidyselect', 'trialr'

Packages suggested but not available for checking:
  'gt', 'gtsummary', 'mmrm', 'rstan', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rstan', 'ggplot2', 'loo', 'posterior', 'bayesplot', 'bridgesampling'

Packages suggested but not available for checking:
  'testthat', 'cmdstanr', 'projpred', 'shinystan', 'mice', 'lme4',
  'arm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘Cyclops’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'lme4', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'mice', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'fabletools', 'ggplot2', 'purrr', 'tibble', 'tidyr',
  'tsibble', 'vctrs'

Packages suggested but not available for checking:
  'gapminder', 'gghighlight', 'lme4', 'modelr', 'testthat',
  'tsibbledata', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'dplyr', 'labelled', 'purrr', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'brms', 'broom.mixed', 'effects', 'forcats', 'geepack', 'ggplot2',
  'ggstats', 'glmmTMB', 'gt', 'gtsummary', 'lme4', 'logitr', 'margins',
  'mice', 'mmrm', 'parsnip', 'patchwork', 'rstanarm', 'testthat',
  'tidycmprsk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'dplyr', 'forcats', 'purrr', 'stringr', 'tibble', 'tidyr',
  'furrr'

Packages suggested but not available for checking:
  'brms', 'dotwhisker', 'testthat', 'ggplot2', 'glmmADMB', 'glmmTMB',
  'lmerTest', 'lme4', 'mediation', 'pbkrtest', 'posterior', 'rstan',
  'rstanarm', 'R2jags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'AER', 'btergm', 'car', 'caret', 'drc', 'epiR', 'ergm', 'geepack',
  'ggplot2', 'Hmisc', 'joineRML', 'Lahman', 'lme4', 'mediation',
  'mlogit', 'modeldata', 'modeltests', 'network', 'rsample',
  'systemfit', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘benchmarks.Rmd’ using rmarkdown

Quitting from lines 24-36 [unnamed-chunk-1] (benchmarks.Rmd)
Error: processing vignette 'benchmarks.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘benchmarks.Rmd’

--- re-building ‘brotli-2015-09-22.pdf.asis’ using asis
--- finished re-building ‘brotli-2015-09-22.pdf.asis’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'multidplyr'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rio', 'dplyr', 'tidyr', 'stringr', 'ggplot2', 'afex', 'mediation',
  'interactions', 'jtools', 'lmerTest'

Packages suggested but not available for checking:
  'tibble', 'forcats', 'haven', 'readxl', 'cowplot', 'ggtext', 'see',
  'car', 'lme4', 'phia', 'BayesFactor', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Packages required but not available:
  'dplyr', 'ggplot2', 'hardhat', 'tibble'

Packages suggested but not available for checking:
  'modeldata', 'purrr', 'recipes', 'testthat', 'yardstick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘usage.Rmd’ using rmarkdown

Quitting from lines 59-63 [unnamed-chunk-3] (usage.Rmd)
Error: processing vignette 'usage.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'tidyr', 'dplyr', 'gsheet', 'httr2', 'stringr', 'tibble',
  'highcharter', 'rvest', 'lubridate'

Package suggested but not available for checking: ‘roxygen2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'blavaan', 'blme', 'rstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'tibble'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'thematic'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'tibble', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'readr', 'stringr', 'reactable.extras'
Running examples in ‘bscui-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bscui
> ### Title: Build SVG Custom User Interface
> ### Aliases: bscui
> 
> ### ** Examples
> 
> ##################################@
> ### Preparing data ----
> 
> library(bscui)
> library(xml2)
> library(readr)
Error in library(readr) : there is no package called ‘readr’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bscui.Rmd’ using rmarkdown

Quitting from lines 22-38 [setup] (bscui.Rmd)
Error: processing vignette 'bscui.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘bscui.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'tidyr'
Package required but not available: ‘Epi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'cowplot', 'tidyr', 'tibble', 'dplyr', 'ggplot2', 'ggpubr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'brms', 'rstan', 'loo', 'dplyr', 'sitar'

Packages suggested but not available for checking:
  'ggplot2', 'bayesplot', 'posterior', 'testthat', 'tidyr', 'purrr',
  'forcats', 'jtools', 'patchwork', 'tibble', 'kableExtra', 'Hmisc',
  'ggtext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'httr2', 'lubridate', 'purrr', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'httptest2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'thematic'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'stringr'

Package suggested but not available for checking: ‘mixtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘C50’
checkRd: (-1) bscontrol.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{opt.solver}{a character string in the set {'enum', 'enum_c', 'gurobi', 'cplex', 'lpSolve', 'greedy'} indicating the optimization solver to be used in the program. The choice of 'cplex' requires the package \code{cplexAPI}, 'gurobi' requires the package \code{gurobi}, and 'lpSolve' requires the package \code{lpSolve}. These solver options are only available in the full version at \url{https://github.com/profyliu/bsnsing/}. The default (and the best) is 'enum_c'.}
       |                                                 ^
checkRd: (-1) bscontrol.Rd:45: Lost braces; missing escapes or markup?
    45 | \item{opt.model}{a character string in the set {'gini','error'} indicating the optimization model to solve in the program. The default is 'gini'. The 'error' option is not available in the current version.}
       |                                                ^
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'progress', 'BayesFactor', 'purrr', 'dplyr', 'furrr', 'ggplot2',
  'ggmcmc', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) bsc.Rd:51: Lost braces; missing escapes or markup?
    51 | {splines::bs()}, {splines2::bSpline()}
       |                  ^
checkRd: (-1) bsp.Rd:37: Lost braces; missing escapes or markup?
    37 | {bsc}, {par2bsp}
       |        ^
checkRd: (-1) bspline.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bspline.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bspline.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bspline.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bspline.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bspline.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bspline.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bspline.Rd:30: Lost braces in \itemize; meant \describe ?
Packages required but not available: 'purrr', 'lubridate', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bayesplot', 'diagis', 'dplyr', 'posterior', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'sde', 'testthat'

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages suggested but not available for checking: 'igraph', 'ggplot2'
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (requireNamespace("BSW")) {
  +   library(BSW)
  +   library(testthat)
  +   test_check("BSW")
  + }
  Loading required namespace: BSW
  Loading required package: Matrix
  Loading required package: matrixStats
  Loading required package: quadprog
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Validation.Rmd’ using rmarkdown

Quitting from lines 28-37 [unnamed-chunk-1] (Validation.Rmd)
Error: processing vignette 'Validation.Rmd' failed with diagnostics:
there is no package called 'testthat'
--- failed re-building ‘Validation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'optimx', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'network', 'sna', 'ergm', 'igraph'

Packages suggested but not available for checking:
  'testthat', 'Bergm', 'ggplot2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) terms.BTM.Rd:23-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) terms.BTM.Rd:26-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) terms.data.frame.Rd:25-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) terms.data.frame.Rd:32-38: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'ggforce', 'reshape2', 'R2jags'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'optimx', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) bubbleHMLegends.Rd:42: Lost braces; missing escapes or markup?
    42 | function. If {sizeBreaks} vector is supplied then this will be ignored and
       |              ^
checkRd: (-1) bubbleHeatmap.Rd:96: Lost braces; missing escapes or markup?
    96 | function. If {sizeBreaks} vector is supplied then this will be ignored and
       |              ^
checkRd: (-1) multiPlotInput.Rd:117: Lost braces; missing escapes or markup?
   117 | \code{unitBase}. This will be supplied to pretty function. If {sizeBreaks} is
       |                                                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘lme4’

Packages suggested but not available for checking:
  'gamm4', 'glmertree', 'glmmTMB', 'lmerTest', 'pbkrtest', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'usethis', 'readr', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'pkgdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'gprofiler2', 'DESeq2', 'ggrepel', 'dplyr', 'ggforce',
  'noisyr', 'tibble', 'ggnewscale', 'ggrastr', 'GENIE3', 'tidyr',
  'UpSetR', 'stringr', 'ggVennDiagram'

Packages suggested but not available for checking:
  'AnnotationDbi', 'org.Hs.eg.db', 'org.Mm.eg.db', 'readxl', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'dplyr', 'googlesheets4', 'haven', 'inspectdf', 'labelled',
  'lubridate', 'readr', 'readxl', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'googledrive', 'testthat'

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'reshape2', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'Hmisc'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'purrr', 'broom', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'car', 'rsq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'roxygen2'
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘purrr’

Packages suggested but not available for checking:
  'bonsai', 'butcher', 'caret', 'embed', 'keras', 'luz', 'modeldata',
  'parsnip', 'recipes', 'stacks', 'tensorflow', 'testthat', 'vetiver',
  'workflows'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'pillar', 'purrr', 'tidyr', 'tibble', 'forcats', 'stringr',
  'lubridate', 'ggplot2'

Packages suggested but not available for checking: 'edeaR', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bupaR', 'edeaR', 'processcheckR', 'processmapR', 'purrr'

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

Package suggested but not available for checking: ‘flexsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forcats', 'ggplot2', 'reshape2', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'rvest', 'stringr', 'readr'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lubridate’

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'tibble', 'vctrs'

Packages suggested but not available for checking:
  'C50', 'caret', 'ClusterR', 'clustMixType', 'dplyr', 'flexsurv',
  'kknn', 'klaR', 'modeldata', 'nestedmodels', 'parsnip', 'recipes',
  'rsample', 'sparklyr', 'testthat', 'tidyr', 'usethis', 'xrf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'riskRegression'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'tidyr', 'tibble', 'dplyr', 'purrr', 'posterior',
  'bayesplot'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rstan’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright 2016 Steven E. Pav. All Rights Reserved.
  > # Author: Steven E. Pav
  > 
  > # This file is part of BWStest.
  > #
  > # BWStest is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU Lesser General Public License as published by
  > # the Free Software Foundation, either version 3 of the License, or
  > # (at your option) any later version.
  > #
  > # BWStest is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU Lesser General Public License for more details.
  > #
  > # You should have received a copy of the GNU Lesser General Public License
  > # along with BWStest.  If not, see <http://www.gnu.org/licenses/>.
  > 
  > # env var:
  > # nb: 
  > # see also:
  > # todo:
  > # changelog: 
  > #
  > # Created: 2016.03.25
  > # Copyright: Steven E. Pav, 2016-2016
  > # Author: Steven E. Pav
  > # Comments: Steven E. Pav
  > 
  > # because Hadley says it should be like this.
  > # see https://github.com/hadley/devtools/wiki/Testing
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'igraph', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lubridate', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'purrr', 'rvest', 'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking: 'readr', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'viridis'

Packages suggested but not available for checking: 'testthat', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'igraph'

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

Packages suggested but not available for checking: 'modeldata', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'plotly', 'ggforce', 'ggrepel', 'multichull'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tibble', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Seurat', 'reshape2', 'dplyr'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tidyr', 'tibble', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'RLRsim'

Package suggested but not available for checking: ‘gamm4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'FactoMineR', 'ggplot2', 'ggrepel', 'Hmisc', 'RcmdrMisc', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'smoof', 'car', 'dplyr', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'taxize', 'dendextend', 'heatmaply', 'ggplot2', 'plotly', 'pkgdown'

Packages suggested but not available for checking: 'AnnotationDbi', 'GO.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'lubridate', 'plotly'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) calcUnique.Rd:24: Lost braces
    24 | functions, and often the /code{cut()} function are relatively slow when working with tens of millions of rows or more.
       |                               ^
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lubridate', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forcats', 'gggibbous', 'ggimage', 'ggplot2', 'suncalc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'forcats', 'suncalc', 'ggimage', 'gggibbous'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggpubr', 'ggExtra', 'Hmisc', 'rms', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'optimx', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ReGenesees', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'tibble', 'dplyr', 'tidyr', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rms', 'ggplot2', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'kableExtra', 'stringr', 'tidyr', 'haven'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'asciicast', 'mockery', 'testthat'
Packages required but not available: 'dplyr', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggnetwork', 'ggplot2', 'network', 'patchwork'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) heage.Rd:18: Lost braces
    18 | B{\"o}hning, D.  and Schlattmann, P. and Lindsay, B. (1992). \dQuote{Computer-Assisted Analysis of Mixtures (C.A.MAN): Statistical Algorithms}. \emph{Biometrics}. \bold{48}, 283--303.
       |  ^
checkRd: (-1) hepab.Rd:5: Lost braces
     5 | Hepatitis B data from Schlattmann and B{\"o}hning (1993).
       |                                        ^
checkRd: (-1) hepab.Rd:19: Lost braces
    19 | Schlattmann, P. and B{\"o}hning, D. (1993). \dQuote{Mixture models and disease mapping}. \emph{Statistics in Medicine}. \bold{12}, 1943--1950.
       |                      ^
checkRd: (-1) mixalg.Rd:117: Lost braces
   117 | D. B{\"o}hning, P. Schlattmann, B.G. Lindsay: C.A.MAN - Computer Assisted
       |     ^
checkRd: (-1) thai_cohort.Rd:19: Lost braces
    19 | Schelp, F., P. Vivatanasept, P. Sitaputra, S. Sornmani, P. Pongpaew, N. Vudhivai, S. Egormaiphol, and D. B{\"o}hning.  \dQuote{Relationship of the morbidity of under-fives to anthropometric measurements and community health intervention.} \emph{Trop Med Parasitol}, 1990, 41(2), 121--126.
       |                                                                                                           ^
Packages required but not available: 'ggplot2', 'magick'

Packages suggested but not available for checking:
  'testthat', 'patchwork', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Seurat', 'org.Hs.eg.db', 'org.Dr.eg.db', 'org.Mm.eg.db',
  'AnnotationDbi'

Package suggested but not available for checking: ‘sctransform’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'purrr', 'readr', 'stringr',
  'tibble'

Packages suggested but not available for checking: 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'readr', 'tibble'

Packages suggested but not available for checking:
  'devtools', 'pkgdown', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'campsismod', 'dplyr', 'ggplot2', 'furrr', 'purrr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'devtools', 'mrgsolve', 'pkgdown', 'roxygen2', 'rxode2', 'stringr',
  'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'roxygen2', 'testthat'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'frictionless', 'purrr', 'readr'

Packages suggested but not available for checking: 'lubridate', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'lubridate', 'secr'

Packages suggested but not available for checking:
  'magick', 'nimble', 'nimbleEcology', 'plotly', 'reshape2', 'RSQLite',
  'ritis', 'taxize', 'testthat', 'tibble', 'unmarked'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rmapshaper', 'dplyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggrepel', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'assertr', 'dplyr', 'phyloregion', 'purrr', 'tibble'

Packages suggested but not available for checking:
  'patchwork', 'testthat', 'stringr', 'readr', 'usethis',
  'colorBlindness'

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

Packages suggested but not available for checking:
  'ggplot2', 'readr', 'tidyr'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'systemfit', 'qvalue', 'reshape2', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'dplyr'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'khisr', 'lubridate', 'pillar', 'purrr', 'stringr', 'tidyr',
  'vctrs'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'heplots', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bluster', 'igraph'

Packages suggested but not available for checking:
  'testthat', 'Seurat', 'scater', 'batchelor', 'scran', 'patchwork',
  'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘MDA231_tree.pdf’
Packages required but not available: 'reshape2', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'readr', 'rvest', 'stringr', 'purrr', 'tibble', 'RSQLite'

Packages suggested but not available for checking:
  'tidyr', 'ggplot2', 'dbplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'tibble', 'tidyr', 'usethis'
Packages suggested but not available for checking:
  'dplyr', 'readr', 'stringr', 'testthat', 'tibble', 'tidyr', 'ggplot2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'igraph', 'qtl2', 'qtl2convert'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) macrocaic.Rd:31: Lost braces; missing escapes or markup?
    31 |      {RRD = ln(N_1/N_2)}
       |      ^
checkRd: (-1) macrocaic.Rd:34: Lost braces; missing escapes or markup?
    34 |      {PDI = (N_1/(N_1 + N_2))-0.5}
       |      ^
checkRd: (-1) pd.calc.Rd:33: Lost braces
    33 |   \item{Length of tip branch lengths (TIPS)}{Length of tip branch lengths (TIPS)}{Unlike UEH, this measure does not use the unique paths to each tips on the \strong{subtree} and instead gives the sum of the unique branches leading to the tips on the \strong{complete tree}.}
       |                                                                                  ^
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'readxl', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘doBy’

Packages suggested but not available for checking: 'testthat', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'stringr'

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'GGally', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'GGally', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'magick', 'rtweet'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
File ‘carbondate/libs/carbondate.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lme4', 'arm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot.ca.rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ca.rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ca.rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ca.rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:66: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘car’
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) fitweibull.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitweibull.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitweibull.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lutz', 'ggplot2', 'tidyr', 'dplyr', 'purrr', 'tibble', 'readr',
  'lubridate', 'stringr', 'broom', 'hardhat', 'recipes', 'Hmisc',
  'ggrepel'

Packages suggested but not available for checking: 'kableExtra', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr', 'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cards', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'broom', 'broom.helpers', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tibble', 'purrr', 'tidyr', 'tidyselect', 'ggplot2'

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

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'caret'

Packages suggested but not available for checking:
  'testthat', 'klaR', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'caret', 'dplyr'

Packages suggested but not available for checking: 'Cubist', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'recipes', 'reshape2'

Packages suggested but not available for checking:
  'BradleyTerry2', 'Cubist', 'dplyr', 'klaR', 'testthat', 'themis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘roxygen2’
checkRd: (-1) build_for_cran.Rd:13: Lost braces
    13 | The exit status code{R CMD build}, invisibly.
       |                     ^
Packages required but not available: 'igraph', 'ggraph', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'patchwork'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘rstan’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSQLite’
Running examples in ‘caroline-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bestBy
> ### Title: Find the "best" record within subgroups of a dataframe.
> ### Aliases: bestBy
> 
> ### ** Examples
> 
> 
> blast.results <- data.frame(score=c(1,2,34,4,5,3,23), 
+                             query=c('z','x','y','z','x','y','z'), 
+                             target=c('a','b','c','d','e','f','g')
+                             )
> best.hits.R <- bestBy(blast.results, by='query', best='score', inverse=TRUE)
> best.hits.R
  score query target
y    34     y      c
z    23     z      g
x     5     x      e
> ## or using SQLite
> best.hits.sql <- bestBy(blast.results, by='query', best='score', inverse=TRUE, sql=TRUE)
Loading required namespace: RSQLite
Failed with error:  ‘there is no package called ‘RSQLite’’
Error in loadNamespace(x) : there is no package called ‘RSQLite’
Calls: bestBy ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'dplyr', 'tidyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pbkrtest', 'lme4'

Packages suggested but not available for checking: 'alr4', 'effects', 'rio'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'plotly', 'reshape2', 'igraph'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'ggplot2', 'rnaturalearthhires'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gsheet', 'rvest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'animation', 'igraph', 'tnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'igraph'
Running examples in ‘CASCORE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SCORE
> ### Title: Spectral Clustering On Ratios-of-Eigenvectors.
> ### Aliases: SCORE
> 
> ### ** Examples
> 
> 
> # Simulate the Network
> n = 10; K = 2;
> theta = 0.4 + (0.45-0.05)*(seq(1:n)/n)^2; Theta = diag(theta);
> P  = matrix(c(0.8, 0.2, 0.2, 0.8), byrow = TRUE, nrow = K)
> set.seed(2022)
> l = sample(1:K, n, replace=TRUE); # node labels
> Pi = matrix(0, n, K) # label matrix
> for (k in 1:K){
+   Pi[l == k, k] = 1
+ }
> Omega = Theta %*% Pi %*% P %*% t(Pi) %*% Theta;
> Adj = matrix(runif(n*n, 0, 1), nrow = n);
> Adj = Omega - Adj;
> Adj = 1*(Adj >= 0)
> diag(Adj) = 0
> Adj[lower.tri(Adj)] = t(Adj)[lower.tri(Adj)]
> library(igraph)
Error in library(igraph) : there is no package called ‘igraph’
Execution halted
Packages required but not available:
  'rms', 'ggplot2', 'cowplot', 'dplyr', 'purrr', 'tidyr', 'pryr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'dplyr', 'lubridate', 'progress', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'readr', 'badger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tibble', 'tidyr', 'purrr', 'ggplot2'

Package suggested but not available for checking: ‘beepr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'bipartite', 'reshape2', 'purrr', 'dplyr', 'tidyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'alphahull', 'dplyr', 'ggplot2', 'progress', 'tibble',
  'tidyselect'

Packages suggested but not available for checking:
  'GGally', 'tidyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘nloptr’
Packages required but not available: 'caret', 'ggplot2', 'forcats'

Packages suggested but not available for checking:
  'lubridate', 'viridis', 'tmap', 'clustMixType', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'caret', 'dplyr', 'forcats', 'testthat', 'tidyr'
Running examples in ‘cat2cat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cat2cat_agg
> ### Title: Manual mapping for an aggregated panel dataset
> ### Aliases: cat2cat_agg
> 
> ### ** Examples
> 
> data("verticals", package = "cat2cat")
> agg_old <- verticals[verticals$v_date == "2020-04-01", ]
> agg_new <- verticals[verticals$v_date == "2020-05-01", ]
> 
> # cat2cat_agg - can map in both directions at once
> # although usually we want to have the old or the new representation
> 
> agg <- cat2cat_agg(
+   data = list(
+     old = agg_old,
+     new = agg_new,
+     cat_var_old = "vertical",
+     cat_var_new = "vertical",
+     time_var = "v_date",
+     freq_var = "counts"
+   ),
+   Automotive %<% c(Automotive1, Automotive2),
+   c(Kids1, Kids2) %>% c(Kids),
+   Home %>% c(Home, Supermarket)
+ )
> 
> ## possible processing
> library("dplyr")
Error in library("dplyr") : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cat2cat.Rmd’ using rmarkdown

Quitting from lines 71-81 [unnamed-chunk-1] (cat2cat.Rmd)
Error: processing vignette 'cat2cat.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘cat2cat.Rmd’

SUMMARY: processing the following file failed:
  ‘cat2cat.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'sparklyr'

Package suggested but not available for checking: ‘roxygen2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'httr2', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'slippymath', 'testthat', 'tidyterra'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rms', 'mlogit', 'Ecdat', 'geepack', 'lme4', 'vcdExtra'
Note: skipping ‘loglinear-leukoplakia.Rnw’ due to unavailable dependencies:
  'vcdExtra'
Note: skipping ‘multinomial-travel.Rnw’ due to unavailable dependencies:
  'mlogit', 'Ecdat'
Note: skipping ‘multivariate-knee.Rnw’ due to unavailable dependencies:
  'geepack'
Note: skipping ‘ordinal-knee1.Rnw’ due to unavailable dependencies: 'rms'
Note: skipping ‘random-knee2.Rnw’ due to unavailable dependencies: 'lme4'
Package required but not available: ‘optimx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'DescTools', 'Hmisc', 'broom'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'forcats'

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

Packages suggested but not available for checking: 'entropart', 'mice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'viridis', 'lubridate', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) catmapdata.Rd:9-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:20-21: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
checkRd: (-1) colAUC.Rd:79: Lost braces
    79 |      Meteorol. Soc. textbf{30} 291-303. 
       |                           ^
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++14: please drop specification unless essential
Packages suggested but not available for checking:
  'tidyverse', 'ggplot2', 'ggpubr', 'Epi', 'dplyr', 'lme4'
Running examples in ‘catregs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: count.fit
> ### Title: Fits four different count models and compares them.
> ### Aliases: count.fit
> 
> ### ** Examples
> 
> data("LF06art")
> p1 <- glm(art ~ fem + mar + kid5 + phd + ment , family = "poisson", data = LF06art)
> table(LF06art$art)

  0   1   2   3   4   5   6   7   8   9  10  11  12  16  19 
275 246 178  84  67  27  17  12   1   2   1   1   2   1   1 
> fit<-count.fit(p1,0:19)
Error in loadNamespace(x) : there is no package called ‘ggplot2’
Calls: count.fit -> suppressMessages -> withCallingHandlers
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘compare.margins.Rmd’ using rmarkdown
--- finished re-building ‘compare.margins.Rmd’

--- re-building ‘count.fit.Rmd’ using rmarkdown

Quitting from lines 16-26 [unnamed-chunk-1] (count.fit.Rmd)
Error: processing vignette 'count.fit.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘count.fit.Rmd’

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

--- re-building ‘first.diff.fitted.Rmd’ using rmarkdown
--- finished re-building ‘first.diff.fitted.Rmd’

--- re-building ‘list.coef.Rmd’ using rmarkdown
--- finished re-building ‘list.coef.Rmd’

--- re-building ‘lr.test.Rmd’ using rmarkdown
--- finished re-building ‘lr.test.Rmd’

--- re-building ‘margins.dat.Rmd’ using rmarkdown
--- finished re-building ‘margins.dat.Rmd’

--- re-building ‘margins.dat.clogit.Rmd’ using rmarkdown

Quitting from lines 16-27 [unnamed-chunk-1] (margins.dat.clogit.Rmd)
Error: processing vignette 'margins.dat.clogit.Rmd' failed with diagnostics:
there is no package called 'Epi'
--- failed re-building ‘margins.dat.clogit.Rmd’

--- re-building ‘margins.des.Rmd’ using rmarkdown
--- finished re-building ‘margins.des.Rmd’

--- re-building ‘rubins.rule.Rmd’ using rmarkdown
--- finished re-building ‘rubins.rule.Rmd’

--- re-building ‘second.diff.fitted.Rmd’ using rmarkdown
--- finished re-building ‘second.diff.fitted.Rmd’

SUMMARY: processing the following files failed:
  ‘count.fit.Rmd’ ‘margins.dat.clogit.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘testthat’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'ggplot2', 'plotly', 'tidyr', 'forcats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘nloptr’

Packages suggested but not available for checking: 'geiger', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DiagrammeR', 'dplyr', 'ggplot2', 'purrr', 'tidyr', 'igraph',
  'stringr', 'cowplot', 'forcats'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sva', 'dplyr'

Packages suggested but not available for checking:
  'tidyr', 'testthat', 'roxygen2', 'ggplot2'

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

Packages suggested but not available for checking:
  'tidyverse', 'ggalt', 'cobalt', 'ggsci', 'naniar', 'Hmisc',
  'hrbrthemes', 'summarytools'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pcalg', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'Hmisc', 'reshape2', 'testthat', 'tidyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'Ecume', 'cowplot'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DiagrammeR', 'stringr', 'useful', 'cna'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'causaldata', 'geepack'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'loo'

Packages suggested but not available for checking: 'testthat', 'rkeops'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggdag', 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'rstan', 'stringr', 'ggdag', 'latex2exp', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'bayesplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'hdm', 'fastDummies'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cowplot', 'dplyr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggforce', 'ggrepel', 'ggplot2', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tibble', 'stringr', 'ggplot2', 'tidyr', 'readr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'fastDummies', 'ggplot2', 'idefix', 'logitr'

Packages suggested but not available for checking: 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tibble', 'purrr', 'tidyr', 'dplyr', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘igraph’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dplyr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'stringr', 'tidyr', 'tibble'

Packages suggested but not available for checking:
  'countcolors', 'devtools', 'ggplot2', 'httptest', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'haven', 'dplyr', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'diceR', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'tibble'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tibble', 'forcats'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'readr', 'ufs', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'lsbclust'

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

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

Packages suggested but not available for checking: 'testthat', 'nnTensor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘R2jags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'dplyr', 'readxl', 'readr'

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSQLite’
Packages required but not available:
  'cdmTools', 'GDINA', 'ggplot2', 'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'httr2', 'tidyr', 'tigris', 'usa'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'stringr', 'dplyr', 'readr', 'lubridate'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'rvest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'dbplyr', 'purrr', 'tidyselect', 'readr', 'waldo',
  'stringr', 'tidyr', 'omopgenerics'

Packages suggested but not available for checking:
  'RSQLite', 'RPostgres', 'odbc', 'ggplot2', 'bigrquery',
  'DatabaseConnector', 'lubridate', 'tibble', 'testthat', 'snakecase',
  'visR'

Packages which this enhances but not available for checking:
  'arrow', 'Capr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BIFIEsurvey', 'miceadds'

Package which this enhances but not available for checking: ‘GDINA’
checkRd: (-1) data.dtmr.Rd:57: Lost braces; missing escapes or markup?
    57 | \code{RU}: {Referent units}
       |            ^
checkRd: (-1) data.dtmr.Rd:59: Lost braces; missing escapes or markup?
    59 | \code{PI}: {Partitioning and iterating attribute}
       |            ^
checkRd: (-1) data.dtmr.Rd:61: Lost braces; missing escapes or markup?
    61 | \code{APP}: {Appropriateness attribute}
       |             ^
checkRd: (-1) data.dtmr.Rd:63: Lost braces; missing escapes or markup?
    63 | \code{MC}: {Multiplicative Comparison attribute}
       |            ^
Packages required but not available: 'GDINA', 'ggplot2', 'fungible'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tidyr', 'broom'

Package suggested but not available for checking: ‘eemR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'freqparcoord', 'partools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'tidyr', 'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'httr2', 'lubridate', 'lutz'

Package suggested but not available for checking: ‘tibble’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'readxl'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mixtools', 'ggplot2', 'dplyr', 'ggsci', 'ggridges', 'ggprism'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'LSTS', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘nloptr’
Running examples in ‘CEGO-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: createSimulatedTestFunction
> ### Title: Simulation-based Test Function Generator, Object Interface
> ### Aliases: createSimulatedTestFunction
> 
> ### ** Examples
> 
> nsim <- 10
> seed <- 12345
> n <- 6
> set.seed(seed)
> #target function:
> fun <- function(x){
+   exp(-20* x) + sin(6*x^2) + x
+ }
> # "vectorize" target
> f <- function(x){sapply(x,fun)}
> # distance function
> dF <- function(x,y)(sum((x-y)^2)) #sum of squares 
> #start pdf creation
> # plot params
> par(mfrow=c(4,1),mar=c(2.3,2.5,0.2,0.2),mgp=c(1.4,0.5,0))
> #test samples for plots
> xtest <- as.list(seq(from=-0,by=0.005,to=1))
> plot(xtest,f(xtest),type="l",xlab="x",ylab="Obj. function")
> #evaluation samples (training)
> xb <- as.list(runif(n)) 
> yb <- f(xb)
> # support samples for simulation
> x <- as.list(sort(c(runif(100),unlist(xb))))
> # fit the model	
> fit <- modelKriging(xb,yb,dF,control=list(
+    algThetaControl=list(method="NLOPT_GN_DIRECT_L",funEvals=100),useLambda=FALSE))
Error in loadNamespace(x) : there is no package called ‘nloptr’
Calls: modelKriging ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
Packages required but not available: 'sdcHierarchies', 'sdcTable', 'ptable'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'scUtils', 'ggplot2', 'viridis', 'cowplot', 'dplyr', 'scattermore'

Packages suggested but not available for checking:
  'testthat', 'Seurat', 'DESeq2', 'tibble'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'dendextend', 'ggplot2', 'ggbeeswarm'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'reshape2', 'ggplot2'

Packages suggested but not available for checking:
  'robustHD', 'rospca', 'GSE'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble', 'stringr', 'purrr'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'purrr'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'dbplyr', 'ggplot2', 'chilemapas'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arrow', 'dplyr'

Packages suggested but not available for checking:
  'geobr', 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Packages required but not available:
  'parsnip', 'dials', 'dplyr', 'hardhat', 'purrr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'flexsurv', 'pec', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AER’

Package which this enhances but not available for checking: ‘sampleSelection’
Running examples in ‘censReg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: censReg
> ### Title: Censored Regression (Tobit) Model
> ### Aliases: censReg print.censReg
> ### Keywords: models regression
> 
> ### ** Examples
> 
> ## Kleiber & Zeileis ( 2008 ), page 142
> data( "Affairs", package = "AER" )
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Note: skipping ‘censReg.Rnw’ due to unavailable dependencies: 'AER'
Package required but not available: ‘optimx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'ggrepel', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Census2016.Rmd’ using rmarkdown

Quitting from lines 63-74 (Census2016.Rmd)
Error: processing vignette 'Census2016.Rmd' failed with diagnostics:
object '.CensusDataTables' not found
--- failed re-building ‘Census2016.Rmd’

SUMMARY: processing the following file failed:
  ‘Census2016.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) listCensusApis.Rd:10: Lost braces; missing escapes or markup?
    10 | Scrapes {https://api.census.gov/data.json} and returns a dataframe
       |         ^
Packages required but not available: 'dplyr', 'stringr'

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

Package suggested but not available for checking: ‘linkcomm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'haven', 'dplyr', 'stringr'

Packages suggested but not available for checking:
  'ggplot2', 'tidyr', 'vtable', 'compareGroups'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gravity’
Packages required but not available: 'tibble', 'dplyr', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'janitor', 'purrr', 'readr', 'readxl', 'stringr', 'tidyr',
  'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) cequre.Rd:31: Lost braces; missing escapes or markup?
    31 |   {epsi}^{# regression coefficients} times the initial value,
       |   ^
checkRd: (-1) cequre.Rd:31: Lost braces; missing escapes or markup?
    31 |   {epsi}^{# regression coefficients} times the initial value,
       |          ^
Packages required but not available:
  'dplyr', 'purrr', 'slippymath', 'tibble', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'vctrs'

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'batchtools', 'dplyr', 'ggplot2', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'dplyr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'haven', 'readr', 'labelled', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'DALEX'

Packages suggested but not available for checking: 'ggiraph', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) cfc.tbasis.Rd:23: Lost braces
    23 | Assuming one-dimensional \code{p1} and \code{p2} for clarity, the algorithm calculates cumulative incidence function for cuase 1 using a recursive formula: \code{ci1[n+1] = ci1[n] + dci1[n]}, where \code{dci1[n] = 0.5*(p2[n] + p2[n+1])*(p1[n] - p1[n+1])}. The increment in cumulative incidence function for cause 2 is similarly calculated, \code{dci2[n] = 0.5*(p1[n] + p1[n+1])*(p2[n] - p2[n+1])}. These equations guarantee that \code{dci1[n] + dci2[n] = p1[n]*p2[n] - p1[n+1]*p2[n+1]}. Event-free probability is simply calculated as code{efp[n] = p1[n]*p2[n]}. Taken together, this numerical integration ensures that \code{efp[n+1] - efp[n] + dci1[n] + dci2[n] = 0}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           ^
Packages required but not available: 'fda', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'usethis'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bibtex_cff.Rmd’ using rmarkdown
--- finished re-building ‘bibtex_cff.Rmd’

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

--- re-building ‘crosswalk.Rmd’ using rmarkdown

Quitting from lines 632-635 [title] (crosswalk.Rmd)
Error: processing vignette 'crosswalk.Rmd' failed with diagnostics:
`x` not valid. If it is a package you may need to install it with
`install.packages()`.
--- failed re-building ‘crosswalk.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'igraph', 'mockery', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'purrr', 'forcats', 'ggplot2', 'testthat',
  'incidence2', 'distributional'
Running examples in ‘cfr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: prepare_data
> ### Title: Prepare common epidemiological data formats for CFR estimation
> ### Aliases: prepare_data prepare_data.incidence2
> 
> ### ** Examples
> 
> #### For <incidence2> data ####
> # load Covid-19 data from incidence2
> covid_uk <- incidence2::covidregionaldataUK
Error in loadNamespace(x) : there is no package called ‘incidence2’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
cfr_time_varying 4.668  0.038   6.649
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > # nolint start
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cfr.Rmd’ using rmarkdown
--- finished re-building ‘cfr.Rmd’

--- re-building ‘data_from_incidence2.Rmd’ using rmarkdown

Quitting from lines 27-31 [setup] (data_from_incidence2.Rmd)
Error: processing vignette 'data_from_incidence2.Rmd' failed with diagnostics:
there is no package called 'incidence2'
--- failed re-building ‘data_from_incidence2.Rmd’

--- re-building ‘delay_distributions.Rmd’ using rmarkdown

Quitting from lines 27-33 [setup] (delay_distributions.Rmd)
Error: processing vignette 'delay_distributions.Rmd' failed with diagnostics:
there is no package called 'distributional'
--- failed re-building ‘delay_distributions.Rmd’

--- re-building ‘estimate_ascertainment.Rmd’ using rmarkdown

Quitting from lines 54-64 [unnamed-chunk-1] (estimate_ascertainment.Rmd)
Error: processing vignette 'estimate_ascertainment.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘estimate_ascertainment.Rmd’

--- re-building ‘estimate_static_severity.Rmd’ using rmarkdown

Quitting from lines 52-56 [unnamed-chunk-1] (estimate_static_severity.Rmd)
Error: processing vignette 'estimate_static_severity.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘estimate_static_severity.Rmd’

--- re-building ‘estimate_time_varying_severity.Rmd’ using rmarkdown

Quitting from lines 59-67 [unnamed-chunk-2] (estimate_time_varying_severity.Rmd)
Error: processing vignette 'estimate_time_varying_severity.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘estimate_time_varying_severity.Rmd’

SUMMARY: processing the following files failed:
  ‘data_from_incidence2.Rmd’ ‘delay_distributions.Rmd’
  ‘estimate_ascertainment.Rmd’ ‘estimate_static_severity.Rmd’
  ‘estimate_time_varying_severity.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'testthat', 'stringr'
Running examples in ‘CFtime-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bounds
> ### Title: Bounds of the time offsets
> ### Aliases: bounds bounds,CFtime-method bounds<- bounds<-,CFtime-method
> 
> ### ** Examples
> 
> cf <- CFtime("days since 2024-01-01", "standard", seq(0.5, by = 1, length.out = 366))
> as_timestamp(cf)[1:3]
[1] "2024-01-01 12:00:00" "2024-01-02 12:00:00" "2024-01-03 12:00:00"
> bounds(cf) <- rbind(0:365, 1:366)
> bounds(cf)[, 1:3]
     [,1] [,2] [,3]
[1,]    0    1    2
[2,]    1    2    3
> bounds(cf, "%d-%b-%Y")[, 1:3]
Error in loadNamespace(x) : there is no package called ‘stringr’
Calls: bounds ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'osmdata', 'tidync', 'furrr', 'tidyr'

Packages suggested but not available for checking: 'lubridate', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cgam', 'gratia'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'reshape2'
Running examples in ‘CGGP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CGGPplotblockselection
> ### Title: Plot CGGP block selection over time
> ### Aliases: CGGPplotblockselection
> 
> ### ** Examples
> 
> gs <- CGGPcreate(d=3, batchsize=100)
> # All dimensions will look similar
> CGGPplotblockselection(gs)
Error in loadNamespace(x) : there is no package called ‘reshape2’
Calls: CGGPplotblockselection ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CGGP.Rmd’ using rmarkdown

Quitting from lines 178-179 [plotblocks] (CGGP.Rmd)
Error: processing vignette 'CGGP.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘CGGP.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'lubridate', 'readxl', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyverse', 'ggplot2', 'hms'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BayesFactor', 'DescTools', 'dplyr', 'forcats', 'ggmosaic',
  'ggplot2', 'ggrepel', 'paletteer', 'purrr', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'ggthemes', 'hrbrthemes', 'janitor', 'productplots', 'tibble',
  'testthat', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr', 'tibble'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘chain_glm.Rmd’ using rmarkdown

Quitting from lines 32-39 [initialize] (chain_glm.Rmd)
Error: processing vignette 'chain_glm.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘chain_glm.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 117-127 [data2] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘chain_glm.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'systemfit', 'cplm', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'vdiffr'
checkRd: (-1) ftse100.Rd:8: Lost braces; missing escapes or markup?
     8 |  This dataset gives the daily returns (c_{t+1}/c_t -1) of the UK FTSE 100 index from 2nd April 1984 until the 13th September 2012.
       |                                          ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘DiagrammeR’
checkRd: (-1) Hausdorff.dist.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{vec1}{A \code{integer} vector forms a subset of {1, 2, ..., n}.}
       |                                                       ^
checkRd: (-1) Hausdorff.dist.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{vec2}{A \code{integer} vector forms a subset of {1, 2, ..., n}.}
       |                                                       ^
checkRd: (-1) online.univar.multi.Rd:47-57: Lost braces
    47 | online.univar.one2 = function(y_vec, gamma, tau_gamma, ...){
       |                                                            ^
checkRd: (-1) online.univar.multi.Rd:50-55: Lost braces
    50 |   while(FLAG == 0 & t <= length(y_vec)){
       |                                        ^
checkRd: (-1) online.univar.multi.Rd:71-89: Lost braces
    71 | online.univar.one3 = function(y_vec, tau_vec, ...){
       |                                                   ^
checkRd: (-1) online.univar.multi.Rd:72-74: Lost braces
    72 |   if(length(y_vec) != length(tau_vec)){
       |                                       ^
checkRd: (-1) online.univar.multi.Rd:77-87: Lost braces
    77 |   while(FLAG == 0 & t <= length(y_vec)){
       |                                        ^
checkRd: (-1) online.univar.multi.Rd:81-86: Lost braces
    81 |     while(j < J & FLAG == 0){
       |                             ^
Running examples in ‘changepoints-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: WBS.univar
> ### Title: Wild binary segmentation for univariate mean change points
> ###   detection.
> ### Aliases: WBS.univar
> 
> ### ** Examples
> 
> set.seed(0)
> cpt_true = c(20, 50, 170)
> y = rnorm(300) + c(rep(0,20),rep(2,30),rep(0,120),rep(2,130))
> intervals = WBS.intervals(M = 300, lower = 1, upper = length(y))
> temp = WBS.univar(y, 1, length(y), intervals$Alpha, intervals$Beta, delta = 5)
> plot.ts(y)
> points(x = tail(temp$S[order(temp$Dval)],4),
+        y = y[tail(temp$S[order(temp$Dval)],4)], col = "red")
> WBS_result = thresholdBS(temp, tau = 4)
> print(WBS_result$BS_tree, "value")
                                      levelName     value
1 Binary Segmentation Tree Trimmed with tau = 4        NA
2  °--N170                                      15.667978
3      °--N50                                    9.957747
4          °--N20                                7.301167
> plot(WBS_result$BS_tree)
Error in plot.Node(WBS_result$BS_tree) : 
  Package "DiagrammeR" is required to plot a `data.tree::Node`object. Please install it.
Calls: plot -> plot.Node
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
WBS.uni.nonpar             4.969  0.004   6.082
DP.SEPP                    4.246  0.003   6.024
CV.search.DP.LR.regression 4.011  0.003   5.744
DP.poly                    3.580  0.000   5.210
Packages required but not available:
  'phylobase', 'dplyr', 'rangeModelMetadata'

Packages suggested but not available for checking:
  'tidyverse', 'testthat', 'wallace'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'available', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nls.multstart', 'ggplot2', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'AER', 'progress', 'purrr'

Packages suggested but not available for checking: 'testthat', 'lax'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

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

Packages suggested but not available for checking: 'testthat', 'ipaddress'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'rvest'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) create_unit_tests.Rd:17: Lost braces; missing escapes or markup?
    17 | Create `{testthat}` test cases for the code.
       |         ^
Packages required but not available: 'httr2', 'purrr'

Packages suggested but not available for checking: 'testthat', 'shinytest2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'bench', 'testthat', 'vctrs'
Running examples in ‘cheapr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gcd
> ### Title: Greatest common divisor and smallest common multiple
> ### Aliases: gcd scm gcd2 scm2
> 
> ### ** Examples
> 
> library(cheapr)
> library(bench)
Error in library(bench) : there is no package called ‘bench’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) as.data.frame.checkglobals.Rd:43: Lost braces; missing escapes or markup?
    43 | \item \code{type}, the type of the detected entity, either \code{"global"} or {"import"}.
       |                                                                               ^
checkRd: (-1) as.matrix.checkglobals.Rd:32: Lost braces; missing escapes or markup?
    32 | \item \code{type}, the type of the detected entity, either \code{"global"} or {"import"}.
       |                                                                               ^
Packages required but not available:
  'devtools', 'dplyr', 'purrr', 'roxygen2', 'stringr'

Packages suggested but not available for checking:
  'attachment', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'testthat', 'tibble'
Running examples in ‘checkmate-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: checkTibble
> ### Title: Check if an argument is a tibble
> ### Aliases: checkTibble check_tibble assertTibble assert_tibble testTibble
> ###   test_tibble expect_tibble
> 
> ### ** Examples
> 
> library(tibble)
Error in library(tibble) : there is no package called ‘tibble’
Execution halted
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘checkmate.Rmd’ using rmarkdown

Quitting from lines 160-171 [unnamed-chunk-7] (checkmate.Rmd)
Error: processing vignette 'checkmate.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘checkmate.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'testthat', 'darts'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘purrr’

Packages suggested but not available for checking:
  'dplyr', 'lubridate', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) LoadCollection.Rd:7: Lost braces
     7 | for loading and saving code{CommunityCollection} objects to text files.
       |                            ^
checkRd: (-1) ShortestPaths.Rd:25: Lost braces
    25 | \references{Williams, R.J. and Berlow, E.L. and Dunne, J.A. and Barab{\'a}si, 
       |                                                                      ^
checkRd: (-1) YthanEstuary.Rd:19: Lost braces
    19 | Read G., St\"{o}hr S., Walter T.C., Costello M.J. Editors. (2012) World 
       |              ^
Packages required but not available: 'spinifex', 'ggplot2', 'plotly'

Packages suggested but not available for checking:
  'tourr', 'gganimate', 'dplyr', 'tidyr', 'beepr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forcats', 'kableExtra', 'purrr', 'stringr', 'tibble',
  'tidyr', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2', 'phyloseq'

Packages suggested but not available for checking: 'patchwork', 'ggpmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'tibble'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'webchem', 'fmcsR', 'ChemmineR', 'hillR', 'GUniFrac', 'tidygraph',
  'igraph', 'ggraph', 'ggplot2', 'ggdendro', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ChemoSpecUtils', 'readJDX', 'ggplot2'

Packages suggested but not available for checking: 'mlrMBO', 'smoof', 'mlr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ChemoSpecUtils', 'reshape2', 'readJDX', 'patchwork', 'ggplot2',
  'plotly'

Packages suggested but not available for checking:
  'speaq', 'hyperSpec', 'roxut'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggrepel', 'plotly'

Packages suggested but not available for checking:
  'ChemoSpec', 'ChemoSpec2D', 'roxut', 'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Running examples in ‘cherryblossom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: run09
> ### Title: Cherry Blossom Run data, 2009
> ### Aliases: run09
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

Packages suggested but not available for checking:
  'igraph', 'patchwork', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'broom', 'ggplot2', 'tibble', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'dunlin', 'forcats', 'ggplot2', 'nestcolor', 'purrr',
  'rlistings', 'stringr', 'tern', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'vdiffr'

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

Packages suggested but not available for checking:
  'testthat', 'GenomicInteractions', 'Gviz', 'countreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dbplyr', 'dplyr', 'purrr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'tibble', 'reshape2', 'purrr', 'purrrlyr'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rmapshaper', 'dplyr', 'stringr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'chillR', 'dplyr', 'lubridate', 'ggplot2'
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'metR', 'patchwork', 'progress',
  'purrr', 'readxl', 'reshape2', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

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

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

Packages suggested but not available for checking:
  'babynames', 'car', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'drc', 'RDML', 'testthat'
checkRd: (-1) C316.amp.Rd:28-32: Lost braces
    28 |     40 x {
       |          ^
checkRd: (-1) C317.amp.Rd:28-32: Lost braces
    28 |     40 x {
       |          ^
checkRd: (-1) C60.amp.Rd:63-67: Lost braces
    63 |     40 x {
       |          ^
Packages suggested but not available for checking:
  'climatrends', 'testthat'
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘gt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'brms', 'rstan'

Packages suggested but not available for checking: 'cmdstanr', 'posterior'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running examples in ‘chk-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: expect_chk_error
> ### Title: Expect Chk Error
> ### Aliases: expect_chk_error
> 
> ### ** Examples
> 
> expect_chk_error(chk_true(FALSE))
Error in expect_chk_error(chk_true(FALSE)) : `testhat` must be installed.
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Problems with news in ‘NEWS.md’:
No news entries found.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'elevatr', 'ggplot2', 'igraph', 'threejs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Packages required but not available:
  'acs', 'Hmisc', 'stringr', 'ggplot2', 'dplyr', 'ggmap', 'tigris',
  'rvest', 'tidyr', 'tidycensus'

Packages suggested but not available for checking:
  'testthat', 'choroplethrAdmin1'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'testthat', 'igraph', 'ggplot2', 'spatialwarnings'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘chouca-package.Rmd’ using rmarkdown

Quitting from lines 28-31 [unnamed-chunk-3] (chouca-package.Rmd)
Error: processing vignette 'chouca-package.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘chouca-package.Rmd’

SUMMARY: processing the following file failed:
  ‘chouca-package.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggplot2’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'readr', 'readxl', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'entab', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'plotly', 'purrr', 'readr', 'skimr', 'viridis'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'lubridate', 'purrr', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'magick', 'readr', 'tibble', 'tidyr',
  'tidyselect'

Packages suggested but not available for checking:
  'readxl', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Packages required but not available: 'dplyr', 'progress'

Packages suggested but not available for checking:
  'testthat', 'RSQLite', 'dbplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
checkRd: (-1) chunker-methods.Rd:63: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:64: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:70: Lost braces in \enumerate; meant \describe ?
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggraph'

Packages suggested but not available for checking:
  'clustree', 'plotly', 'Seurat', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'roxygen2', 'testthat'
Running ‘run-all.R’ [0s/1s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ggplot2', 'ggpubr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'stringr', 'dplyr', 'tidyr', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'twang', 'arm', 'dplyr', 'WeightIt', 'tidyr', 'ggplot2', 'cowplot',
  'metR', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ChIPseeker', 'DESeq2', 'dplyr', 'fgsea',
  'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene', 'ggplot2', 'ggrepel', 'sva'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidytext', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'network', 'sna', 'centiserve', 'FactoMineR', 'factoextra',
  'GGally', 'dendextend', 'viridis', 'ggplot2', 'intergraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘userfriendlyscience’
checkRd: (-1) CIplot.Rd:58: Lost braces; missing escapes or markup?
    58 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.
       |                       ^
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'gh', 'purrr', 'testthat', 'usethis'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'viridis'
Running examples in ‘circlesplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: circlesplot
> ### Title: circlesplot(): Plots multiple circles with their given ratios
> ### Aliases: circlesplot
> 
> ### ** Examples
> 
> 
> 
> # Proportions among planets
> library('plotrix')
> colors = c('#D1BBD7', '#AE76A3', '#882E72', '#1965B0', '#5289C7', '#7BAFDE', '#4EB265', '#90C987')
> planets = c('Mercury','Venus','Earth','Mars','Jupiter','Saturn','Uranus','Neptune')
> diameter = c(4879.4,12103.6,12756.3,6792.4,142984,120536,51118,49528)
> circlesplot(cp_vals=diameter, cp_text=planets, cp_max=3L, cp_title="Planets", cp_color=colors)
> 
> # For coloring, you can also use viridis package:
> library("viridis")
Error in library("viridis") : there is no package called ‘viridis’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘dendextend’
Running examples in ‘circlize-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: circos.dendrogram
> ### Title: Add circular dendrograms
> ### Aliases: circos.dendrogram
> 
> ### ** Examples
> 
> load(system.file(package = "circlize", "extdata", "bird.orders.RData"))
> 
> labels = hc$labels  # name of birds
> ct = cutree(hc, 6)  # cut tree into 6 pieces
> n = length(labels)  # number of bird species
> dend = as.dendrogram(hc)
> 
> circos.par(cell.padding = c(0, 0, 0, 0))
> circos.initialize(sectors = "a", xlim = c(0, n)) # only one sector
> max_height = attr(dend, "height")  # maximum height of the trees
> circos.trackPlotRegion(ylim = c(0, 1), bg.border = NA, track.height = 0.3,
+     panel.fun = function(x, y) {
+         for(i in seq_len(n)) {
+             circos.text(i-0.5, 0, labels[i], adj = c(0, 0.5),
+                 facing = "clockwise", niceFacing = TRUE,
+                 col = ct[labels[i]], cex = 0.7)
+         }
+ })
> 
> suppressPackageStartupMessages(require(dendextend))
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘dendextend’
> dend = color_branches(dend, k = 6, col = 1:6)
Error in color_branches(dend, k = 6, col = 1:6) : 
  could not find function "color_branches"
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) rstable.Rd:42: Lost braces
    42 | Lo\"{g}ae\"{v}e, M. (1977). Probability Theory I. (fourth edition) Springer-Verlag, New York.
       |     ^
checkRd: (-1) rstable.Rd:42: Lost braces
    42 | Lo\"{g}ae\"{v}e, M. (1977). Probability Theory I. (fourth edition) Springer-Verlag, New York.
       |            ^
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'plotly', 'testthat'

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

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggforce', 'ggplot2', 'htmlTable', 'purrr', 'tibble',
  'tidyr'

Packages suggested but not available for checking:
  'ggrepel', 'kableExtra', 'roxygen2', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) doseFind.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) doseFind.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) doseFind.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
Packages required but not available: 'ggplot2', 'dplyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'MESS', 'networkD3', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'plotly', 'tidyr', 'ggthemes'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'plotly', 'rvest'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arm', 'dplyr', 'lme4'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'parabar', 'progress', 'tibble', 'lme4'

Packages suggested but not available for checking:
  'testthat', 'plotly', 'ggraph', 'igraph', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available:
  'ggplot2', 'GGally', 'clustMixType', 'tibble', 'stringr', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘caret’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'feather', 'ggplot2', 'roxygen2', 'mockery', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘civis_ml.Rmd’ using rmarkdown

Quitting from lines 215-216 [unnamed-chunk-11] (civis_ml.Rmd)
Error: processing vignette 'civis_ml.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘civis_ml.Rmd’

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘AER’

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'dplyr', 'tidyr', 'tibble', 'lubridate', 'progress',
  'vctrs', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'ggplot2', 'randomForestSRC'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'dbplyr'

Packages suggested but not available for checking: 'readxl', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # testthat.R -- automated test cases
  > #
  > # MS
  > # Created: Feb 8, 2015
  > 
  > require("testthat")
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > require("Ckmeans.1d.dp")
  Loading required package: Ckmeans.1d.dp
  > 
  > test_check("Ckmeans.1d.dp")
  Error in test_check("Ckmeans.1d.dp") : 
    could not find function "test_check"
  Execution halted
Packages required but not available:
  'dplyr', 'ggforce', 'ggplot2', 'ggraph', 'igraph', 'purrr', 'readr',
  'stringr', 'tibble', 'tidygraph', 'tidyr', 'vroom'

Package suggested but not available for checking: ‘tidyverse’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘clarabel/libs/clarabel.so’:
  Found non-API calls to R: ‘SET_ENCLOS’, ‘SET_ENVFLAGS’, ‘SET_PRCODE’,
    ‘SET_PRENV’, ‘SET_PRVALUE’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) get_langs.Rd:13: Lost braces
    13 | character vector listing all the languages that tag API call supports. See \code{\link{tag_images}} and code{\link{tag_image_urls}}
       |                                                                                                             ^
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'logistf', 'geepack', 'rms', 'AER', 'ivreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'caret'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'cellWise'

Packages suggested but not available for checking:
  'reshape2', 'robCompositions'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'readtext'
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'pillar', 'vctrs'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'cowplot', 'AER', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘cleaner’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'devtools', 'testthat', 'usethis'
Running examples in ‘cleanr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check_package
> ### Title: Check a Package
> ### Aliases: check_package
> 
> ### ** Examples
> 
> # create a fake package first:
> package_path <- file.path(tempdir(), "fake")
> usethis::create_package(package_path, fields = NULL,
+                         rstudio = FALSE, open = FALSE)
Error in loadNamespace(x) : there is no package called ‘usethis’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'gganimate', 'ggplot2', 'ggtext', 'transformr', 'imputeTestbench',
  'imputeTS', 'lubridate', 'stringr', 'tibble'

Package suggested but not available for checking: ‘timetk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘AER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'progress', 'selectr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplotify', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘seqHMM’
Package required but not available: ‘arrow’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'reshape2', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'rvest', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'lubridate', 'ggplot2', 'reshape2', 'rvest', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'readr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'gganimate', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rangeBuilder', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘readxl’
Running examples in ‘climatol-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: csv2climatol
> ### Title: Convert data in a single CSV file to 'climatol' input format
> ### Aliases: csv2climatol
> ### Keywords: manip
> 
> ### ** Examples
> 
> ## Set a temporal working directory:
> wd <- tempdir()
> wd0 <- setwd(wd)
> 
> ## Create origin and destination directories and copy example input files:
> dir.create('dir1'); dir.create('dir2')
> file.copy(exampleFiles('p064.xlsx'),'dir1')
[1] TRUE
> file.copy(exampleFiles('p082.xlsx'),'dir1')
[1] TRUE
> file.copy(exampleFiles('p084.xlsx'),'dir1')
[1] TRUE
> 
> ## Create input files for csv2climatol with the function xls2csv:
> xls2csv('dir1','dir2','RR')
Error in xls2csv("dir1", "dir2", "RR") : 
  Please, install the package 'readxl' and run this function again
Execution halted
Package required but not available: ‘nasapower’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘SPEI’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'climatrends', 'gosset', 'nasapower', 'PlackettLuce', 'testthat'
Note: skipping ‘Overview.Rmd’ due to unavailable dependencies:
  'PlackettLuce'
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'ggplot2', 'lubridate', 'lme4'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'clinUtils', 'ggplot2', 'haven', 'plotly', 'stringr'

Packages suggested but not available for checking:
  'inTextSummaryTable', 'patientProfilesVis', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rstan', 'DoseFinding', 'ggplot2', 'tidyr', 'purrr', 'tibble',
  'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BayesFactor', 'dplyr', 'ggplot2', 'lme4', 'purrr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'tidyverse', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'ggplot2', 'cowplot', 'nloptr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) clinsig.Rd:129: Lost braces
   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                   ^
checkRd: (-1) clinsig.Rd:129: Lost braces
   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                                 ^
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'ggplot2', 'dplyr'

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

Packages suggested but not available for checking:
  'tibble', 'ggplot2', 'plotly', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'igraph', 'qgraph', 'ohenery'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'mockery', 'testthat', 'tibble'
File ‘cli/libs/cli.so’:
  Found non-API calls to R: ‘SET_ENCLOS’, ‘SET_FRAME’, ‘SET_HASHTAB’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘cli-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: test_that_cli
> ### Title: Test cli output with testthat
> ### Aliases: test_that_cli
> 
> ### ** Examples
> 
> # testthat cannot record or compare snapshots when you run these
> # examples interactively, so you might want to copy them into a test
> # file
> 
> # Default configurations
> cli::test_that_cli("success", {
+   testthat::local_edition(3)
+   testthat::expect_snapshot({
+     cli::cli_alert_success("wow")
+   })
+ })
Error in loadNamespace(x) : there is no package called ‘testthat’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lme4', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'StMoMo', 'ChainLadder', 'ggplot2', 'forecast', 'reshape2'

Packages suggested but not available for checking: 'apc', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'janitor', 'lubridate', 'purrr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'pillar', 'slider', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) print.clogitL1.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.clogitL1.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.clogitL1.Rd:23: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘rstan’

Packages suggested but not available for checking:
  'car', 'ggplot2', 'ggsurvfit', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mc2d’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'googledrive', 'dplyr'

Packages suggested but not available for checking:
  'googlesheets4', 'haven', 'readr', 'readxl', 'testthat'

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

Packages suggested but not available for checking:
  'tensorflow', 'keras', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'httptest', 'kableExtra', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lubridate', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'geepack', 'mlmRev', 'AER', 'lme4', 'testthat', 'ivreg'
checkRd: (-1) impute_covariance_matrix.Rd:74-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_covariance_matrix.Rd:80-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_covariance_matrix.Rd:88-98: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'patchwork', 'roxygen2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright (c) 2020-2023 Nuno Fachada
  > # Distributed under the MIT License (http://opensource.org/licenses/MIT)
  > 
  > library(clugenr)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Note: skipping ‘examples2d.Rmd’ due to unavailable dependencies:
  'ggplot2', 'patchwork'
Note: skipping ‘examplesmrg.Rmd’ due to unavailable dependencies:
  'ggplot2', 'patchwork'
Note: skipping ‘examplesnd.Rmd’ due to unavailable dependencies:
  'ggplot2', 'patchwork'
Packages required but not available: 'ggplot2', 'dplyr', 'tableone'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggplot2', 'plotly', 'viridis', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggpubr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'igraph', 'progress', 'reshape2', 'stringr'

Packages suggested but not available for checking:
  'dendextend', 'Seurat', 'readr', 'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘FactoMineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DescTools', 'ggplot2', 'ggseqlogo', 'network', 'stringr', 'sna'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qrcm', 'fda', 'ggpubr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Found the following files/directories:
  ‘clusterhap_reports’
Specified C++11: please drop specification unless essential
checkRd: (-1) HTKmeans.Rd:62: Lost braces
    62 | \item{centers }{A matrix of cluster centres.}
       |      ^
checkRd: (-1) HTKmeans.Rd:62: Lost braces
    62 | \item{centers }{A matrix of cluster centres.}
       |                ^
checkRd: (-1) HTKmeans.Rd:63: Lost braces
    63 | \item{cluster }{A vector of integers (from 1:\code{k}) indicating the cluster to which each point is allocated.}
       |      ^
checkRd: (-1) HTKmeans.Rd:63: Lost braces
    63 | \item{cluster }{A vector of integers (from 1:\code{k}) indicating the cluster to which each point is allocated.}
       |                ^
checkRd: (-1) HTKmeans.Rd:64: Lost braces
    64 | \item{itnb }{The number of iterations executed until convergence}
       |      ^
checkRd: (-1) HTKmeans.Rd:64: Lost braces
    64 | \item{itnb }{The number of iterations executed until convergence}
       |             ^
checkRd: (-1) HTKmeans.Rd:65: Lost braces
    65 | \item{converged }{Whether the algorithm stopped by converging or through reaching the maximum number of itertions.}
       |      ^
checkRd: (-1) HTKmeans.Rd:65: Lost braces
    65 | \item{converged }{Whether the algorithm stopped by converging or through reaching the maximum number of itertions.}
       |                  ^
Packages required but not available:
  'ClusterR', 'dplyr', 'ggplot2', 'sqldf', 'toOrdinal'

Packages suggested but not available for checking:
  'shinyFiles', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mice', 'micemd', 'ClusterR', 'FactoMineR', 'diceR',
  'NPBayesImputeCat', 'reshape2'

Packages suggested but not available for checking:
  'VIM', 'missMDA', 'clustrd', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'GSEABase', 'GSVA', 'singscore', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'narray', 'progress'

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-clusternomics.Rmd’ using rmarkdown

Quitting from lines 37-42 [unnamed-chunk-1] (using-clusternomics.Rmd)
Error: processing vignette 'using-clusternomics.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘using-clusternomics.Rmd’

SUMMARY: processing the following file failed:
  ‘using-clusternomics.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'car', 'dendextend', 'reshape2', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'AER', 'mlogit', 'dfidx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) cluster.Gen.rd:82: Lost braces
    82 | Steinley, D., Henson, R. (2005), \emph{OCLUS: an analytic method for generating clusters with known overlap}, "Journal of Classification", vol. 22, 221-250. Available at: \\doi{10.1007/s00357-005-0015-6}.
       |                                                                                                                                                                                 ^
checkRd: (-1) index.DB.rd:23: Lost braces; missing escapes or markup?
    23 | \item{R}{R matrix $(S_r+S_s)/d_{rs}$}
       |                                ^
checkRd: (-1) index.GAP.rd:12: Lost braces; missing escapes or markup?
    12 | "pc" - generate the reference variables from a uniform distribution over a box aligned with the principal components of the data. In detail, if $X=\{x_{ij}\}$  is our   n x m data matrix, assume that the columns have mean 0 and compute the singular value decomposition $X=UDV^T$. We transform via $X'=XV$ and then draw uniform features Z'  over the ranges of the columns of X' , as in method a) above. Finally we back-transform via $Z=Z'V^T$   to give reference data Z 
       |                                                                                                                                                        ^
checkRd: (-1) pattern.GDM1.rd:77: Lost braces
    77 | Jajuga, K., Walesiak, M., Bak, A. (2003), \emph{On the general distance measure}, In: M. Schwaiger, O. Opitz (Eds.), Exploratory data analysis in empirical research, Springer-Verlag, Berlin, Heidelberg, 104-109. Available at: doi{10.1007/978-3-642-55721-7_12}.
       |                                                                                                                                                                                                                                      ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'fastDummies', 'parabar'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ClusterR', 'dplyr', 'tidyr', 'ggplot2'

Packages suggested but not available for checking:
  'ggExtra', 'testthat', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BiDAG', 'pcalg', 'igraph'

Packages suggested but not available for checking:
  'ggraph', 'ggpubr', 'ggplot2', 'reshape2', 'car', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BAMBI', 'igraph', 'purrr', 'ggplot2', 'cowplot'

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘haven’
Packages required but not available:
  'ggplot2', 'tibble', 'GGally', 'dplyr', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggraph', 'igraph', 'dplyr', 'ggplot2', 'viridis', 'tidygraph',
  'ggrepel'

Packages suggested but not available for checking:
  'testthat', 'Seurat', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'stringr', 'igraph', 'forcats', 'tidygraph', 'ggraph',
  'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'klaR', 'dplyr', 'psycho'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'annotate', 'GO.db', 'moe430a.db'
Note: skipping ‘clValid.Rnw’ due to unavailable dependencies: 'annotate'
Packages required but not available:
  'ggplot2', 'lubridate', 'optimx', 'testthat'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'smoof', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) CMAPSS.Rd:10: Lost braces
    10 | \item \code{train}{ a list of class "hhsmm.data" as the train dataset}
       |                   ^
checkRd: (-1) CMAPSS.Rd:11: Lost braces
    11 | \item \code{test}{ a list of class "hhsmm.data" as the test dataset}
       |                  ^
checkRd: (-1) CMAPSS.Rd:12: Lost braces
    12 | \item \code{subsets}{ a matrix containig the number of units in each subset of the CMAPSS data set (FD001-FD004) for the train and test datasets}
       |                     ^
Packages required but not available:
  'readxl', 'ggplot2', 'dplyr', 'reshape2', 'stringr'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) cmb.search.Rd:50: Lost braces; missing escapes or markup?
    50 |   \item{order}{applied conditioning order {length p}}
       |                                           ^
checkRd: (-1) gp.realize.Rd:20: Lost braces; missing escapes or markup?
    20 | The list \code{l.v} is created by \code{makedistlist()} from a {n x p} design matrix on which to generate the unconditional GP realization.  The correlation parameters take on values in \code{(0,1)} and use the Gaussian correlation model, calculated as \code{rho^d(xi,xj)^2}.  This helper function is used to create the demonstration data used in the example for \code{calibrate()}.
       |                                                                ^
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'x3ptools', 'dplyr', 'ggplot2', 'imager', 'purrr', 'stringr',
  'ggnewscale', 'tibble', 'tidyr', 'patchwork', 'ggplotify'

Packages suggested but not available for checking:
  'testthat', 'magick', 'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
File ‘CMF/libs/CMF.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘kableExtra’
Error(s) in re-building vignettes:
  ...
--- re-building ‘cmfrec_vignette.Rmd’ using rmarkdown

Quitting from lines 350-366 [unnamed-chunk-13] (cmfrec_vignette.Rmd)
Error: processing vignette 'cmfrec_vignette.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘cmfrec_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'readr', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'cancensus', 'ggplot2', 'tidyr'

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fastDummies', 'robCompositions', 'ggplot2', 'forcats', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2'
checkRd: (-1) bvp.Rd:24: Lost braces
    24 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
checkRd: (-1) ivp.Rd:38: Lost braces
    38 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
checkRd: (-1) ivpsys.Rd:29: Lost braces
    29 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘ggplot2’
Packages required but not available: 'ggplot2', 'twang'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
Packages required but not available: 'dplyr', 'ggplot2'

Packages suggested but not available for checking:
  'purrr', 'tidyverse', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘progress’

Packages suggested but not available for checking:
  'cmsaf', 'cmsafvis', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cmsafops', 'cmsafvis', 'colourpicker', 'shinyFiles'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cmsafops', 'progress'

Packages suggested but not available for checking: 'animation', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'rvest'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'testthat'

Packages suggested but not available for checking:
  'cmstatr', 'testthat', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'purrr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'AER', 'tobit1'
Running examples in ‘cmtest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cmtest
> ### Title: Conditional moments test
> ### Aliases: cmtest cmtest.tobit cmtest.tobit1 cmtest.censReg cmtest.glm
> ### Keywords: htest
> 
> ### ** Examples
> 
> # replication of Wells (2003) and Pagan and Vella (1989) using Fair's data
> library("AER")
Error in library("AER") : there is no package called ‘AER’
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'readxl', 'testthat', 'widgetframe'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cna', 'ggplot2', 'dplyr'

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

Packages suggested but not available for checking:
  'dplyr', 'frscore', 'causalHyperGraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) cnlt.reg.Rd:43: Lost braces
    43 | \emph{Technometrics}, bold{60} (1), 48-60, DOI 10.1080/00401706.2017.1281846.\cr\cr
       |                           ^
checkRd: (-1) fwtnppermC.Rd:35: Lost braces
    35 | Given \eqn{n} points on a line, \env{x}, each with a corresponding env{f} value this function computes
       |                                                                       ^
Package suggested but not available for checking: ‘ggplot2’
Running examples in ‘cnmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getMap
> ### Title: China Map Data from AutoNavi Map
> ### Aliases: getMap
> 
> ### ** Examples
> 
> library(cnmap)
> 
> map1 <- getMap(code = "110000") # get the map data of Beijing City
Error in process_cpl_read_ogr(x, quiet, check_ring_dir = check_ring_dir,  : 
  package tibble not available: install first?
Calls: getMap ... st_read -> st_read.character -> process_cpl_read_ogr
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown

Quitting from lines 29-35 [unnamed-chunk-3] (Introduction.Rmd)
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'readxl', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'tidyr', 'reshape2', 'GenomicInteractions', 'biomaRt',
  'dplyr', 'stringr', 'Hmisc'

Packages suggested but not available for checking:
  'HiCseg', 'igraph', 'plotly', 'GenomicFeatures', 'heatmaply',
  'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'PopGenome', 'testthat'
Package required but not available: ‘phangorn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyr', 'readxl', 'ggplot2', 'progress'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggparty', 'ggtext'

Package suggested but not available for checking: ‘disttree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'WeightIt', 'twang', 'optmatch', 'optweight', 'mice', 'MatchThem',
  'caret', 'testthat'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'tibble', 'ggplot2', 'ggtern', 'forcats'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’

Package which this enhances but not available for checking: ‘rkward’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # the tests are realized using the "testthat" package
  > # and can be found in testthat/tests.r
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > ## Test `analogue` using the `testthat` package
  > 
  > ## Setup
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’

Package which this enhances but not available for checking: ‘rkward’
Running ‘test.cocron.package.R’ [0s/1s]
Running the tests in ‘tests/test.cocron.package.R’ failed.
Complete output:
  > # the tests are realized using the "testthat" package
  > # and can be found in ../inst/tests
  > 
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > test_package("cocron")
  Error in test_package("cocron") : could not find function "test_package"
  Execution halted
Packages required but not available: 'ggpubr', 'ggplot2', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Packages required but not available: 'tensorflow', 'keras'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) educFM.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:28: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'broom'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forcats', 'vctrs', 'ggplot2', 'stringr', 'dplyr', 'tidyr',
  'tidyselect', 'haven', 'purrr', 'tibble', 'likert', 'skimr',
  'labelled'

Packages suggested but not available for checking:
  'testthat', 'shinytest', 'lme4', 'roxygen2', 'rio', 'ufs',
  'userfriendlyscience'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'haven', 'dplyr', 'purrr', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'hms', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'omopgenerics', 'stringr', 'tidyselect', 'tidyr', 'purrr',
  'lubridate', 'PatientProfiles', 'vctrs', 'visOmopResults'

Packages suggested but not available for checking:
  'CDMConnector', 'testthat', 'RPostgres', 'odbc', 'tibble', 'gt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'gh', 'purrr'

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tibble’
Packages suggested but not available for checking: 'bvpSolve', 'testthat'
Package required but not available: ‘tibble’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'httptest', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'purrr', 'ggplot2', 'readr', 'imputeTS', 'tensorflow', 'keras',
  'narray', 'fastDummies', 'greybox', 'lubridate'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'kableExtra', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'readr', 'REDCapR', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'reshape2'

Package suggested but not available for checking: ‘wTO’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'car', 'ggplot2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘codingMatrices.Rnw’ using knitr

Quitting from lines 20-32 [unnamed-chunk-1] (codingMatrices.Rnw)
Error: processing vignette 'codingMatrices.Rnw' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘codingMatrices.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'pillar', 'reshape2', 'devtools', 'dplyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat) 
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Community_Stability_Metrics.Rmd’ using rmarkdown
--- finished re-building ‘Community_Stability_Metrics.Rmd’

--- re-building ‘Temporal_Diversity_Indices.Rmd’ using rmarkdown

Quitting from lines 108-110 [unnamed-chunk-8] (Temporal_Diversity_Indices.Rmd)
Error: processing vignette 'Temporal_Diversity_Indices.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘Temporal_Diversity_Indices.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'reshape2', 'useful', 'dplyr', 'tibble', 'purrr', 'plotly'

Packages suggested but not available for checking:
  'testthat', 'workflows', 'parsnip'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > ## Test `coenocliner` using the `testthat` package
  > 
  > ## Setup
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'dplyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'igraph', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘coglasso.Rmd’ using rmarkdown

Quitting from lines 75-93 [unnamed-chunk-5] (coglasso.Rmd)
Error: processing vignette 'coglasso.Rmd' failed with diagnostics:
there is no package called 'igraph'
--- failed re-building ‘coglasso.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'car'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) kprime.Rd:36: Lost braces; missing escapes or markup?
    36 | kprime is a {p,d,q} set of functions that compute the K-prime distribution. This distribution has many applications,
       |             ^
checkRd: (-1) lsecond.Rd:37: Lost braces; missing escapes or markup?
    37 | lsecond are {p,d,q} functions that compute the Lambda-second (L") distribution. This
       |             ^
checkRd: (-1) pilsecond.Rd:39: Lost braces; missing escapes or markup?
    39 | pilsecond are {p,d,q} functions that compute the prior-informed Lambda-second (L") distribution. This
       |               ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'DatabaseConnector', 'dplyr'

Packages suggested but not available for checking: 'Andromeda', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'tibble', 'dplyr', 'tidyr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CDMConnector', 'dplyr', 'tidyr', 'stringr', 'omopgenerics',
  'visOmopResults', 'PatientProfiles', 'ggpubr', 'snakecase',
  'DiagrammeR'

Packages suggested but not available for checking:
  'testthat', 'CodelistGenerator', 'odbc', 'ggplot2', 'RPostgres',
  'dbplyr', 'PaRe', 'magick', 'plotly', 'ggraph', 'cowplot', 'gt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CDMConnector', 'dbplyr', 'dplyr', 'omopgenerics', 'PatientProfiles',
  'purrr', 'tidyr'

Packages suggested but not available for checking:
  'DrugUtilisation', 'CodelistGenerator', 'testthat', 'tibble',
  'stringr', 'IncidencePrevalence', 'omock', 'RPostgres', 'odbc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DatabaseConnector', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'ggplot2', 'plotly', 'tidyr', 'forcats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'dtplyr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CDMConnector', 'omopgenerics', 'dplyr', 'dbplyr', 'lubridate',
  'broom', 'PatientProfiles', 'visOmopResults', 'stringr', 'tibble',
  'tidyr'

Packages suggested but not available for checking:
  'testthat', 'CodelistGenerator', 'roxygen2', 'ggplot2', 'patchwork',
  'gt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CDMConnector', 'dplyr', 'ggplot2', 'PatientProfiles', 'stringr',
  'tibble', 'visOmopResults', 'tidyr', 'omock', 'omopgenerics'

Packages suggested but not available for checking:
  'testthat', 'DrugUtilisation', 'CodelistGenerator', 'odbc',
  'RPostgres', 'tidyselect', 'gt', 'dbplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Epi', 'ggplot2', 'DiagrammeR'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'readxl'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'tibble', 'dplyr', 'ggplot2', 'testthat'
File ‘collapse/libs/collapse.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_ENVFLAGS’,
    ‘SET_S4_OBJECT’, ‘SET_TRUELENGTH’, ‘UNSET_S4_OBJECT’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # rm(list = ls())
  > # Sys.setenv(R_TESTS = "")
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'tibble'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'purrr', 'pillar'

Packages suggested but not available for checking:
  'dplyr', 'tibble', 'tidyr', 'furrr', 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'devtools', 'pkgdown'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'stringr'

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'network', 'latentnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'coloc'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'viridis', 'susieR'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'imager', 'magick'

Packages suggested but not available for checking:
  'testthat', 'shinytest', 'devtools', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rcartocolor', 'testthat', 'vdiffr'
Running examples in ‘colorblindcheck-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: palette_bivariate_plot
> ### Title: Plot Bivariate Palette And Its Color Vision Deficiencies
> ### Aliases: palette_bivariate_plot
> 
> ### ** Examples
> 
> palette_bivariate_plot(x = rcartocolor::carto_pal(4, "Sunset"))
Error in loadNamespace(x) : there is no package called ‘rcartocolor’
Calls: palette_bivariate_plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'cowplot'

Package suggested but not available for checking: ‘reshape2’

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

Packages suggested but not available for checking:
  'testthat', 'tibble', 'dplyr', 'tidyr'

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'stringr', 'tibble', 'treemap', 'dplyr', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tidyr'

Package suggested but not available for checking: ‘tigris’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'magick', 'purrr', 'dplyr', 'stringr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr'

Packages suggested but not available for checking:
  'tibble', 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'plotly', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'rcartocolor', 'viridis'
Running examples in ‘colorspace-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_colour_binned_diverging
> ### Title: HCL-Based Binned Diverging Color Scales for ggplot2
> ### Aliases: scale_colour_binned_diverging scale_color_binned_diverging
> ###   scale_fill_binned_diverging
> 
> ### ** Examples
> 
> # adapted from stackoverflow: https://stackoverflow.com/a/20127706/4975218
> 
> library("ggplot2")
Error in library("ggplot2") : there is no package called ‘ggplot2’
Execution halted
Note: skipping ‘colorspace.Rmd’ due to unavailable dependencies: 'ggplot2'
Packages required but not available: 'stringr', 'testthat'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'httptest', 'testthat', 'vdiffr'
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) colour_values.Rd:143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values.Rd:144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values_rgb.Rd:143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values_rgb.Rd:144: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'kableExtra', 'ggplot2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘cols4all.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cols4all.Rcheck/vign_test/cols4all/vignettes/cols4all_files/figure-html/unnamed-chunk-11-1.png
576x192 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 5081 bytes
Input file size = 5159 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 4845
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 4473
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 4473

Output IDAT size = 4473 bytes (608 bytes decrease)
Output file size = 4551 bytes (608 bytes = 11.79% decrease)


Quitting from lines 178-193 [unnamed-chunk-12] (cols4all.Rmd)
Error: processing vignette 'cols4all.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘cols4all.Rmd’

SUMMARY: processing the following file failed:
  ‘cols4all.Rmd’

Error: Vignette re-building failed.
Execution halted
Unexported object imported by a ':::' call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
Package required but not available: ‘igraph’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) xsimplex.Rd:6: Lost braces; missing escapes or markup?
     6 |              Generates all points on a {p,n} simplex lattice (i.e. a p-part
       |                                        ^
Packages required but not available: 'lubridate', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'tidyr', 'dplyr', 'ggplot2', 'stringr'

Packages suggested but not available for checking: 'testthat', 'Seurat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tidyr', 'SAMBA'

Package suggested but not available for checking: ‘kableExtra’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'httptest', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tidyr', 'dplyr'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'stringr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggnewscale', 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DatabaseConnector', 'stringr', 'dplyr', 'readr'

Packages suggested but not available for checking: 'testthat', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Packages required but not available:
  'purrr', 'GGally', 'useful', 'ggplot2', 'reshape2', 'wrassp',
  'igraph'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'pcalg', 'backShift', 'CAM', 'testthat', 'huge', 'flare'
Packages required but not available: 'ggplot2', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'htmlTable', 'tidyr', 'stringr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'HardyWeinberg', 'kableExtra'

Packages suggested but not available for checking: 'readxl', 'haven'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nimble', 'ggplot2', 'reshape2'

Packages suggested but not available for checking: 'testthat', 'rstan'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'progress', 'testthat', 'ggplot2', 'GGally', 'ggpubr', 'tibble',
  'reshape2'
Running examples in ‘comparer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: R6_hype
> ### Title: Hyperparameter optimization
> ### Aliases: R6_hype
> 
> ### ** Examples
> 
> 
> # Have df output, but only use one value from it
> h1 <- hype(
+   eval_func = function(a, b) {data.frame(c=a^2+b^2, d=1:2)},
+   extract_output_func = function(odf) {odf$c[1]},
+   a = par_unif('a', -1, 2),
+   b = par_unif('b', -10, 10),
+   n_lhs = 10
+ )
> h1$run_all()
Error in loadNamespace(x) : there is no package called ‘progress’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘comparer.Rmd’ using rmarkdown

Quitting from lines 88-90 [unnamed-chunk-2] (comparer.Rmd)
Error: processing vignette 'comparer.Rmd' failed with diagnostics:
there is no package called 'progress'
--- failed re-building ‘comparer.Rmd’

--- re-building ‘hype-intro.Rmd’ using rmarkdown
--- finished re-building ‘hype-intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘CVglasso’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) atomdeps.Rd:9: Lost braces
     9 |  \item{"tangle"}: {Dihedral angle defined by atoms A-B-C-D as described below. \code{NA}'s represent the free side chain dihedral angles \emph{chi} for that amino acid.}
       |                   ^
checkRd: (-1) atomdeps.Rd:10: Lost braces; missing escapes or markup?
    10 |  \item{"names"}: {The component atoms of the amino acid side chain.  Represents atom D in the dihedral.}
       |                  ^
checkRd: (-1) atomdeps.Rd:11: Lost braces; missing escapes or markup?
    11 |  \item{"matx"}: {The names of atoms A,B,C in the dihedral, with rows corresponding to the atoms in "names".}
       |                 ^
checkRd: (-1) atomdeps.Rd:12: Lost braces; missing escapes or markup?
    12 |  \item{"bangle"}: {Planar bond angle formed between B-C-D}
       |                   ^
checkRd: (-1) atomdeps.Rd:13: Lost braces; missing escapes or markup?
    13 |  \item{"blength"}: {Bond length between C-D}
       |                    ^
Packages required but not available: 'comperes', 'dplyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'car', 'dplyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Hmisc', 'nonparaeff', 'FactoMineR', 'Rcompadre'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tibble', 'progress', 'stringr'

Packages suggested but not available for checking: 'lubridate', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggforce', 'ggplot2', 'reshape2'
Running ‘complex_rlm.R’ [0s/1s]
Running the tests in ‘tests/complex_rlm.R’ failed.
Complete output:
  > ####
  > #### William Ryan
  > #### 12 September, 2021
  > #### Test script for complex robust linear fit (rlm).
  > #### Modified from rlm in MASS.
  > #### Test script based on Wuber's answer on stackexchange https://stats.stackexchange.com/questions/66088/analysis-with-complex-data-anything-different#
  > ####
  > 
  > 
  > library(complexlm)
  Loading required package: MASS
  
  Attaching package: 'complexlm'
  
  The following objects are masked from 'package:MASS':
  
      psi.bisquare, psi.hampel, psi.huber, rlm
  
  The following objects are masked from 'package:stats':
  
      cor, cov, lm, lm.fit, lm.wfit, mad, mahalanobis, var
  
  The following object is masked from 'package:base':
  
      range
  
  > library(MASS, include.only = "mvrnorm")
  > library(ggplot2)
  Error in library(ggplot2) : there is no package called 'ggplot2'
  Execution halted
Packages required but not available: 'greybox', 'legion', 'nloptr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'patchwork'

Packages suggested but not available for checking:
  'testthat', 'tibble', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'higlasso', 'bkmr', 'qgcomp', 'gWQS', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown

Quitting from lines 285-291 [unnamed-chunk-10] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'lme4', 'reshape2', 'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Directional', 'pchc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'readr', 'httr2', 'stringr', 'lubridate', 'purrr'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'httptest2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'testthat', 'dplyr'
'LazyData' is specified without a 'data' directory
Running examples in ‘con2lki-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: con2lki
> ### Title: Calculate lki from contaminants
> ### Aliases: con2lki
> 
> ### ** Examples
> 
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'igraph', 'tibble', 'readxl', 'stringr'

Packages suggested but not available for checking: 'tidyverse', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available: 'dplyr', 'ggplot2', 'trackeR', 'SiZer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'stringr', 'tibble', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'sna'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'devtools', 'kableExtra', 'ggplot2', 'testthat'
checkRd: (-1) concstats_hhi.Rd:13: Lost braces; missing escapes or markup?
    13 | value is required. Ranges from {0, 1} and often used for comparison over
       |                                ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘simulatedData.Rmd’ using rmarkdown

Quitting from lines 22-26 [setup] (simulatedData.Rmd)
Error: processing vignette 'simulatedData.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘simulatedData.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'htmlTable', 'tibble', 'tidyselect'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > withr::with_package("testthat", {
  +     testthat::test_check("condGEE")
  + })
  Error in (get("library"))(package, pos = pos, lib.loc = lib.loc, character.only = character.only,  : 
    there is no package called 'testthat'
  Calls: <Anonymous> ... suppressPackageStartupMessages -> withCallingHandlers -> <Anonymous>
  Execution halted
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) KCI.Rd:44: Lost braces
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                ^
checkRd: (-1) KCI.Rd:44: Lost braces
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                      ^
checkRd: (-1) KCI.Rd:44: Lost braces; missing escapes or markup?
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                                    ^
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘BayesFactor’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'purrr', 'tidyverse', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'dplyr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Packages suggested but not available for checking: 'roxygen2', 'testthat'
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/1s]
  Running ‘tests.R’ [0s/1s]
Running the tests in ‘tests/tests.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'shinytest2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > shinytest2::test_app()
  Error in loadNamespace(x) : there is no package called 'shinytest2'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package required but not available: ‘bigrquery’

Packages suggested but not available for checking: 'testthat', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'hdrcde', 'keras', 'parsnip', 'mlr', 'C50', 'caret', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'hdrcde', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'mockery', 'vctrs', 'ggplot2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction_to_confcons.Rmd’ using rmarkdown

Quitting from lines 103-115 [unnamed-chunk-7] (introduction_to_confcons.Rmd)
Error: processing vignette 'introduction_to_confcons.Rmd' failed with diagnostics:
Please install these packages for function to work: ggplot2
--- failed re-building ‘introduction_to_confcons.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'cellWise', 'dplyr', 'forcats', 'ggplot2', 'purrr', 'tibble',
  'tidyr', 'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘stringr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lme4', 'tidyr'

Packages suggested but not available for checking:
  'robustlmm', 'robustvarComp', 'lmerTest', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'dplyr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘purrr’

Packages suggested but not available for checking: 'mockery', 'testthat'

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

Packages suggested but not available for checking:
  'rstanarm', 'brms', 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'fda', 'ggplot2', 'ggnewscale', 'ggpubr'

Package suggested but not available for checking: ‘roahd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'hrbrthemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'repr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'tidyr', 'caret', 'purrr', 'furrr'

Package suggested but not available for checking: ‘FeatureTerminatoR’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'httr2', 'purrr', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'httptest2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'phangorn', 'TreeSearch', 'usethis'
Packages required but not available:
  'ggplot2', 'dplyr', 'stringr', 'miceadds'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'ggplot2', 'forcats', 'dplyr', 'tibble', 'genefilter',
  'ggrepel', 'tidyr', 'Hmisc', 'tidyselect'

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'broom', 'ggplot2', 'ggfortify'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available:
  'purrr', 'summarytools', 'stringr', 'dplyr', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'tibble', 'vctrs'

Packages suggested but not available for checking:
  'dbplyr', 'dplyr', 'ggplot2', 'httptest', 'lubridate', 'progress',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rmgarch', 'rugarch', 'igraph', 'progress', 'riskParityPortfolio'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pins', 'dplyr', 'dbplyr'

Packages suggested but not available for checking: 'RSQLite', 'testthat'

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'dplyr', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘igraph’
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'igraph', 'cowplot', 'dendextend', 'dplyr', 'ggplot2', 'ggrepel',
  'leidenAlg', 'reshape2', 'sccore'

Packages suggested but not available for checking:
  'AnnotationDbi', 'conosPanel', 'DESeq2', 'ggrastr', 'GO.db',
  'org.Hs.eg.db', 'org.Mm.eg.db', 'p2data', 'pagoda2', 'Seurat',
  'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'kableExtra', 'stringr', 'tidyr',
  'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘httr2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cowplot', 'GGally', 'ggplot2', 'ggrepel', 'network', 'sna'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'DiagrammeR'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'DiagrammeR', 'tibble', 'dplyr', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ConsRank', 'janitor'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'nloptr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'devtools', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘waldo’

Packages suggested but not available for checking:
  'DiagrammeR', 'dm', 'dplyr', 'forcats', 'ggplot2', 'lubridate',
  'pixarfilms', 'roxygen2', 'testthat', 'tibble', 'tidyselect', 'vctrs'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'tibble', 'testthat'
Error(s) in re-building vignettes:
  ...
--- re-building ‘code-development.Rmd’ using rmarkdown
--- finished re-building ‘code-development.Rmd’

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

--- re-building ‘deque-set-dict.Rmd’ using rmarkdown
--- finished re-building ‘deque-set-dict.Rmd’

--- re-building ‘manage-data-columns.Rmd’ using rmarkdown

Quitting from lines 19-37 [knitr-setup] (manage-data-columns.Rmd)
Error: processing vignette 'manage-data-columns.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘manage-data-columns.Rmd’

--- re-building ‘parameter-list.Rmd’ using rmarkdown
--- finished re-building ‘parameter-list.Rmd’

--- re-building ‘reference-semantics.Rmd’ using rmarkdown
--- finished re-building ‘reference-semantics.Rmd’

SUMMARY: processing the following file failed:
  ‘manage-data-columns.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'vroom'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'reshape2', 'fastDummies', 'stringr', 'tidyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > testthat::test_check("contingencytables")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package suggested but not available for checking: ‘ggplot2’
Specified C++11: please drop specification unless essential
checkRd: (-1) getConvexHull.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getConvexHull.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getConvexHull.Rd:30: Lost braces in \itemize; meant \describe ?
Running examples in ‘contoureR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: contourLinesR
> ### Title: Get Contour Lines (list)
> ### Aliases: contourLinesR
> 
> ### ** Examples
> 
> library(contoureR)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages suggested but not available for checking: 'ggplot2', 'testthat'
checkRd: (-1) cf_grid.Rd:38: Lost braces; missing escapes or markup?
    38 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
checkRd: (-1) cf_highdim.Rd:58: Lost braces; missing escapes or markup?
    58 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
checkRd: (-1) gcf_grid.Rd:51: Lost braces; missing escapes or markup?
    51 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
Running examples in ‘ContourFunctions-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gcf
> ### Title: Make contour plot from data or function using ggplot2
> ### Aliases: gcf
> 
> ### ** Examples
> 
> gcf(function(x){x[1]^2 - x[2]})
Error in loadNamespace(x) : there is no package called ‘ggplot2’
Calls: gcf ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rms’

Packages suggested but not available for checking:
  'kableExtra', 'dplyr', 'ggplot2', 'tidyr', 'testthat', 'geepack'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr', 'gh'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'dplyr', 'riskRegression'

Packages suggested but not available for checking:
  'pammtools', 'gganimate', 'transformr', 'plotly', 'reshape2',
  'testthat', 'vdiffr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'pryr', 'dplyr', 'tidyr', 'ggplot2', 'SHELF'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tibble', 'ggplot2', 'eurostat', 'tidyr', 'purrr', 'broom',
  'stringr', 'ggpubr', 'tidyselect'

Packages suggested but not available for checking:
  'devtools', 'kableExtra', 'readr', 'readxl', 'tidyverse', 'rvest',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'AnnotationDbi', 'org.Hs.eg.db', 'org.Mm.eg.db', 'stringr',
  'biomaRt', 'BiocFileCache'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'geiger', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'vardpoor', 'RSQLite'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘StatMatch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cowplot', 'ggplot2'

Package suggested but not available for checking: ‘cooccur’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'readr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'vctrs'

Packages suggested but not available for checking: 'httr2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'clock', 'purrr', 'vctrs'

Packages suggested but not available for checking:
  'pkgdown', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'ggtree', 'imager'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'rgbif', 'tidyselect'

Packages suggested but not available for checking: 'testthat', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidytable', 'lubridate', 'igraph'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) condQestCopC.Rd:45: Lost braces; missing escapes or markup?
    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                          ^
checkRd: (-1) condQestCopC.Rd:45: Lost braces; missing escapes or markup?
    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                                      ^
checkRd: (-1) condQestCopC.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                  ^
checkRd: (-1) condQestCopC.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                              ^
checkRd: (-1) ComputeCope.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:57-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DrawContour.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Draws the contour {f=c}.}
       |                          ^
checkRd: (-1) DrawContour.Rd:20: Lost braces; missing escapes or markup?
    20 | Draws the contour {f=c}.
       |                   ^
checkRd: (-1) cope.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:35: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking: 'fitbitViz', 'tmap'
Packages required but not available:
  'dplyr', 'httr2', 'purrr', 'readr', 'rvest', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'ncmeta', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'coloc', 'ggplot2', 'ggrepel', 'viridis', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dirichletprocess’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'smacof', 'nloptr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'flexsurv', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rugarch’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘mc2d’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'beepr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘igraph’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'vcfR', 'adegenet', 'ggfortify'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'StatMatch'
Running ‘test.R’ [0s/1s]
Running the tests in ‘tests/test.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘ExplainPrediction’
checkRd: (-1) cvGen.Rd:29: Lost braces
    29 | The function code{gatherFromList} returns a list with components containing elements of the same name.
       |                  ^
Specified C++11: please drop specification unless essential
Packages required but not available:
  'ggplot2', 'ggrepel', 'plotly', 'reshape2'

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

Packages suggested but not available for checking: 'car', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'nloptr', 'phangorn', 'viridis', 'igraph', 'phytools'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'testthat', 'vdiffr'
checkRd: (-1) CorMID.Rd:54: Lost braces; missing escapes or markup?
    54 |  individual compound containing 2 carbons and observe a vector of {978,22,0}.
       |                                                                   ^
checkRd: (-1) CorMID.Rd:58: Lost braces; missing escapes or markup?
    58 |  The equivalent corMID vector would be {1,0,0}, indicating that the non-labeled
       |                                        ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'optimx', 'phyloseq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'roxygen2', 'testthat'
checkRd: (-1) carstats.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:14: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitFunction.Rmd’ using rmarkdown

Quitting from lines 17-22 [setup] (fitFunction.Rmd)
Error: processing vignette 'fitFunction.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘fitFunction.Rmd’

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

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gganimate', 'ggplot2', 'qicharts2', 'reshape2'

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

Packages suggested but not available for checking:
  'dplyr', 'plotly', 'readr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'padr', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'shinytest', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'igraph', 'RNewsflow', 'rsyntax'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'profr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘Hmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'pkgdown'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘New-Credible-Set.Rmd’ using rmarkdown

Quitting from lines 166-169 [unnamed-chunk-8] (New-Credible-Set.Rmd)
Error: processing vignette 'New-Credible-Set.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘New-Credible-Set.Rmd’

--- re-building ‘Useful-Info.Rmd’ using rmarkdown
--- finished re-building ‘Useful-Info.Rmd’

--- re-building ‘a01_gwas_to_cs.Rmd’ using rmarkdown
--- finished re-building ‘a01_gwas_to_cs.Rmd’

--- re-building ‘corrected-coverage.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/corrcoverage.Rcheck/vign_test/corrcoverage/vignettes/corrected-coverage_files/figure-html/unnamed-chunk-6-1.png
384x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15263 bytes
Input file size = 15353 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 11684
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 11684

Output IDAT size = 11684 bytes (3579 bytes decrease)
Output file size = 11762 bytes (3591 bytes = 23.39% decrease)

--- finished re-building ‘corrected-coverage.Rmd’

SUMMARY: processing the following file failed:
  ‘New-Credible-Set.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘xcms’
Packages suggested but not available for checking: 'pkgdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'recipes', 'plotly', 'tibble', 'dplyr', 'tidyr',
  'ggrepel', 'stringr', 'forcats', 'purrr'

Packages suggested but not available for checking: 'lubridate', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BayesFactor', 'ggplot2', 'ggraph', 'gt', 'Hmisc', 'lme4',
  'rstanarm', 'see', 'testthat', 'tidygraph'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ingredients', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'DALEX'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'purrr', 'tibble'

Packages suggested but not available for checking:
  'dbplyr', 'RSQLite', 'sparklyr', 'testthat'

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

Packages suggested but not available for checking: 'waldo', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'plotly', 'gganimate', 'igraph', 'ggraph', 'GGally',
  'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'forecast', 'hts', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # file corset/tests/testthat.R
  > # Copyright (C) 2016 Merck Sharp & Dohme Corp. a subsidiary of Merck & Co.
  > # , Inc., Kenilworth, NJ, USA.
  > #
  > # This program is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU General Public License as published by
  > # the Free Software Foundation, either version 3 of the License, or
  > # (at your option) any later version.
  > #
  > # This program is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU General Public License for more details.
  > #
  > # You should have received a copy of the GNU General Public License
  > # along with this program.  If not, see <http://www.gnu.org/licenses/>.
  > 
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'igraph', 'ggplot2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggcorrplot', 'tidyselect', 'ggpubr', 'ggplot2'

Packages suggested but not available for checking: 'papaja', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'R2jags', 'bayesplot', 'ggplot2', 'viridis', 'reshape2', 'ggnewscale'

Packages suggested but not available for checking: 'testthat', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cosinor', 'cowplot', 'stringr', 'purrr', 'ggplot2', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ICAMS', 'usethis'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
Packages required but not available:
  'ggplot2', 'nloptr', 'cowplot', 'animation', 'ggquiver'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ctsem', 'MBESS', 'zcurve', 'scholar'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tram', 'mlt'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'StatMatch', 'iml'

Packages suggested but not available for checking:
  'GGally', 'trtf', 'testthat', 'cowplot', 'ggplot2', 'keras', 'mlt',
  'tidymodels', 'caret', 'mlr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'dplyr', 'reshape2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'tidyverse', 'viridis', 'igraph', 'Seurat', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) fasttrakg.Rd:18: Lost braces
    18 |     \item{\code{killip}}{Killip level of cardiac event severity (1-4)age75}{1= Age>75; 0=Age<=75}
       |                                                                            ^
Packages required but not available:
  'tidyr', 'stringr', 'dplyr', 'lubridate', 'ggplot2', 'viridis'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'flexsurv', 'optimx', 'car', 'dplyr', 'standardize'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'eurostat', 'testthat', 'tibble'
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > ## Test `countrycode` using the `testthat` package
  > 
  > ## Setup
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘spikeSlabGAM’

Package suggested but not available for checking: ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fastDummies', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dslabs', 'ggformula', 'ggplot2', 'mosaic', 'purrr', 'supernova',
  'vctrs'

Packages suggested but not available for checking:
  'lubridate', 'mockery', 'readr', 'readxl', 'usethis', 'testthat',
  'tibble', 'tidyr', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lubridate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'qgraph', 'igraph'
Packages required but not available: 'ggplot2', 'latex2exp', 'reshape2'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'colourpicker', 'egg', 'ggplot2'

Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'shinymeta', 'mrgsolve', 'GGally', 'ggridges',
  'ggrepel', 'ggstance', 'patchwork', 'plotly', 'ggdist', 'ggh4x',
  'ggpmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'autothresholdr', 'dplyr', 'lubridate', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following files/directories:
  ‘covfefe_inauguration.txt’
Packages required but not available: 'readxl', 'plotly', 'dplyr'

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'ggrepel', 'kableExtra', 'plotly', 'testthat', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘networkD3’
Error(s) in re-building vignettes:
  ...
--- re-building ‘covid19dbcand.Rmd’ using rmarkdown

Quitting from lines 78-190 [unnamed-chunk-8] (covid19dbcand.Rmd)
Error: processing vignette 'covid19dbcand.Rmd' failed with diagnostics:
there is no package called 'networkD3'
--- failed re-building ‘covid19dbcand.Rmd’

SUMMARY: processing the following file failed:
  ‘covid19dbcand.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'lubridate', 'readr', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'EpiEstim', 'gt', 'janitor', 'stringr'

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

Packages suggested but not available for checking: 'readr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'RSQLite', 'wbstats'
Packages required but not available:
  'devtools', 'dplyr', 'lubridate', 'plotly'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'readr', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'snakecase', 'stringr', 'tibble',
  'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'purrr', 'tidyr'

Packages suggested but not available for checking:
  'httptest', 'mockery', 'testthat', 'tibble', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'projmgr', 'readr', 'readxl', 'tibble'

Packages suggested but not available for checking: 'SIPDIBGE', 'srvyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'cowplot', 'stringr', 'ggpubr', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'pins', 'readr', 'readxl', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'cowplot', 'dbplyr', 'EpiEstim', 'ggformula', 'ggplot2', 'ggstream',
  'ggtext', 'lubridate', 'MetBrewer', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘usethis’

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'mockery'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ops <- options("crayon.enabled" = FALSE, warn = 1)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'GGally', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘purrr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'dplyr', 'forcats', 'magick', 'patchwork', 'testthat', 'tidyr',
  'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'randomForestSRC', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rms', 'dplyr', 'tidyr', 'ggplot2', 'mediation'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'caret', 'cowplot', 'furrr', 'ggrepel', 'ggplot2', 'ggpubr',
  'mixOmics', 'progress', 'purrr', 'scattermore', 'survminer', 'tidyr'

Packages suggested but not available for checking:
  'nsROC', 'ggforce', 'RColorConesa'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) gen_data.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gen_data.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gen_data.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MESS', 'qvalue'

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

Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qvalue’
checkRd: (-1) Sample.data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:21: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking: 'testthat', 'vctrs'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'BEST', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rms', 'Hmisc', 'benchmarkme'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'crops', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'mockery', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'bench', 'decor', 'ggplot2', 'mockery', 'progress', 'testthat',
  'tibble', 'vctrs'
Running examples in ‘cpp11-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cpp_register
> ### Title: Generates wrappers for registered C++ functions
> ### Aliases: cpp_register
> 
> ### ** Examples
> 
> # create a minimal package
> dir <- tempfile()
> dir.create(dir)
> 
> writeLines("Package: testPkg", file.path(dir, "DESCRIPTION"))
> writeLines("useDynLib(testPkg, .registration = TRUE)", file.path(dir, "NAMESPACE"))
> 
> # create a C++ file with a decorated function
> dir.create(file.path(dir, "src"))
> writeLines("[[cpp11::register]] int one() { return 1; }", file.path(dir, "src", "one.cpp"))
> 
> # register the functions in the package
> cpp_register(dir)
Error: The decor, tibble, vctrs package(s) are required for this functionality
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘FAQ.Rmd’ using rmarkdown

Quitting from lines 39-50 [unnamed-chunk-2] (FAQ.Rmd)
Error: processing vignette 'FAQ.Rmd' failed with diagnostics:
The decor, tibble, vctrs package(s) are required for this functionality
--- failed re-building ‘FAQ.Rmd’

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

--- re-building ‘cpp11.Rmd’ using rmarkdown
--- finished re-building ‘cpp11.Rmd’

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

--- re-building ‘motivations.Rmd’ using rmarkdown

Quitting from lines 449-461 [unnamed-chunk-19] (motivations.Rmd)
Error: processing vignette 'motivations.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘motivations.Rmd’

SUMMARY: processing the following files failed:
  ‘FAQ.Rmd’ ‘motivations.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘shinyFiles’
Packages suggested but not available for checking: 'bench', 'testthat'
Running examples in ‘cppdoubles-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: all_equal
> ### Title: Are all values of x nearly equal (within a tolerance) to all
> ###   values of y?
> ### Aliases: all_equal
> 
> ### ** Examples
> 
> library(cppdoubles)
> library(bench)
Error in library(bench) : there is no package called ‘bench’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘mc2d’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘igraph’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Packages required but not available: 'car', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'lme4'

Packages suggested but not available for checking:
  'geepack', 'ggpubr', 'qwraps2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'dplyr', 'tidyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'dplyr', 'stringr', 'forcats'

Packages suggested but not available for checking: 'srvyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lme4', 'broom', 'dplyr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tibble', 'patchwork', 'latex2exp', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'rvest', 'stringr', 'dplyr', 'igraph'

Packages suggested but not available for checking: 'ggplot2', 'tibble'

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

Packages suggested but not available for checking: 'mockery', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'igraph', 'stringr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘NMF’
Packages required but not available:
  'dplyr', 'tibble', 'lubridate', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'mockery', 'testthat'
checkRd: (-1) make_style.Rd:51: Lost braces
    51 | The style (the code{...} argument) can be anything of the
       |                    ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(crayon)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'palette'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘distributions3’
Packages required but not available:
  'ggplot2', 'ggpubr', 'stringr', 'lme4', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Packages suggested but not available for checking: 'rvest', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2'

Packages suggested but not available for checking: 'pdp', 'pmml'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'ggplot2', 'ggstance'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'crew', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'crew', 'vctrs'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'janitor', 'lubridate', 'readr', 'rvest', 'stringr',
  'tibble', 'tidyr'

Packages suggested but not available for checking:
  'gghighlight', 'ggplot2', 'ggtext', 'paletteer', 'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'forecast', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'osfr', 'purrr', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'stringr', 'ggplot2', 'readr', 'gt', 'tidyr'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'dplyr', 'ggplot2', 'keras'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'igraph', 'stringr', 'tibble'

Packages suggested but not available for checking: 'DiagrammeR', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DiagrammeR', 'ggplot2', 'reshape2', 'dplyr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'ggforce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'ggbeeswarm', 'ggplot2', 'ggpmisc', 'ggpubr',
  'ggrepel', 'sccore', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'conos', 'pagoda2', 'Seurat', 'SoupX', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) normFit.Rd:39: Lost braces; missing escapes or markup?
    39 | {analytes}}
       | ^
checkRd: (-1) normPred.Rd:27: Lost braces
    27 | ode{standards}, \code{analytes}}
       |    ^
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggmcmc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘shinyFiles’
Packages required but not available: 'magick', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lubridate', 'dplyr', 'tibble', 'purrr', 'purrrlyr'

Packages suggested but not available for checking: 'furrr', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyverse', 'ggplot2', 'cowplot', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'PowerSDI', 'lubridate'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'geepack', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr'

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'clustree', 'dplyr', 'ggdist', 'ggplot2', 'ggpp', 'patchwork',
  'tibble', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gamm4', 'ggplot2', 'rms', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'vctrs'

Packages suggested but not available for checking:
  'broom', 'furrr', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'meta', 'netmeta', 'dplyr', 'tidyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forcats', 'purrr', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'gt', 'expss', 'ggplot2', 'Hmisc', 'hms', 'lubridate', 'sloop',
  'tidyselect', 'testthat', 'waldo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'readr', 'dplyr', 'stringr', 'tidyr', 'tibble', 'igraph',
  'ensembldb', 'ggplot2', 'STRINGdb'

Packages suggested but not available for checking:
  'tidygraph', 'ggraph', 'testthat', 'EnsDb.Hsapiens.v86'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'tibble', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'openVA'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-crossva-and-openva.Rmd’ using rmarkdown

Quitting from lines 14-17 [unnamed-chunk-1] (using-crossva-and-openva.Rmd)
Error: processing vignette 'using-crossva-and-openva.Rmd' failed with diagnostics:
there is no package called 'openVA'
--- failed re-building ‘using-crossva-and-openva.Rmd’

SUMMARY: processing the following file failed:
  ‘using-crossva-and-openva.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'haven', 'labelled', 'readr', 'readxl', 'tibble'

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) confRegCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                                                                                    ^
checkRd: (-1) confRegCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                                                                                      ^
checkRd: (-1) confRegUCRandUCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
Packages required but not available:
  'dplyr', 'ggplot2', 'httptest', 'purrr', 'tibble', 'stringr',
  'tidyselect'

Packages suggested but not available for checking: 'vdiffr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ## load dependencies
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'purrr', 'readr', 'tidytext', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr'

Packages suggested but not available for checking:
  'mapboxapi', 'tigris', 'tidycensus', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'geepack', 'tidyr', 'dplyr', 'lme4'

Packages suggested but not available for checking: 'INLA', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'roxygen2'
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'devtools', 'haven', 'httptest', 'styler', 'testthat'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(httptest)
  Error in library(httptest) : there is no package called 'httptest'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘abstract-categories.Rmd’ using rmarkdown
--- finished re-building ‘abstract-categories.Rmd’

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

--- re-building ‘array-variables.Rmd’ using rmarkdown
--- finished re-building ‘array-variables.Rmd’

--- re-building ‘crunch-internals.Rmd’ using rmarkdown
--- finished re-building ‘crunch-internals.Rmd’

--- re-building ‘crunch.Rmd’ using rmarkdown

Quitting from lines 18-21 [unnamed-chunk-2] (crunch.Rmd)
Error: processing vignette 'crunch.Rmd' failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘crunch.Rmd’

--- re-building ‘deck-cookbook.Rmd’ using rmarkdown
--- finished re-building ‘deck-cookbook.Rmd’

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

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

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

--- re-building ‘fork-and-merge.Rmd’ using rmarkdown

Quitting from lines 19-23 [unnamed-chunk-2] (fork-and-merge.Rmd)
Error: processing vignette 'fork-and-merge.Rmd' failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘fork-and-merge.Rmd’

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

--- re-building ‘subtotals.Rmd’ using rmarkdown

Quitting from lines 18-38 [unnamed-chunk-2] (subtotals.Rmd)
Error: processing vignette 'subtotals.Rmd' failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘subtotals.Rmd’

--- re-building ‘variable-order.Rmd’ using rmarkdown
--- finished re-building ‘variable-order.Rmd’

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

SUMMARY: processing the following files failed:
  ‘crunch.Rmd’ ‘fork-and-merge.Rmd’ ‘subtotals.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'httptest', 'shinytest', 'testthat'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'stringr', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'marmap', 'stringr', 'swfscDAS'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘clusterSEs’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'tibble', 'tidyr', 'purrr', 'progress', 'lubridate'

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking: 'testthat', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘lubridate’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'cstidy', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'ggrepel', 'plnr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'reshape2', 'ggpubr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rms', 'Hmisc'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyverse', 'dplyr', 'purrr', 'stringr', 'tibble', 'riskRegression',
  'caret', 'recipes', 'furrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'broom', 'dplyr', 'forcats', 'geojsonio', 'ggplot2',
  'gt', 'lubridate', 'purrr', 'readxl', 'reshape2', 'rmapshaper',
  'stringr', 'tidyr'
Running examples in ‘csdata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_granularity_geo_to_data_set
> ### Title: Adds granularity_geo to a given data set
> ### Aliases: add_granularity_geo_to_data_set
> 
> ### ** Examples
> 
> library(data.table)
> data <- data.table(location_code = c("norge", "county03", "blah"))
> csdata::add_granularity_geo_to_data_set(data)
Error in loadNamespace(x) : there is no package called ‘stringr’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘csdata.Rmd’ using rmarkdown

Quitting from lines 31-121 [unnamed-chunk-2] (csdata.Rmd)
Error: processing vignette 'csdata.Rmd' failed with diagnostics:
there is no package called 'gt'
--- failed re-building ‘csdata.Rmd’

--- re-building ‘locations_norway.Rmd’ using rmarkdown

Quitting from lines 27-41 [unnamed-chunk-2] (locations_norway.Rmd)
Error: processing vignette 'locations_norway.Rmd' failed with diagnostics:
there is no package called 'gt'
--- failed re-building ‘locations_norway.Rmd’

--- re-building ‘population_norway.Rmd’ using rmarkdown

Quitting from lines 13-21 [unnamed-chunk-1] (population_norway.Rmd)
Error: processing vignette 'population_norway.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘population_norway.Rmd’

SUMMARY: processing the following files failed:
  ‘csdata.Rmd’ ‘locations_norway.Rmd’ ‘population_norway.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘purrr’

Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'plotly', 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'fuzzyjoin', 'purrr', 'stringr', 'dplyr', 'ggplot2', 'furrr'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lubridate', 'stringr', 'ggplot2', 'ggspatial', 'dplyr', 'tidyhydat',
  'OpenStreetMap'

Packages suggested but not available for checking: 'testthat', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CSTools', 'SPEI'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'ggrepel'
Running examples in ‘csmaps-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nor_county_map_bxxxx_default_dt
> ### Title: Maps of Norwegian counties in data.table format
> ### Aliases: nor_county_map_bxxxx_default_dt
> ###   nor_county_map_b2024_default_dt nor_county_map_b2020_default_dt
> ###   nor_county_map_b2019_default_dt nor_county_map_b2017_default_dt
> ###   nor_county_position_geolabels_b2024_default_dt
> ###   nor_county_position_geolabels_b2020_default_dt
> ###   nor_county_position_geolabels_b2019_default_dt
> ###   nor_county_position_geolabels_b2017_default_dt
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # 2024 borders
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘csmaps.Rmd’ using rmarkdown

Quitting from lines 24-28 [setup] (csmaps.Rmd)
Error: processing vignette 'csmaps.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘csmaps.Rmd’

--- re-building ‘customization.Rmd’ using rmarkdown

Quitting from lines 23-27 [setup] (customization.Rmd)
Error: processing vignette 'customization.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘customization.Rmd’

--- re-building ‘layout.Rmd’ using rmarkdown

Quitting from lines 23-27 [setup] (layout.Rmd)
Error: processing vignette 'layout.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘layout.Rmd’

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

--- re-building ‘sf_interactive.Rmd’ using rmarkdown

Quitting from lines 22-25 [setup] (sf_interactive.Rmd)
Error: processing vignette 'sf_interactive.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘sf_interactive.Rmd’

SUMMARY: processing the following files failed:
  ‘csmaps.Rmd’ ‘customization.Rmd’ ‘layout.Rmd’ ‘sf_interactive.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'Hmisc', 'rms', 'forestmodel', 'ggplot2', 'ggpubr', 'survminer'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'reshape2', 'lubridate', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'stringr', 'readr', 'tidyselect', 'ggplot2', 'haven',
  'purrr', 'ggcorrplot'

Packages suggested but not available for checking:
  'testthat', 'ggraph', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'gt', 'dplyr', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'readxl', 'lubridate'
Running examples in ‘cstime-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: date_to_calmonth_c
> ### Title: Date -> calmonth (character)
> ### Aliases: date_to_calmonth_c date_to_calmonth_c.default
> ###   date_to_calmonth_c.character date_to_calmonth_c.Date
> 
> ### ** Examples
> 
> date_to_calmonth_c("2021-08-11")
[1] "08"
> date_to_calmonth_c(lubridate::today())
Error in loadNamespace(x) : there is no package called ‘lubridate’
Calls: date_to_calmonth_c ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cstime.Rmd’ using rmarkdown
--- finished re-building ‘cstime.Rmd’

--- re-building ‘date_conversion.Rmd’ using rmarkdown

Quitting from lines 40-50 [unnamed-chunk-2] (date_conversion.Rmd)
Error: processing vignette 'date_conversion.Rmd' failed with diagnostics:
there is no package called 'lubridate'
--- failed re-building ‘date_conversion.Rmd’

--- re-building ‘season.Rmd’ using rmarkdown

Quitting from lines 35-44 [unnamed-chunk-2] (season.Rmd)
Error: processing vignette 'season.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘season.Rmd’

SUMMARY: processing the following files failed:
  ‘date_conversion.Rmd’ ‘season.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'reshape2', 'ggplot2', 'lubridate'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cgam', 'purrr', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'readr', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘igraph’

Packages suggested but not available for checking:
  'huge', 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'roxygen2', 'testthat'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'readr', 'stringr', 'tibble', 'purrr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'gdistance'

Package suggested but not available for checking: ‘crawl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'dplyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown

Quitting from lines 36-71 [unnamed-chunk-1] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'animation', 'dplyr', 'suncalc'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘fda’

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

Packages suggested but not available for checking:
  'kableExtra', 'readxl', 'testthat', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘asciicast’
Error(s) in re-building vignettes:
  ...
--- re-building ‘get_started.Rmd’ using rmarkdown
--- finished re-building ‘get_started.Rmd’

--- re-building ‘reproducibility.Rmd’ using rmarkdown

Quitting from lines 14-26 [unnamed-chunk-1] (reproducibility.Rmd)
Error: processing vignette 'reproducibility.Rmd' failed with diagnostics:
there is no package called 'asciicast'
--- failed re-building ‘reproducibility.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ClusterR’

Packages suggested but not available for checking:
  'phytools', 'viridis', 'progress'

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

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tibble', 'lubridate', 'dplyr', 'readr'

Packages suggested but not available for checking:
  'devtools', 'RSQLite', 'RPostgres'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'plotly', 'purrr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'usethis'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'rstan', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'lme4', 'papaja'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'latex2exp', 'tsibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Hello.csv’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) cubintegrate.Rd:67: Lost braces; missing escapes or markup?
    67 | evaluated} - {returnCode}{the actual integer return code
       |              ^
checkRd: (-1) cubintegrate.Rd:67-69: Lost braces
    67 | evaluated} - {returnCode}{the actual integer return code
       |                          ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'stringr', 'tibble', 'tidyr',
  'tidyselect', 'tsibble', 'vctrs'

Packages suggested but not available for checking:
  'testthat', 'ozmaps', 'GGally', 'ggrepel', 'ggforce', 'purrr',
  'plotly', 'concaveman', 'vdiffr', 'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'pillar', 'purrr', 'tibble', 'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘reshape2’

Packages suggested but not available for checking:
  'dplyr', 'modeldata', 'testthat', 'tidyrules'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'stringr', 'testthat', 'tibble'

Packages suggested but not available for checking: 'mockery', 'shinytest2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'hardhat', 'parsnip'

Packages suggested but not available for checking: 'purrr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lmerTest', 'haven', 'dplyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'readr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'tibble'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘devtools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘curephEM-vignette.Rmd’ using rmarkdown

Quitting from lines 14-17 [unnamed-chunk-1] (curephEM-vignette.Rmd)
Error: processing vignette 'curephEM-vignette.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘curephEM-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'relsurv', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘engine.R’ [0s/1s]
  Comparing ‘engine.Rout’ to ‘engine.Rout.save’ ...4d3
< Using libcurl 8.8.0 with GnuTLS/3.8.5
  Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'readr', 'stringr', 'broom', 'tibble', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'ggthemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
Specified C++11: please drop specification unless essential
Package required but not available: ‘hdrcde’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'

Package which this enhances but not available for checking: ‘vdiffr’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'set', 'do'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyselect', 'tidyr', 'purrr', 'tibble', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'pkgmaker', 'vctrs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'censable', 'dplyr', 'readr', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'stringr', 'dplyr', 'tibble', 'purrr', 'furrr', 'tidyr', 'ggplot2',
  'lemna', 'lubridate'

Packages suggested but not available for checking:
  'testthat', 'morse', 'roxyglobals'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'stringr', 'purrr', 'tibble', 'ggplot2', 'ggpubr'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘RGtk2’
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'dplyr', 'tidyr', 'ggbeeswarm'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘how_to_test_CVs.Rmd’ using rmarkdown

Quitting from lines 108-116 [unnamed-chunk-3] (how_to_test_CVs.Rmd)
Error: processing vignette 'how_to_test_CVs.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘how_to_test_CVs.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'geepack', 'pkgdown'
Running examples in ‘cvGEE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cv_gee
> ### Title: Proper Scoring Rules for Generalized Estimating Equations
> ### Aliases: cv_gee
> 
> ### ** Examples
> 
> library("geepack")
Error in library("geepack") : there is no package called ‘geepack’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Scoring_Rules_GEE.Rmd’ using rmarkdown

Quitting from lines 15-23 [setup] (Scoring_Rules_GEE.Rmd)
Error: processing vignette 'Scoring_Rules_GEE.Rmd' failed with diagnostics:
there is no package called 'geepack'
--- failed re-building ‘Scoring_Rules_GEE.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'dplyr'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'StMoMo', 'forecast', 'tmap'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'groupdata2', 'lme4', 'purrr', 'rearrr',
  'recipes', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'furrr', 'ggimage', 'ggnewscale', 'merDeriv', 'testthat', 'xpectr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'glmmTMB', 'lme4'

Packages suggested but not available for checking:
  'dplyr', 'effects', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'tibble'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’

Packages which this enhances but not available for checking:
  'gurobi', 'rcbc'
Running ‘group00.R’ [0s/1s]
  Running ‘group01.R’ [0s/1s]
  Running ‘group02.R’ [0s/1s]
  Running ‘group03.R’ [0s/1s]
  Running ‘group04.R’ [0s/1s]
  Running ‘group05.R’ [0s/1s]
Running the tests in ‘tests/group00.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/group01.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/group02.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/group03.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/group04.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/group05.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘zen4R’

Packages suggested but not available for checking:
  'tidytext', 'testthat', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘optimx’

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'nloptr', 'stringr', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'stringr'

Packages suggested but not available for checking: 'od', 'stplanr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'flexsurv', 'lubridate'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Andromeda', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'readr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'purrr', 'dplyr', 'stringr', 'ggplot2', 'viridis', 'plotly',
  'cowplot', 'mixR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'dplyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'igraph', 'cowplot'

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'dplyr', 'purrr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'dbplyr', 'readr', 'RSQLite', 'stringr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'MetBrewer', 'patchwork', 'reshape2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'magick', 'patchwork', 'Seurat', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'devtools', 'dplyr', 'ggplot2', 'ggrepel', 'questionr',
  'recipes'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'purrr'

Package suggested but not available for checking: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr'

Packages suggested but not available for checking: 'purrr', 'testthat'

Packages which this enhances but not available for checking:
  'igraph', 'treemap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'tidyselect', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'usethis'
checkRd: (-1) D4TAlinkTask.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:25-26: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following HTML validation problems:
saveReportTable.html:80:1 (saveReportTable.Rd:36): Warning: trimming empty <dt>
Package suggested but not available for checking: ‘lme4’
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{  A small, positive scalar that determines when iterations
       |               ^
checkRd: (-1) fpiter.Rd:60-61: Lost braces
    60 |     \code{maxiter}{  An integer denoting the maximum limit on the number of
       |                   ^
checkRd: (-1) fpiter.Rd:63-65: Lost braces
    63 |     \code{trace}{  A logical variable denoting whether some of the intermediate
       |                 ^
Packages required but not available:
  'ggplot2', 'cowplot', 'tidyr', 'dplyr', 'tibble', 'ggbeeswarm',
  'ggsci', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RMariaDB', 'tibble'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'beepr', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'mockery'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'AmesHousing', 'babynames', 'dplyr', 'forcats', 'gapminder',
  'ggplot2', 'Lahman', 'nycflights13', 'tibble', 'tidyr', 'pixarfilms'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'DescTools'

Package suggested but not available for checking: ‘multigroup’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggpubr'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘more_tests.R’ [3s/4s]
  Comparing ‘more_tests.Rout’ to ‘more_tests.Rout.save’ ... OK
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'mixtools', 'readr', 'readxl',
  'stringr', 'tibble', 'tidyr', 'tidyselect', 'vroom'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) formatScientificTeX.Rd:33: Lost braces; missing escapes or markup?
    33 | function will return  " 3.0\\\\times 10^{2}"
       |                                         ^
Packages suggested but not available for checking:
  'igraph', 'testthat', 'fastDummies'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘ggdag’
Running examples in ‘dagwood-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dagwood
> ### Title: DAGs with Omitted Objects Displayed (DAGWOOD)
> ### Aliases: dagwood
> ### Keywords: DAG DAGWOOD causal inference
> 
> ### ** Examples
> 
> 
> # Generate a DAGWOOD from an example root DAG:
> DAG.root <-"Chocolate -> Alzheimers
+ Chocolate <- Education -> Alzheimers
+ Chocolate -> CV
+ CV -> Alzheimers"
> 
> # Identify the exposure and outcome of interest
> exposure <- "Chocolate"
> outcome <- "Alzheimers"
> 
> # Run the DAGWOOD algorithm and store results
> choc.alz.dagwood <- dagwood(DAG.root,exposure,outcome)
DAGWOOD has identified the following key assumptions, With respect to the root DAG:

. There are no common causes of both Alzheimers and CV that are not already adjusted- or controlled-for.
. There are no common causes of both Alzheimers and Chocolate that are not already adjusted- or controlled-for.
. There are no pathways through which CV causes Education except through nodes already accounted-for.
. There are no pathways through which Alzheimers can cause CV.
. There are no pathways through which both Alzheimers can cause Chocolate, and CV can cause Chocolate.
. There are no pathways through which CV can cause Chocolate.
. There are no pathways through which both Alzheimers can cause Education, and Chocolate can cause Education.
. There are no pathways through which Chocolate can cause Education.> 
> # Get the branch DAGs from the DAGWOOD object
> branch.DAGs <- choc.alz.dagwood$DAGs.branch
> 
> # Display the first branch DAG in the list
> library(ggdag)
Error in library(ggdag) : there is no package called ‘ggdag’
Execution halted
Packages required but not available:
  'deflateBR', 'dplyr', 'janitor', 'lubridate', 'readr', 'stringr',
  'tidytext'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'ggplot2', 'cowplot'

Packages suggested but not available for checking: 'testthat', 'codemetar'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'beepr', 'magick', 'purrr', 'readtext', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'phylobase', 'ggplot2', 'ggtree', 'DAISIE', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'corHMM', 'tidyr', 'dplyr', 'ggimage'

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

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2', 'ggtree', 'tidytree', 'tidyr',
  'purrr', 'phytools', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'iBreakDown', 'ingredients'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DALEX', 'ggplot2'

Packages suggested but not available for checking:
  'auditor', 'ggrepel', 'iml', 'ingredients', 'lime', 'localModel',
  'mlr', 'recipes', 'stacks', 'testthat', 'tidymodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'daltoolbox', 'doBy', 'smotefamily'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'dplyr', 'forecast', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DDD', 'Hmisc'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'testthat', 'ggetho', 'zeitgebr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'janitor', 'readxl'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rtweet’
Packages suggested but not available for checking:
  'car', 'DescTools', 'reshape2'
Running examples in ‘DanielBiostatistics10th-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Chapter08
> ### Title: Chapter 8: Analysis of Variance
> ### Aliases: Chapter08
> 
> ### ** Examples
> 
> library(DanielBiostatistics10th)
> library(reshape2)
Error in library(reshape2) : there is no package called ‘reshape2’
Execution halted
Package required but not available: ‘Epi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tibble', 'ggplot2', 'stringr', 'purrr', 'hardhat'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'recipes'

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

Packages suggested but not available for checking:
  'testthat', 'purrr', 'dplyr', 'ggplot2', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'stringr', 'tidyr', 'xesreadR', 'bupaR',
  'readr', 'edeaR', 'purrr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'adegenet', 'klaR', 'plotly'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'ggplot2', 'dplyr', 'dartR.data', 'patchwork',
  'reshape2', 'StAMPP', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'devtools', 'gdistance', 'gganimate', 'ggrepel', 'ggthemes',
  'HardyWeinberg', 'hierfstat', 'igraph', 'mmod', 'networkD3',
  'plotly', 'poppr', 'purrr', 'qvalue', 'SIBER', 'tibble', 'vcfR',
  'viridis', 'testthat', 'ggtern'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'dartR.base', 'dartR.data', 'ggplot2', 'patchwork',
  'stringr'

Packages suggested but not available for checking:
  'SIBER', 'igraph', 'reshape2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'dartR.base', 'dartR.data', 'dplyr', 'patchwork',
  'ggplot2', 'stringr'

Packages suggested but not available for checking:
  'SIBER', 'igraph', 'purrr', 'qvalue', 'reshape2', 'tidyr', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'ggplot2', 'dplyr', 'dartR.data', 'patchwork',
  'PopGenReport', 'reshape2', 'StAMPP', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'devtools', 'gdistance', 'ggtern', 'gganimate', 'ggrepel',
  'ggthemes', 'HardyWeinberg', 'hierfstat', 'igraph', 'mmod',
  'networkD3', 'plotly', 'poppr', 'purrr', 'qvalue', 'SIBER', 'tibble',
  'vcfR', 'viridis', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'dartR.base', 'dartR.data', 'ggplot2', 'stringr',
  'hierfstat', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'dartR.base', 'dartR.data', 'StAMPP', 'tidyr', 'ggplot2'

Packages suggested but not available for checking:
  'mmod', 'gdistance', 'PopGenReport'

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

Packages suggested but not available for checking:
  'dartR.base', 'dartR.data', 'dartR.sim', 'dartR.captive',
  'dartR.popgen', 'dartR.spatial'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Resolves environment issues when running devtools::check()
  > Sys.setenv(R_TESTS = "")
  > 
  > testthat::test_check(package = "dashboardthemes")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'readr', 'dbplyr'

Packages suggested but not available for checking:
  'testthat', 'DBItest', 'RSQLite', 'Andromeda', 'dplyr', 'RPostgres',
  'odbc'

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

Packages suggested but not available for checking:
  'DataVisualizations', 'ProjectionBasedClustering', 'dendextend'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'httr2', 'magick', 'purrr', 'rvest', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'readr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'tibble', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'summarytools', 'dplyr', 'plotly', 'purrr', 'lubridate', 'shinyFiles'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking: 'devtools', 'testthat'

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

Packages suggested but not available for checking: 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'admiraldev', 'dplyr', 'lubridate', 'purrr', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'devtools', 'pkgdown', 'testthat', 'roxygen2', 'styler', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'haven', 'labelled', 'lubridate', 'tibble', 'tidyr',
  'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'stringr', 'tidyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) data_edit.Rd:137: Lost braces
   137 | code{data_edit} is a shiny application built on \code{rhandsontable} that is
       |     ^
Packages required but not available: 'reshape2', 'ggplot2', 'networkD3'

Packages suggested but not available for checking:
  'testthat', 'nycflights13'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'tidygraph', 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'charlatan', 'stringr', 'mockery', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'dplyr', 'tidyr', 'stringr'

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

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr', 'purrr'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'haven'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readxl', 'rio', 'tibble'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'dplyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'httr2', 'readr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'datapack'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'roxygen2', 'usethis'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking: 'testthat', 'igraph'

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

Packages suggested but not available for checking: 'tibble', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lubridate', 'stringr', 'progress'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lme4', 'lubridate', 'patchwork', 'rio', 'readr'

Packages suggested but not available for checking:
  'GGally', 'cowplot', 'testthat', 'tibble', 'vdiffr', 'plotly',
  'ggvenn', 'rvest'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'haven'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Running examples in ‘dataresqc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_decimals
> ### Title: Plot decimals
> ### Aliases: plot_decimals
> 
> ### ** Examples
> 
> plot_decimals(Rosario$Tx, outfile = paste0(tempdir(),"/test.pdf"))
Error: Package "ggplot2" needed for this function to work. Please install it.
Execution halted
Packages required but not available: 'lubridate', 'readr'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lubridate', 'testthat', 'AmesHousing', 'doBy', 'ggplot2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘tidyr’

Packages suggested but not available for checking: 'testthat', 'RSDA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'haven'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat) # nolint: undesirable_function_linter
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'pryr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'purrr', 'EML', 'readr', 'stringr', 'tibble', 'dplyr', 'tidyr',
  'ggplot2'

Packages suggested but not available for checking: 'testthat', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'dplyr'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘data.table/libs/data_table.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_S4_OBJECT’,
    ‘SET_TRUELENGTH’, ‘UNSET_S4_OBJECT’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'testthat', 'networkD3', 'treemap', 'DiagrammeR', 'mockery'

Package which this enhances but not available for checking: ‘igraph’
Running examples in ‘data.tree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.Node
> ### Title: Plot a graph, or get a graphviz dot representation of the tree
> ### Aliases: plot.Node ToDiagrammeRGraph SetNodeStyle SetEdgeStyle
> ###   SetGraphStyle GetDefaultTooltip
> 
> ### ** Examples
> 
> data(acme)
> SetGraphStyle(acme, rankdir = "TB")
> SetEdgeStyle(acme, arrowhead = "vee", color = "blue", penwidth = 2)
> #per default, Node style attributes will be inherited:
> SetNodeStyle(acme, style = "filled,rounded", shape = "box", fillcolor = "GreenYellow", 
+              fontname = "helvetica", tooltip = GetDefaultTooltip)
> SetNodeStyle(acme$IT, fillcolor = "LightBlue", penwidth = "5px")
> #inheritance can be avoided:
> SetNodeStyle(acme$Accounting, inherit = FALSE, fillcolor = "Thistle", 
+              fontcolor = "Firebrick", tooltip = "This is the accounting department")
> SetEdgeStyle(acme$Research$`New Labs`, 
+              color = "red", 
+              label = "Focus!", 
+              penwidth = 3, 
+              fontcolor = "red")
> #use Do to set style on specific nodes:
> Do(acme$leaves, function(node) SetNodeStyle(node, shape = "egg"))
> plot(acme)
Error in plot.Node(acme) : 
  Package "DiagrammeR" is required to plot a `data.tree::Node`object. Please install it.
Calls: plot -> plot.Node
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘applications.Rmd’ using rmarkdown

Quitting from lines 57-64 [unnamed-chunk-2] (applications.Rmd)
Error: processing vignette 'applications.Rmd' failed with diagnostics:
there is no package called 'treemap'
--- failed re-building ‘applications.Rmd’

--- re-building ‘data.tree.Rmd’ using rmarkdown

Quitting from lines 121-124 [unnamed-chunk-3] (data.tree.Rmd)
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
there is no package called 'treemap'
--- failed re-building ‘data.tree.Rmd’

SUMMARY: processing the following files failed:
  ‘applications.Rmd’ ‘data.tree.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'assertr', 'shiny.semantic', 'purrr', 'dplyr', 'tidyr', 'tibble'

Packages suggested but not available for checking:
  'fixtuRes', 'readr', 'targets', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'arrow', 'dplyr', 'dbplyr', 'RSQLite', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘readr’

Packages suggested but not available for checking:
  'haven', 'purrr', 'testthat', 'devtools', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

Packages suggested but not available for checking:
  'ggmap', 'choroplethr', 'dplyr', 'ggExtra', 'plotly', 'ggrepel',
  'viridis'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'brms', 'dplyr', 'gamm4', 'ggplot2', 'gt', 'haven', 'lme4',
  'mediation', 'readxl', 'readr', 'rio', 'rstanarm', 'see', 'testthat',
  'tibble', 'tidyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'Hmisc', 'janitor', 'purrr', 'readr', 'readxl', 'sidrar',
  'stringr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘googledrive’

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

Packages suggested but not available for checking:
  'readxl', 'shinytest2', 'testthat', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'phangorn', 'phytools', 'ips', 'geiger', 'stringr', 'rotl',
  'paleotree', 'knitcitations', 'phylobase', 'taxize', 'phylocomr'

Packages suggested but not available for checking:
  'testthat', 'usethis', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'clock', 'purrr', 'vctrs'

Packages suggested but not available for checking:
  'lubridate', 'parttime', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'stringr', 'lubridate'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'babynames', 'dplyr', 'forcats', 'gapminder', 'ggplot2', 'Lahman',
  'nycflights13', 'modeldata', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'dplyr', 'forcats', 'ggplot2', 'ggridges', 'reshape2',
  'stringr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘data_preparation.Rmd’ using rmarkdown

Quitting from lines 24-32 [unnamed-chunk-2] (data_preparation.Rmd)
Error: processing vignette 'data_preparation.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘data_preparation.Rmd’

--- re-building ‘how-to.Rmd’ using rmarkdown

Quitting from lines 12-29 [unnamed-chunk-1] (how-to.Rmd)
Error: processing vignette 'how-to.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘how-to.Rmd’

SUMMARY: processing the following files failed:
  ‘data_preparation.Rmd’ ‘how-to.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'progress', 'aoos'

Packages suggested but not available for checking:
  'dplyr', 'nycflights13', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'odbc', 'dplyr', 'RSQLite'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'caret', 'TSdist', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot.mleBb.Rd:48: Lost braces
    48 |   \ code{size} is extracted from argument \code{x}.
       |         ^
Packages required but not available: 'blob', 'flobr', 'RSQLite'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readxl', 'tidyr', 'dplyr', 'ggplot2', 'purrr', 'questionr',
  'tibble', 'labelled', 'naniar'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidypredict', 'tidyverse', 'dbplyr', 'vctrs', 'dplyr', 'purrr',
  'tibble', 'tidyr', 'stringr'

Packages suggested but not available for checking:
  'RSQLite', 'bigrquery', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'seqHMM', 'reshape2', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'arrow', 'blob', 'DBItest', 'dbplyr', 'downlit', 'dplyr', 'hms',
  'RMariaDB', 'RSQLite', 'testthat', 'vctrs'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'blob', 'hms', 'lubridate', 'testthat'

Packages suggested but not available for checking:
  'constructive', 'devtools', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) CI_mc.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{i}{the row index of the interest entry X_{i,j}}
       |                                                ^
checkRd: (-1) CI_mc.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{j}{the row index of the interest entry X_{i,j}}
       |                                                ^
Packages required but not available: 'ggplot2', 'reshape2', 'tibble'

Packages suggested but not available for checking: 'testthat', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bnviewer', 'ggplot2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
checkRd: (-1) Velocity.Rd:9: Lost braces; missing escapes or markup?
     9 | \item{probs}{the weight of each value {-1,0,1}. They define the probability that each of them will be picked}
       |                                       ^
checkRd: (-1) cte_times_vel_cpp.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{abs_op}{the final number of {1,-1} operations}
       |                                   ^
checkRd: (-1) natVelocity.Rd:15: Lost braces; missing escapes or markup?
    15 | \item{probs}{the weight of each value {-1,0,1}. They define the probability that each of them will be picked}
       |                                       ^
checkRd: (-1) nat_cte_times_vel_cpp.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{abs_op}{the final number of {1,-1} operations}
       |                                   ^
checkRd: (-1) nat_vel_plus_vel_cpp.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{abs_op1}{the number of {1,-1} operations in the first velocity}
       |                              ^
checkRd: (-1) nat_vel_plus_vel_cpp.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{abs_op2}{the number of {1,-1} operations in the second velocity}
       |                              ^
checkRd: (-1) randomize_vl_cpp.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{probs}{the probabilities of each value in the set {-1,0,1}}
       |                                                         ^
checkRd: (-1) vel_plus_vel_cpp.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{abs_op}{the final number of {1,-1} operations}
       |                                   ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'progress', 'purrr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'purrr'

Packages suggested but not available for checking:
  'dbplyr', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'blob', 'dplyr', 'pillar', 'purrr', 'tibble', 'tidyr', 'tidyselect',
  'vctrs'

Packages suggested but not available for checking:
  'Lahman', 'nycflights13', 'odbc', 'RMariaDB', 'RPostgres', 'RSQLite',
  'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'dendextend', 'igraph'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dada2', 'ggplot2', 'taxonomizr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DBTC', 'ggplot2', 'leaflet.extras', 'shinyFiles'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'testthat', 'RSQLite', 'RMariaDB', 'RPostgres', 'hms', 'blob', 'odbc'
Running examples in ‘dbx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dbxConnect
> ### Title: Create a database connection
> ### Aliases: dbxConnect
> 
> ### ** Examples
> 
> # SQLite
> db <- dbxConnect(adapter="sqlite", dbname=":memory:")
Error in requireLib("RSQLite") : Could not load adapter: RSQLite
Calls: dbxConnect -> findAdapter -> requireLib
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'c3net', 'igraph', 'RedeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Ecdat’
Running examples in ‘DCchoice-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dbchoice
> ### Title: Parametric approach to analyze double-bounded dichotomous choice
> ###   contingent valuation data
> ### Aliases: dbchoice print.dbchoice vcov.dbchoice logLik.dbchoice
> ### Keywords: DCchoice double-bounded nonlinear
> 
> ### ** Examples
> 
> ## Examples are based on a data set NaturalPark in the package 
> ## Ecdat (Croissant 2011): DBDCCV style question for measuring 
> ## willingness to pay for the preservation of the Alentejo Natural 
> ## Park. The data set (dataframe) contains seven variables: 
> ## bid1 (bid in the initial question), bidh (higher bid in the follow-up 
> ## question), bidl (lower bid in the follow-up question), answers 
> ## (response outcomes in a factor format with four levels of "nn", 
> ## "ny", "yn", "yy"), respondents' characteristic variables such 
> ## as age, sex and income (see NaturalPark for details).
> data(NaturalPark, package = "Ecdat")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘Ecdat’
Calls: data -> find.package
Execution halted
Packages required but not available: 'rumidas', 'rugarch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘mlogit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Packages required but not available:
  'readxl', 'idefix', 'tidyr', 'mlogit', 'dfidx', 'adjustedcranlogs',
  'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'devtools'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'tensorflow', 'dplyr', 'phangorn', 'igraph', 'purrr', 'stringr',
  'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'modelr', 'purrr', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'GDINA', 'roxygen2', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'rstan', 'beepr', 'dplyr', 'forcats', 'janitor', 'purrr', 'tibble',
  'tidyr'

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'broom', 'dplyr', 'ggplot2', 'purrr', 'tibble'

Packages suggested but not available for checking:
  'gtsummary', 'testthat', 'tidyr'

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking: 'testthat', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'rifreg', 'Hmisc'

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tibble'
Running examples in ‘ddi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ddc
> ### Title: Data Defect Correlation
> ### Aliases: ddc
> 
> ### ** Examples
> 
> library(tibble)
Error in library(tibble) : there is no package called ‘tibble’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'tidyr'
Packages required but not available: 'haven', 'readxl'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) detectAgeInterval.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Age}, or code{age}.}
       |                                                                              ^
checkRd: (-1) detectSex.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Sex}, or code{sex}.}
       |                                                                              ^
checkRd: (-1) ggbgetAgesFit.Rd:28: Lost braces
    28 | code{\link{ggbChooseAges}}
       |     ^
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'ggplot2', 'mixtools', 'readr', 'tibble'

Packages suggested but not available for checking: 'ggExtra', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'tidyr', 'gapminder'
Running examples in ‘ddplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: barChart
> ### Title: Create a bar chart.
> ### Aliases: barChart
> 
> ### ** Examples
> 
> library(ggplot2) #needed for the mpg data frame
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Start.Rmd’ using rmarkdown

Quitting from lines 28-40 [unnamed-chunk-2] (Start.Rmd)
Error: processing vignette 'Start.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘Start.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ggplot2', 'ggalt', 'MEGENA', 'igraph', 'Hmisc'

Packages suggested but not available for checking: 'WGCNA', 'ggfortify'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available:
  'ggplot2', 'ggpubr', 'ggtext', 'ggtree', 'phylobase', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'tidyr', 'plotly', 'igraph', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘flexsurv’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'devtools'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tibble', 'vctrs'

Packages suggested but not available for checking:
  'ggplot2', 'ggraph', 'igraph', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'mockery', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'chillR', 'dplyr', 'ggplot2', 'patchwork', 'rriskDistributions',
  'stringr', 'tidyr', 'tidyselect'

Packages suggested but not available for checking: 'mc2d', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'AER', 'dplyr', 'tibble', 'ggplot2', 'broom', 'reshape2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
File ‘declared/libs/declared.so’:
  Found non-API call to R: ‘SET_ENVFLAGS’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'tidyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘decoder.Rmd’ using rmarkdown
--- finished re-building ‘decoder.Rmd’

--- re-building ‘sjukhus.Rmd’ using rmarkdown

Quitting from lines 54-70 [unnamed-chunk-2] (sjukhus.Rmd)
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘sjukhus.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'keras', 'tensorflow', 'tsutils', 'TSdeeplearning'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'usethis', 'StratigrapheR', 'dplyr'

Packages suggested but not available for checking: 'Rssa', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following significant warnings:
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 3 at (1)
  Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 25 at (1)
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 4 at (1)
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 16 at (1)
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 5 at (1)
  Warning: Fortran 2018 deleted feature: Shared DO termination label 9 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/decon.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-25) 13.2.0’
* used Fortran compiler: ‘GNU Fortran (Debian 13.2.0-25) 13.2.0’
Packages suggested but not available for checking: 'cowplot', 'ggplot2'
checkRd: (-1) deconv.Rd:85: Lost braces; missing escapes or markup?
    85 |     \code{tg}, std. error of \eqn{g}, \eqn{G} (the cdf of {g}),
       |                                                           ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘deconvolution.Rmd’ using rmarkdown

Quitting from lines 116-133 [unnamed-chunk-7] (deconvolution.Rmd)
Error: processing vignette 'deconvolution.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘deconvolution.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'vctrs'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'car', 'effects'

Package suggested but not available for checking: ‘Hmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'reshape2', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'purrr', 'readr', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'kableExtra', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘usage-and-algorithm-explained.Rmd’ using rmarkdown

Quitting from lines 19-23 [setup] (usage-and-algorithm-explained.Rmd)
Error: processing vignette 'usage-and-algorithm-explained.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘usage-and-algorithm-explained.Rmd’

SUMMARY: processing the following file failed:
  ‘usage-and-algorithm-explained.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'ggraph', 'graphlayouts', 'igraph',
  'miniCRAN', 'testthat'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'fastDummies', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'purrr'

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) deepNN-package.Rd:18: Lost braces
    18 | section{Dependencies}{
       |        ^
checkRd: (-1) deepNN-package.Rd:18-21: Lost braces
    18 | section{Dependencies}{
       |                      ^
checkRd: (-1) deepNN-package.Rd:23: Lost braces
    23 | section{Citation}{
       |        ^
checkRd: (-1) deepNN-package.Rd:23-25: Lost braces
    23 | section{Citation}{
       |                  ^
checkRd: (-1) deepNN-package.Rd:27-38: Lost braces
    27 | references{
       |           ^
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'ggplot2', 'ggthemes', 'keras', 'purrr', 'tensorflow'

Packages suggested but not available for checking:
  'kableExtra', 'stringr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tensorflow', 'tfprobability', 'keras', 'dplyr', 'tfruns'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(deepRstudio)
  > 
  > # Setting
  > options(testthat.use_colours = FALSE)
  > 
  > testthat::test_file("testthat/test_deepRstudio.R")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available:
  'ggplot2', 'ggnewscale', 'ggforce', 'ggfittext', 'phytools',
  'geomtextpath'

Packages suggested but not available for checking:
  'dplyr', 'palaeoverse', 'paleotree', 'dispRity', 'ggtree',
  'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tensorflow', 'keras', 'tfprobability', 'deepregression', 'mlt',
  'purrr'

Packages suggested but not available for checking:
  'testthat', 'tram', 'cotram'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ActivePathways', 'dplyr', 'ggplot2', 'ggrepel'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'readxl', 'reporter', 'libr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'lubridate'

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'cimir', 'dplyr', 'testthat', 'tidyr'
Running examples in ‘degday-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dd_calc
> ### Title: Estimate degree days from daily data
> ### Aliases: dd_calc dd_simp_avg dd_sng_tri dd_sng_sine dd_dbl_tri
> ###   dd_dbl_sine
> 
> ### ** Examples
> 
> daily_temps <- system.file("extdata/espartoa-weather-2020.csv", package = "degday") %>%
+   read.csv() %>%
+     dplyr::mutate(date = as.Date(date)) %>%
+     dplyr::slice(1:10)
Error in loadNamespace(x) : there is no package called ‘dplyr’
Calls: %>% ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'igraph', 'network'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmmTMB', 'tibble', 'ggplot2', 'ggpubr', 'ggrepel', 'car', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Problems with news in ‘NEWS.md’:
No news entries found.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'igraph', 'progress'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) deltaPlot.Rd:28: Lost braces
    28 |  \item{purify}{logical: should item purification be performed? (Default is code{FALSE}). See \bold{Details}.}
       |                                                                                ^
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) deming.Rd:71: Lost braces
    71 | on whether the code{cv} option is TRUE or FALSE, respectively.
       |                    ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
Packages required but not available:
  'ggplot2', 'purrr', 'tidyr', 'dplyr', 'GGally', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'dplyr'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following files/directories:
  ‘smd_table.docx’
Packages required but not available:
  'forecast', 'ftsa', 'rainbow', 'HMDHFDplus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'purrr', 'progress', 'igraph'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ClusterR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'viridis'

Packages suggested but not available for checking: 'testthat', 'heatmaply'

Packages which this enhances but not available for checking:
  'ggdendro', 'Hmisc', 'WGCNA', 'phangorn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyverse', 'dplyr', 'ggplot2', 'lubridate', 'readxl', 'tibble',
  'tidyr', 'forecast', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > # Run all tests for gphys package
  > #  
  > # Author: jefferis
  > ###############################################################################
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplR', 'igraph', 'stringr', 'reshape2', 'RCy3', 'dplyr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'DiagrammeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'reshape2', 'dplyr', 'plotly', 'Cubist', 'lubridate',
  'viridis', 'dplR'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘gapmap’
Package required but not available: ‘dplyr’

Packages suggested but not available for checking: 'roxygen2', 'tsibble'

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

Packages suggested but not available for checking: 'testthat', 'DiagrammeR'

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

Package suggested but not available for checking: ‘missMDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggdensity', 'purrr', 'tibble', 'vctrs'

Packages suggested but not available for checking:
  'forcats', 'ggplot2', 'readr', 'stringr', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggrepel'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'usethis', 'devtools', 'roxygen2', 'ggplot2', 'cowplot'
Running examples in ‘denvax-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lazou2016
> ### Title: The serosurvey data in L'Azou 2016
> ### Aliases: lazou2016
> ### Keywords: datasets
> 
> ### ** Examples
> 
> require(denvax); require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> data(lazou2016)
> ggplot(lazou2016) + aes(Age, Seropositive/Number*100, color = Country) +
+   geom_point() + labs(y="Seropositive %", x="Age Group") + lims(y=c(0,100)) +
+   theme_minimal()
Error in ggplot(lazou2016) : could not find function "ggplot"
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'ggplot2', 'Hmisc', 'progress', 'purrr', 'readr', 'rms',
  'stringr', 'tibble', 'tidyr', 'usethis'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘Rdonlp2’
checkRd: (-1) discrimination.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) fitdmm.Rd:59: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘Rdonlp2’
checkRd: (-1) responses.Rd:68: Lost braces
    68 |         response.  See code{\link{makeDepmix}} for an example of how to use
       |                            ^
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) crs.Rd:34: Lost braces; missing escapes or markup?
    34 | system, crs) of DeponsRaster and DeponsTrack objects. For {sp} objects the
       |                                                           ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'fda', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'tidyr'

VignetteBuilder packages required for checking but not installed:
  'ggplot2', 'dplyr', 'tidyr'
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) Deriv.Rd:33: Lost braces
    33 | guessed either from\ code{names(formals(f))} (if \code{f} is a function)
       |                          ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'gh', 'testthat'
Packages required but not available:
  'dplyr', 'forcats', 'tibble', 'tidyr', 'purrr', 'broom', 'stringr',
  'haven', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'ggplot2', 'GGally'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dplyr', 'testthat'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'ggpattern', 'paletteer', 'GGally'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'exact2x2', 'DescTools', 'dplyr', 'tibble', 'stringr', 'forcats',
  'kableExtra', 'haven', 'Hmisc'

Packages suggested but not available for checking: 'testthat', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'dplyr', 'tidyr', 'tibble', 'tidyselect', 'forcats'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'tidyr'

Package suggested but not available for checking: ‘purrr’

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

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

Packages suggested but not available for checking:
  'RDCOMClient', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'animation', 'furrr', 'purrr'

Packages suggested but not available for checking:
  'badger', 'smoots', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'dplyr'

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

Packages suggested but not available for checking: 'shinytest2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'ggplot2', 'tibble', 'tidyr', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'pkgdown', 'gt', 'bench', 'tidyverse',
  'devtools', 'ggpattern', 'cowplot', 'bestNormalize'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package which this enhances but not available for checking: ‘gurobi’
Packages required but not available: 'tibble', 'dplyr', 'lme4'

Packages suggested but not available for checking:
  'lmerTest', 'afex', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'readxl', 'testthat'
Package suggested but not available for checking: ‘ggplot2’
Running examples in ‘desla-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HDLP
> ### Title: State Dependent High-Dimensional Local Projection
> ### Aliases: HDLP
> 
> ### ** Examples
> 
> X<-matrix(rnorm(50*50), nrow=50)
> y<-X[,1:4] %*% c(1, 2, 3, 4) + rnorm(50)
> s<-matrix(c(rep(1,25),rep(0,50),rep(1,25)), ncol=2, dimnames = list(NULL, c("A","B")))
> h<-HDLP(x=X[,4], y=y, q=X[,-4], state_variables=s, hmax=5, lags=1)
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
> plot(h)
Error in plot.hdlp(h) : Cannot plot as package ggplot2 not installed.
Calls: plot -> plot.hdlp
Execution halted
Packages required but not available: 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'tibble'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘custom.Rmd’ using rmarkdown
--- finished re-building ‘custom.Rmd’

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

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

--- re-building ‘objects.Rmd’ using rmarkdown

Quitting from lines 39-42 [unnamed-chunk-3] (objects.Rmd)
Error: processing vignette 'objects.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building ‘objects.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dclone', 'dcmle'
Packages required but not available: 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AER’
Packages required but not available:
  'tourr', 'tibble', 'tidyselect', 'purrr'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'liminal'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'autothresholdr', 'dplyr', 'filesstrings', 'ijtiff', 'purrr',
  'stringr'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Package required but not available: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'usethis', 'pkgdown', 'profvis', 'roxygen2', 'testthat'

Packages suggested but not available for checking:
  'foghorn', 'gh', 'gmailr', 'mockery'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dplyr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown

Quitting from lines 38-42 [make_subsets] (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dexter', 'shinyFiles', 'dplyr', 'tidyr', 'tibble', 'readxl',
  'readODS', 'ggplot2', 'ggExtra', 'ggridges', 'networkD3'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dexter', 'dplyr', 'RSQLite', 'igraph', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSQLite', 'tidyr', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BayesFactor', 'MVN'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'vdiffr'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'stringr', 'gprofiler2', 'signatureSearch', 'signatureSearchData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'pryr'

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking: 'AER', 'mlogit'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) mtaBin_next.Rd:27: Lost braces
    27 |   \item{s_1}{A function depending on the number of patients included used for adaptive randomization in plateau determination, only used if the estimation method chosen is "MTA-RA". The default function is function(n_cur,n){0.2}.}
       |                                                                                                                                                                                                                                ^
checkRd: (-1) mtaBin_sim.Rd:30: Lost braces
    30 |   \item{s_1}{A function depending on the number of patients included used for adaptive randomization in plateau determination, only used if the estimation method chosen is "MTA-RA". The default function is function(n_cur){0.2}.}
       |                                                                                                                                                                                                                              ^
Packages required but not available:
  'dplR', 'dplyr', 'forcats', 'ggplot2', 'ggpubr', 'purrr', 'tidyr',
  'tibble'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'ggplot2', 'plotly'

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'MLInterfaces', 'genefilter'

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'biomaRt', 'dplyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DGEobj', 'dplyr', 'stringr'

Packages suggested but not available for checking:
  'biomaRt', 'ggplot2', 'qvalue', 'sva', 'testthat', 'zFPKM'

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

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) AIC.dglars.Rd:47: Lost braces
    47 | \item{comp}{the measures of model complexity used to compute the measure of goodness-of-fit. It is equal to \code{npar} when code{complexity = "df"};}
       |                                                                                                                                  ^
checkRd: (-1) dglars.Rd:258: Lost braces
   258 |                 \item{\code{7}}{maximum number of solution points ('code{np}') reached.}
       |                                                                         ^
Package required but not available: ‘nloptr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'benchmarkme', 'ggplot2', 'ggforce', 'reshape2', 'patchwork', 'clhs',
  'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available: 'gap', 'lme4'

Packages suggested but not available for checking:
  'testthat', 'mgcViz', 'spaMM', 'glmmTMB'

Packages which this enhances but not available for checking:
  'phyr', 'rstan', 'BayesianTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'purrr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) dHSIC-package.Rd:32: Lost braces
    32 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dHSIC-package.Rd:36: Lost braces
    36 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dHSIC-package.Rd:36: Lost braces
    36 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
checkRd: (-1) dhsic.Rd:84: Lost braces
    84 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dhsic.Rd:88: Lost braces
    88 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dhsic.Rd:88: Lost braces
    88 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
checkRd: (-1) dhsic.test.Rd:124: Lost braces
   124 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dhsic.test.Rd:128: Lost braces
   128 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dhsic.test.Rd:128: Lost braces
   128 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
Packages required but not available: 'haven', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'meta', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'igraph', 'purrr', 'readr', 'stringr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'dplyr', 'pillar', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dialr.Rmd’ using rmarkdown

Quitting from lines 18-21 [setup] (dialr.Rmd)
Error: processing vignette 'dialr.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘dialr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'hardhat', 'pillar', 'purrr', 'tibble', 'vctrs'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'tidyr', 'purrr', 'stringr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'pillar', 'purrr', 'tibble', 'tidyr', 'tidyselect', 'vctrs'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ## load dependencies
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'klaR', 'NMF', 'purrr', 'stringr', 'tidyr',
  'yardstick'

Packages suggested but not available for checking: 'progress', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) DIconvex.Rd:40: Lost braces; missing escapes or markup?
    40 |  {Paul Schneider <paul.schneider@usi.ch>}{}
       |  ^
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'ggplot2', 'did', 'staggered', 'didimputation'

Packages suggested but not available for checking: 'haven', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'progress'
Packages required but not available:
  'broom', 'dplyr', 'stringr', 'purrr', 'tidyr'

Packages suggested but not available for checking: 'haven', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'matlib', 'car', 'haven', 'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BMisc', 'ggplot2', 'ggpubr', 'DRDID', 'tidyr'

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

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

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

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

Packages suggested but not available for checking:
  'testthat', 'lubridate', 'purrr', 'dplyr', 'stringr', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arrow', 'dplyr', 'janitor'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'stringr', 'reshape2', 'ggnewscale'

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'BoolNet', 'igraph'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tidyr', 'tidyselect'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'randomNames', 'testthat'
checkRd: (-1) sensitivitySamplerManual-DPMech-function-numeric-numeric-numeric-method.Rd:25: Lost braces
    25 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
checkRd: (-1) sensitivitySamplerManual-DPMechNumeric-function-numeric-numeric-numeric-method.Rd:25: Lost braces
    25 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
checkRd: (-1) sensitivitySamplerManual.Rd:22: Lost braces
    22 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bernstein.Rnw’ using knitr
--- finished re-building ‘bernstein.Rnw’

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

Quitting from lines 296-310 [samplerExponential] (diffpriv.Rnw)
Error: processing vignette 'diffpriv.Rnw' failed with diagnostics:
there is no package called 'randomNames'
--- failed re-building ‘diffpriv.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggdendro', 'ggplot2', 'igraph', 'reshape2', 'viridis'

Packages suggested but not available for checking:
  'cowplot', 'strex', 'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nloptr', 'systemfit', 'optimx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gurobi’
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) simulate_diff_tables.Rd:72: Lost braces; missing escapes or markup?
    72 |   {The Sharma-Song test} {\code{\link[DiffXTables]{sharma.song.test}}}
       |   ^
checkRd: (-1) simulate_diff_tables.Rd:74: Lost braces; missing escapes or markup?
    74 |   {The comparative chi-squared test} {\code{\link[DiffXTables]{cp.chisq.test}}}
       |   ^
checkRd: (-1) simulate_diff_tables.Rd:76: Lost braces; missing escapes or markup?
    76 |   {The heterogeneity test} {\code{\link[DiffXTables]{heterogeneity.test}}}
       |   ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ShinyItemAnalysis’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'difR', 'readxl'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyr', 'readr', 'dplyr', 'ggplot2', 'lubridate', 'stringr'

Packages suggested but not available for checking: 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyr', 'zinbwave', 'dplyr', 'reshape2', 'keras', 'tensorflow',
  'ggplot2', 'ggpubr', 'scran'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'BeyondBenford', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'viridis', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bibliometrix’
Package suggested but not available for checking: ‘tinysnapshot’
checkRd: (-1) DIME.Rd:272: Lost braces; missing escapes or markup?
   272 | \item{name}{the name of the model {"GNG", "iNUDGE","NUDGE"} where
       |                                   ^
Packages required but not available: 'DImodels', 'dplyr', 'reshape2'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DImodels', 'dplyr', 'forcats', 'ggfortify', 'ggplot2', 'ggtext',
  'metR', 'PieGlyph', 'tidyr'

Package suggested but not available for checking: ‘DImodelsMulti’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'NMF', 'cccd', 'diffusionMap', 'ggplot2', 'igraph', 'keras', 'loe',
  'optimx', 'tensorflow', 'testthat', 'tidyr'
checkRd: (-1) DRR-class.Rd:79: Lost braces; missing escapes or markup?
    79 | n^{1/3} up to sacrificing some accuracy, for details see
       |   ^
Unknown package ‘loe’ in Rd xrefs
Running examples in ‘dimRed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Isomap-class
> ### Title: Isomap embedding
> ### Aliases: Isomap-class Isomap
> 
> ### ** Examples
> 
> if(requireNamespace(c("RSpectra", "igraph", "RANN"), quietly = TRUE)) {
+ 
+ dat <- loadDataSet("3D S Curve", n = 500)
+ emb <- embed(dat, "Isomap", knn = 10)
+ plot(emb)
+ 
+ ## or simpler, use embed():
+ samp <- sample(nrow(dat), size = 200)
+ emb2 <- embed(dat[samp], "Isomap", .mute = NULL, knn = 10)
+ emb3 <- predict(emb2, dat[-samp])
+ 
+ plot(emb2, type = "2vars")
+ plot(emb3, type = "2vars")
+ 
+ }
Error in chckpkg("igraph") : 
  require 'igraph' package, install it using install.packages('igraph')
Calls: embed ... embed -> .local -> do.call -> <Anonymous> -> chckpkg
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘biomaRt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘Hmisc’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'lubridate', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dint.Rmd’ using rmarkdown

Quitting from lines 171-176 [unnamed-chunk-9] (dint.Rmd)
Error: processing vignette 'dint.Rmd' failed with diagnostics:
there is no package called 'lubridate'
--- failed re-building ‘dint.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'WGCNA', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'usethis', 'ggplot2', 'lemon', 'dplyr'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'optmatch', 'rrelaxiv'
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'reshape2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DirectEffects.Rmd’ using rmarkdown

Quitting from lines 14-20 [loadpkg] (DirectEffects.Rmd)
Error: processing vignette 'DirectEffects.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘DirectEffects.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'bigstatsr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'alphahull', 'dplyr', 'ggthemes', 'testthat'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plotly’

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

Packages suggested but not available for checking: 'testthat', 'EdSurvey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘mcmcse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 130 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DirStats.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-25) 13.2.0’
* used Fortran compiler: ‘GNU Fortran (Debian 13.2.0-25) 13.2.0’
Package required but not available: ‘nloptr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Packages required but not available:
  'dplyr', 'ggplot2', 'cowplot', 'fmesher', 'tidyterra'

Packages suggested but not available for checking: 'testthat', 'INLA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'shinytest2', 'testthat', 'vdiffr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'tidyr', 'tibble', 'rstan', 'SHELF', 'ggplot2', 'loo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'TSCAN', 'igraph', 'ggplot2', 'AnnotationDbi', 'org.Hs.eg.db'

Packages suggested but not available for checking: 'testthat', 'Seurat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'readxl'
Running examples in ‘disclapmix2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: haplotype_counts
> ### Title: Count the number of times each haplotype occurs
> ### Aliases: haplotype_counts
> 
> ### ** Examples
> 
> # read haplotypes
> h <- readxl::read_excel(system.file("extdata","South_Australia.xlsx",
+ package = "disclapmix2"), 
+ col_types = "text")[-c(1,2)]
Error in loadNamespace(x) : there is no package called ‘readxl’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'ggdendro', 'testthat'
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 31-35 [unnamed-chunk-2] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘introduction.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'lubridate', 'qdap', 'SentimentAnalysis', 'stringr',
  'syuzhet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'haven', 'latex2exp', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'GGally', 'ggplot2', 'ggrepel', 'igraph', 'network'

Packages suggested but not available for checking:
  'ggpubr', 'sna', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'loadeR', 'ggplot2', 'ggdendro', 'echarts4r', 'FactoMineR',
  'colourpicker'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'bench', 'testthat'
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘package_introduction.Rmd’ using rmarkdown

Quitting from lines 28-40 [setup] (package_introduction.Rmd)
Error: processing vignette 'package_introduction.Rmd' failed with diagnostics:
there is no package called 'bench'
--- failed re-building ‘package_introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'parsnip', 'dials', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'klaR', 'modeldata', 'sparsediscrim', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dfidx', 'readr'
checkRd: (-1) mc_attitudes.Rd:52: Lost braces
    52 | P\'{a}ez, A. (2013). Mapping travelers’ attitudes: does space matter?. Journal of Transport Geography, 26, 117-125. (https://doi.org/10.1016/j.jtrangeo.2012.09.002)
       |    ^
checkRd: (-1) mc_commute.csv.Rd:49: Lost braces
    49 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
checkRd: (-1) mc_commute_long.Rd:74: Lost braces
    74 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
checkRd: (-1) mc_commute_wide.Rd:87: Lost braces
    87 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
checkRd: (-1) mc_modality.Rd:50: Lost braces
    50 | Lavery, T., P\'{a}ez, A., & Kanaroglou, P.S. (2013). Driving out of choices: An investigation of transport modality in a university sample. Transportation Research Part A: Policy and Practice, 57:37-46 (https://doi.org/10.1016/j.tra.2013.09.010)
       |                ^
Running examples in ‘discrtr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mc_commute.csv
> ### Title: McMaster Commuting Data Set (csv file).
> ### Aliases: mc_commute.csv
> ### Keywords: datasets
> 
> ### ** Examples
> 
>  library(readr)
Error in library(readr) : there is no package called ‘readr’
Execution halted
Package required but not available: ‘geepack’

Packages suggested but not available for checking: 'caret', 'Ecdat', 'pec'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stm', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tmap’
Package which this enhances but not available for checking: ‘INLA’
Packages required but not available:
  'dbplyr', 'dplyr', 'ISOweek', 'lubridate', 'purrr', 'readr', 'SCDB',
  'stringr', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'devtools', 'odbc', 'RSQLite', 'RPostgres', 'testthat', 'tibble'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyselect', 'purrr', 'tidyr', 'stringr'

Packages suggested but not available for checking: 'ggplot2', 'forcats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'pryr', 'stringr', 'benchmarkme', 'purrr', 'arrow'

Packages suggested but not available for checking:
  'nycflights13', 'readr', 'broom', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) mess.Rd:28: Lost braces
    28 | Elith J., M. Kearney M., and S. Phillips, 2010. The art of modelling range-shifting species. \doi{10.1111/j.2041-210X.2010.00036.x}{Methods in Ecology and Evolution 1:330-342}.
       |                                                                                                                                    ^
Packages suggested but not available for checking: 'mvp', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘disindex.Rmd’ using rmarkdown
--- finished re-building ‘disindex.Rmd’

--- re-building ‘disordR.Rmd’ using rmarkdown

Quitting from lines 172-175 [unnamed-chunk-2] (disordR.Rmd)
Error: processing vignette 'disordR.Rmd' failed with diagnostics:
there is no package called 'mvp'
--- failed re-building ‘disordR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'purrr', 'lubridate', 'progress'

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat', 'tidyr', 'skimr', 'ggplot2',
  'ggridges', 'furrr', 'bench'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Claddis', 'GET', 'phangorn'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'biomartr', 'dplyr', 'reutils', 'RSQLite', 'stringr'
checkRd: (-1) store_in_DB.Rd:89: Lost braces
    89 | link{read_from_DB} function. Those parameters define rows and columns that will be returned.
       |     ^
checkRd: (-1) unite_two_DF.Rd:46: Lost braces; missing escapes or markup?
    46 | \code{data1.shared.var} and {data2.shared.var} must contain unique values within its own data frame.
       |                             ^
Running examples in ‘disprose-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: count_PhCh
> ### Title: Calculate physical and chemical properties
> ### Aliases: count_PhCh count_GC count_REP count_MFE count_TM
> 
> ### ** Examples
> 
> probes <- data.frame (ids = 1:3,  probes = c ("acacacacacaca", "aaaaagggggtttttccccc",
+                                              "atgcgctagctcagc"))
> probes <- count_GC (probe.var = probes$probes, trim.gc = FALSE, GCmin = 40, GCmax = 60,
+                    add.to.data = TRUE, data = probes)
Error: Package "stringr" needed for this function to work. Please install it.
Execution halted
Packages required but not available: 'caret', 'dplyr', 'viridis'

Package suggested but not available for checking: ‘Cubist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mrds', 'dplyr'

Packages suggested but not available for checking:
  'progress', 'testthat', 'optimx', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘viridis’

Packages suggested but not available for checking: 'devtools', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'readxl', 'dplyr', 'tidytext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'dplyr'

Package suggested but not available for checking: ‘opencpu’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) booter.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) ci.booted.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) pbooter.Rd:57: Escaped LaTeX specials: \&
Packages required but not available: 'ggplot2', 'dplyr', 'purrr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'downlit', 'lubridate', 'stringr'

Packages suggested but not available for checking:
  'DiagrammeR', 'progress', 'testthat'

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'factoextra', 'ggplot2', 'broom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'colourpicker', 'dplyr', 'ggplot2', 'rio', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bamlss', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'testthat', 'ggdist', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'AdaptGauss'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'cowplot', 'revdbayes', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'tidyverse', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) moranTest.Rd:37: Lost braces; missing escapes or markup?
    37 |   {M(theta)=-(log(y_1-y_0)+log(y_2-y_1)+...+log(y_m-y_m-1))}
       |   ^
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'dplyr', 'dbplyr', 'nycflights13', 'odbc', 'RMariaDB', 'RPostgres',
  'RSQLite', 'testthat'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘developing-dittodb.Rmd’ using rmarkdown

Quitting from lines 13-22 [unnamed-chunk-1] (developing-dittodb.Rmd)
Error: processing vignette 'developing-dittodb.Rmd' failed with diagnostics:
there is no package called 'testthat'
--- failed re-building ‘developing-dittodb.Rmd’

--- re-building ‘dittodb.Rmd’ using rmarkdown

Quitting from lines 13-22 [unnamed-chunk-1] (dittodb.Rmd)
Error: processing vignette 'dittodb.Rmd' failed with diagnostics:
there is no package called 'testthat'
--- failed re-building ‘dittodb.Rmd’

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

SUMMARY: processing the following files failed:
  ‘developing-dittodb.Rmd’ ‘dittodb.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ggplot2', 'cowplot', 'ggrepel', 'ggridges'

Packages suggested but not available for checking:
  'plotly', 'testthat', 'ggplot.multistats', 'ggrastr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘icosa’
checkRd: (-1) fadlad.Rd:30: Lost braces
    30 | \item{diffbin}{\code{(logical)}: Difference-based duration for discreet time (only applicabble to cases when \code{bin} is provided). If set to \code{TRUE}, single-interval taxa will \code{0} durations. Setting this argument to \code{FALSE} will add code{1} to the durations of all taxa.}
       |                                                                                                                                                                                                                                                               ^
checkRd: (-1) slice.Rd:27: Lost braces
    27 | Due to stratigraphic constraints, we can only process deep time data, when it is sliced to discrete bins. It is suggested that you do this separately for most of your analyses. This function is also used by the code{\link{divDyn}} function when \code{age} entries are provided.
       |                                                                                                                                                                                                                        ^
checkRd: (-1) tabinate.Rd:31: Lost braces
    31 | Setting both \code{bin} If \code{bin=NULL} and code{tax=NULL}, will run \code{FUN} on the entire dataset (no effect). Providing either \code{bin} or \code{tax} and keeping the other \code{NULL} will iterate \code{FUN} for every \code{bin} or \code{tax} entry (whichever is presented).
       |                                                    ^
Packages required but not available: 'plotly', 'uniReg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggmulti', 'loon.ggplot', 'loon.shiny', 'loon.tourr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Packages suggested but not available for checking: 'igraph', 'entropart'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'lubridate', 'geiger'
Packages required but not available: 'ggplot2', 'ggpubr', 'rms'

Packages suggested but not available for checking: 'testthat', 'BOLTSSIRR'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyverse', 'dplyr', 'tibble', 'tidyr', 'stringr', 'ggplot2',
  'plotly', 'pryr', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyselect', 'tibble'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

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

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Hmisc', 'RPostgres'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'stringr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'httptest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nardl', 'dynlm', 'AER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘magick’
Packages required but not available: 'ggplot2', 'reshape2', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MSEtool', 'dplyr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'lme4', 'geepack'
Packages required but not available:
  'dplyr', 'ggplot2', 'hrbrthemes', 'kableExtra', 'mice', 'purrr',
  'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'dbplyr', 'forecast', 'Hmisc', 'ppsr', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'stringr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) dma.Rd:47: Lost braces; missing escapes or markup?
    47 | When y_t is controlled, only y_{t-delay-1} and before 
       |                                ^
checkRd: (-1) dma.Rd:64: Lost braces; missing escapes or markup?
    64 |                  estimate of theta_{j-1} for model k at t}
       |                                    ^
checkRd: (-1) dma.Rd:66: Lost braces; missing escapes or markup?
    66 |                  variance of theta_{j-1} for model k at t}
       |                                    ^
checkRd: (-1) dma.Rd:68: Lost braces; missing escapes or markup?
    68 |                  estimate of theta_{j-1} at t}
       |                                    ^
checkRd: (-1) dma.Rd:70: Lost braces; missing escapes or markup?
    70 |                  variance of thetahat_{j-1} at t}
       |                                       ^
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'bayesplot', 'ggplot2', 'ggrepel'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) dca.Rd:24: Lost braces; missing escapes or markup?
    24 | \eqn{neglinks_{ij} = 1} means chunklet \code{i} and chunklet {j}
       |                                                              ^
checkRd: (-1) dca.Rd:26: Lost braces; missing escapes or markup?
    26 | \eqn{neglinks_{ij} = 0} means chunklet \code{i} and chunklet {j}
       |                                                              ^
checkRd: (-1) rca.Rd:57: Lost braces; missing escapes or markup?
    57 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |            ^
checkRd: (-1) rca.Rd:57: Lost braces; missing escapes or markup?
    57 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |                          ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'stringr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'igraph', 'purrr', 'tibble', 'tidyr', 'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'colourpicker', 'dbplyr', 'DiagrammeR', 'forcats', 'labelled',
  'nycflights13', 'odbc', 'pillar', 'pixarfilms', 'progress',
  'RMariaDB', 'RPostgres', 'RSQLite', 'testthat', 'waldo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test_vtrack.R’ [0s/1s]
Running the tests in ‘tests/test_vtrack.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'readxl', 'purrr', 'lubridate', 'tidyr', 'tibble',
  'progress'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gRaven', 'gRbase'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'testthis'
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'stringr', 'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'rvest', 'tidyr', 'tibble'

Packages suggested but not available for checking: 'httptest', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'GOstats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'network', 'ergm', 'sna', 'igraph', 'arm'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘OutliersO3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) beetle.Rd:13: Lost braces; missing escapes or markup?
    13 |     \item{\code{x}}{dose (log base 10 CS2mgl^{-1})}
       |                                              ^
Packages required but not available:
  'broom', 'cowplot', 'dplyr', 'ggplot2', 'modelr', 'pbkrtest',
  'tibble', 'tidyr'

Packages suggested but not available for checking:
  'geepack', 'lme4', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'textstem'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Package required but not available: ‘usethis’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘stringr’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘magick’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘roxygen2’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘roxygen2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'purrr', 'dplyr'

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

Packages suggested but not available for checking:
  'bench', 'dplyr', 'ggplot2', 'igraph', 'testthat', 'tidygraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'FrF2', 'DoE.wrapper'
Package which this enhances but not available for checking: ‘gurobi’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘FrF2’

Package suggested but not available for checking: ‘skpr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'ggplot2', 'ggthemes', 'igraph'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'tidyr', 'networkD3', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'lme4', 'testthat', 'car', 'dynlm', 'reshape2'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'dplyr', 'dominanceanalysis', 'forcats', 'ggplot2', 'lme4', 'purrr',
  'stringr', 'systemfit', 'testthat', 'tidyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘domir_basics.Rmd’ using rmarkdown

Quitting from lines 45-56 [unnamed-chunk-1] (domir_basics.Rmd)
Error: processing vignette 'domir_basics.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘domir_basics.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'dplyr'

Packages suggested but not available for checking:
  'stringr', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'igraph', 'concaveman', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
Packages required but not available:
  'dplyr', 'stringr', 'tibble', 'tidytext'

Packages suggested but not available for checking:
  'purrr', 'readr', 'rvest', 'sqldf', 'tidyr', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyselect', 'reshape2', 'tidyr', 'rvest', 'usethis', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) redisWorker.Rd:56: Lost braces; missing escapes or markup?
    56 | You can increase it by including a {timeout=n} argument value.
       |                                    ^
checkRd: (-1) startLocalWorkers.Rd:54: Lost braces; missing escapes or markup?
    54 | You can increase it by including a {timeout=n} argument value.
       |                                    ^
Packages required but not available: 'lme4', 'ggplot2', 'lmerTest'

Packages suggested but not available for checking: 'devtools', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'testthat', 'pkgmaker'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘doRNG.Rnw’ using knitr

Quitting from lines 20-21 [pkgmaker_preamble] (doRNG.Rnw)
Error: processing vignette 'doRNG.Rnw' failed with diagnostics:
there is no package called 'pkgmaker'
--- failed re-building ‘doRNG.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘optmatch’
Package suggested but not available for checking: ‘igraph’
Specified C++11: please drop specification unless essential
Packages required but not available:
  'ggplot2', 'purrr', 'stringr', 'DoseFinding', 'readxl', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'RBesT'

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

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'dplyr', 'ggplot2'

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

Package suggested but not available for checking: ‘gurobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
Found the following calls to attach():
File ‘doSNOW/R/doSNOW.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘optmatch’
Package suggested but not available for checking: ‘rms’
Error(s) in re-building vignettes:
  ...
--- re-building ‘dosresmeta.Rnw’ using knitr

Quitting from lines 330-331 [loading.rms] (dosresmeta.Rnw)
Error: processing vignette 'dosresmeta.Rnw' failed with diagnostics:
there is no package called 'rms'
--- failed re-building ‘dosresmeta.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘test_package.R’ [0s/1s]
Running the tests in ‘tests/test_package.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'roxygen2', 'testthat'
Running ‘run-all.R’ [0s/1s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > require("RhpcBLASctl"); omp_set_num_threads(1)
  Loading required package: RhpcBLASctl
  > # to address:
  > # * checking tests ... [10s/1s] NOTE
  > #   Running ‘run-all.R’ [10s/1s]
  > #   Running R code in ‘run-all.R’ had CPU time 10.5 times elapsed time
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) dot.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
Packages required but not available:
  'ggplot2', 'rmapshaper', 'purrr', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'wacolors'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyr', 'stringr', 'dplyr', 'ggplot2', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'patchwork', 'dplyr', 'stringr', 'ggstance', 'purrr'

Packages suggested but not available for checking: 'tibble', 'broom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'testthat', 'patrick', 'dplyr', 'AER'
Running ‘testthat_regression_tests.R’ [0s/0s]
Running the tests in ‘tests/testthat_regression_tests.R’ failed.
Complete output:
  > 
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
checkRd: (-1) PMLE.Weibull.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
checkRd: (-1) PMLE.Weibull.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
checkRd: (-1) PMLE.loglogistic.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
checkRd: (-1) PMLE.loglogistic.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
checkRd: (-1) PMLE.lognormal.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
checkRd: (-1) PMLE.lognormal.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'flexsurv', 'ggplot2', 'tidyverse', 'epicontacts', 'lubridate',
  'plotly', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'shinytest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'kableExtra', 'purrr', 'tibble', 'tidyr'

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'readr', 'bsplus', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rgbif’
checkRd: (-1) downscale.Rd:9: Lost braces; missing escapes or markup?
     9 | \item{occupancies}{Either a data frame containing two columns or an object of class \code{"upgrain"} from the \code{\link{upgrain}} function. If using a data frame the first column must be the grain sizes (cell area in squared units e.g. km^{2}). The second column is the proportion of occupancies at each grain size.}
       |                                                                                                                                                                                                                                                  ^
checkRd: (-1) ensemble.downscale.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
checkRd: (-1) hui.downscale.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{new.areas}{vector of grain sizes as cell area (in same units as cell.width but squared e.g. km^{2}) at fine scales for model prediction.}
       |                                                                                                      ^
checkRd: (-1) predict.downscale.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'alakazam', 'dplyr', 'ggtree', 'phangorn', 'shazam',
  'stringr', 'tidyselect', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'devtools'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘CEoptim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available:
  'exactci', 'ggplot2', 'ggpubr', 'stringr'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking: 'forecast', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyverse', 'tidyr', 'stringr'

Package suggested but not available for checking: ‘nycflights13’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'pillar', 'tibble', 'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'bench', 'broom', 'dbplyr', 'ggplot2', 'Lahman', 'nycflights13',
  'purrr', 'RSQLite', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'panelr', 'stringr', 'dplyr', 'jtools'

Packages suggested but not available for checking:
  'broom', 'tibble', 'testthat'

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

Packages suggested but not available for checking: 'devtools', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'nloptr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Packages required but not available: 'BayesianTools', 'purrr', 'parabar'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'DIZutils', 'DQAstats', 'lubridate', 'shinyFiles'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DIZutils', 'kableExtra'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'bench'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'stringr', 'vroom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'drc', 'devtools', 'roxygen2', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'tidyr', 'tibble', 'dplyr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dragracer-intro.Rmd’ using rmarkdown

Quitting from lines 18-22 [setup] (dragracer-intro.Rmd)
Error: processing vignette 'dragracer-intro.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building ‘dragracer-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘dragracer-intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'igraph', 'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'clustermq', 'disk.frame', 'ggplot2', 'ggraph', 'keras', 'lubridate',
  'networkD3', 'progress', 'styler', 'testthat', 'tibble', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'readr', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'highcharter', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'bsplus', 'stringr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
Packages required but not available: 'dplyr', 'tibble', 'readxl'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rstan', 'sde'

Packages suggested but not available for checking:
  'fda', 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'purrr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'drc', 'drcte', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'drc', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) logistic2_fn.Rd:34: Lost braces; missing escapes or markup?
    34 | This function allows values other than {0, 1, -1} for \code{alpha} and \code{delta} but
       |                                        ^
checkRd: (-1) loglogistic2_fn.Rd:35: Lost braces; missing escapes or markup?
    35 | This function allows values other than {0, 1, -1} for \code{alpha} and \code{delta} but
       |                                        ^
Running ‘spelling.R’ [0s/1s]
  Running ‘testdata.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘BMisc’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'dplyr', 'stringr', 'WGCNA', 'readr', 'tibble', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'tidyr', 'tidyselect'

Packages suggested but not available for checking: 'testthat', 'tibble'

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

Package suggested but not available for checking: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyverse’
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'DALEX', 'dplyr', 'tidyr', 'ingredients'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'tidyverse', 'dplyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'roxygen2'
Packages required but not available:
  'caret', 'GenomicFeatures', 'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Hsapiens.UCSC.hg38.knownGene', 'org.Hs.eg.db'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'mockery', 'testthat', 'tibble', 'vdiffr'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'DESeq2', 'ggplot2', 'ggfortify'

Packages suggested but not available for checking:
  'testthat', 'sva', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'ggsci'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'janitor', 'reshape2', 'stringr', 'tidyr', 'dplyr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'plotly', 'FCPS', 'ProjectionBasedClustering', 'DataVisualizations',
  'ggplot2', 'igraph', 'cccd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'cowplot', 'ggplot2', 'purrr', 'Seurat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'nloptr'
Running examples in ‘drtmle-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ci.adaptive_iptw
> ### Title: Confidence intervals for adaptive_iptw objects
> ### Aliases: ci.adaptive_iptw
> 
> ### ** Examples
> 
> # load super learner
> library(SuperLearner)
Loading required package: nnls
Loading required package: gam
Loading required package: splines
Loading required package: foreach
Loaded gam 1.22-3

Super Learner
Version: 2.0-29
Package created on 2024-02-06

> # fit adaptive_iptw
> set.seed(123456)
> n <- 200
> W <- data.frame(W1 = runif(n), W2 = rnorm(n))
> A <- rbinom(n, 1, plogis(W$W1 - W$W2))
> Y <- rbinom(n, 1, plogis(W$W1 * W$W2 * A))
> 
> fit1 <- adaptive_iptw(
+   W = W, A = A, Y = Y, a_0 = c(1, 0),
+   SL_g = c("SL.glm", "SL.mean", "SL.step"),
+   SL_Qr = "SL.glm"
+ )
Loading required package: nloptr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘nloptr’
Error in if (r$status < 1 || r$status > 4) { : 
  missing value where TRUE/FALSE needed
Calls: adaptive_iptw ... resolve.list -> signalConditionsASAP -> signalConditions
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_drtmle.Rmd’ using rmarkdown

Quitting from lines 524-532 [unnamed-chunk-5] (using_drtmle.Rmd)
Error: processing vignette 'using_drtmle.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘using_drtmle.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'purrr', 'stringr', 'plotly', 'eventPred'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'kableExtra', 'devtools'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'CDMConnector', 'dplyr', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'testthat', 'odbc', 'lubridate', 'tibble', 'PaRe', 'magick',
  'ggplot2', 'cowplot', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'doseminer', 'tidyr', 'sqldf', 'stringr', 'purrr',
  'DescTools'

Packages suggested but not available for checking: 'testthat', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'ChemmineR', 'rvest', 'tidyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CDMConnector', 'dbplyr', 'dplyr', 'lubridate', 'tidyr',
  'PatientProfiles', 'purrr', 'omopgenerics', 'visOmopResults'

Packages suggested but not available for checking:
  'testthat', 'odbc', 'RPostgres', 'CodelistGenerator', 'PaRe',
  'magick', 'ggplot2', 'cowplot', 'plotly', 'tibble'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GSVA', 'clusterProfiler', 'igraph', 'ChemmineR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'unikn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'nloptr', 'plotly'

Packages suggested but not available for checking:
  'devtools', 'emoji', 'pkgdown', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'nloptr', 'plotly'

Packages suggested but not available for checking:
  'devtools', 'emoji', 'pkgdown', 'roxygen2', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'tsoutliers', 'forecast', 'reshape2', 'seastests'

Package suggested but not available for checking: ‘stR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'cowplot'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘additional_topics.Rmd’ using rmarkdown
--- finished re-building ‘additional_topics.Rmd’

--- re-building ‘end_to_end_workflow.rmd’ using rmarkdown
--- finished re-building ‘end_to_end_workflow.rmd’

--- re-building ‘no_empty_drops.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dsb.Rcheck/vign_test/dsb/vignettes/no_empty_drops_files/figure-html/unnamed-chunk-3-1.png
720x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 32196 bytes
Input file size = 32310 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 27228
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 27228

Output IDAT size = 27228 bytes (4968 bytes decrease)
Output file size = 27306 bytes (5004 bytes = 15.49% decrease)

--- finished re-building ‘no_empty_drops.Rmd’

--- re-building ‘understanding_dsb.Rmd’ using rmarkdown

Quitting from lines 24-28 [unnamed-chunk-2] (understanding_dsb.Rmd)
Error: processing vignette 'understanding_dsb.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘understanding_dsb.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'stringr', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'ggplot2', 'kableExtra', 'lme4', 'patchwork', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sem', 'igraph'

Packages suggested but not available for checking:
  'AER', 'phylopath', 'dynlm', 'ggplot2', 'ggpubr', 'ggraph',
  'testthat'

Packages which this enhances but not available for checking:
  'rstan', 'tmbstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dssd', 'mrds', 'Distance', 'ggplot2', 'purrr', 'dplyr'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'tibble', 'tidyr', 'ggplot2', 'dplyr', 'testthat', 'forcats',
  'viridis'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DSjobtracker.Rmd’ using rmarkdown

Quitting from lines 62-63 [unnamed-chunk-5] (DSjobtracker.Rmd)
Error: processing vignette 'DSjobtracker.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building ‘DSjobtracker.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DSI', 'stringr'

Packages suggested but not available for checking:
  'dsBaseClient', 'mockery', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mrds', 'ggplot2'

Packages suggested but not available for checking: 'Distance', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'httr2', 'imager'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'opalr', 'DSI'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'exactci', 'asht'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'readr', 'stringr', 'tibble', 'tidyr',
  'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'tibble', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mcmcse', 'posterior'

Packages suggested but not available for checking:
  'cowplot', 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

Packages suggested but not available for checking:
  'igraph', 'tidyverse', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mixtools', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'epiR'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Hmisc', 'dplyr'

Packages suggested but not available for checking:
  'widgetframe', 'tidyr', 'rms'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'epiR', 'ggplot2', 'ggpubr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) DTDAcif.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) efron.petrosian.Rd:22: Lost braces
    22 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
checkRd: (-1) lynden.Rd:21: Lost braces
    21 |    \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                                ^
checkRd: (-1) shen.Rd:24: Lost braces
    24 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) extract-methods.Rd:105: Lost braces
   105 |   argument \code{what}.  For code{"["} the cutted object.
       |                                  ^
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) applied_crm.Rd:64: Lost braces; missing escapes or markup?
    64 | The empiric model is specified as F(d, beta) = d^{exp(beta)}. The logistic model is
       |                                                  ^
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'tibble', 'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'bench', 'testthat', 'tidyr', 'waldo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Mena.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:19: Lost braces in \itemize; meant \describe ?
Packages required but not available:
  'dplyr', 'stringr', 'tibble', 'tidyr', 'purrr'

Packages suggested but not available for checking:
  'tidyselect', 'devtools', 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tibble’
Packages required but not available:
  'dplyr', 'fgsea', 'igraph', 'tibble', 'tidyr', 'stringr'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_DTwrappers2.Rmd’ using knitr
Warning in eng_r(options) :
  Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.


Quitting from lines 20-21 [unnamed-chunk-2] (Introduction_to_DTwrappers2.Rmd)
Error: processing vignette 'Introduction_to_DTwrappers2.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘Introduction_to_DTwrappers2.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction_to_DTwrappers2.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) DTWUMI_1gap_imputation.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTWUMI_1gap_imputation.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTWUMI_1gap_imputation.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTWUMI_1gap_imputation.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTWUMI_1gap_imputation.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available: 'ggplot2', 'ggrepel'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'haven', 'readxl', 'readr', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dbplyr', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'arrow', 'DBItest', 'dbplyr', 'dplyr', 'testthat', 'tibble', 'vctrs'
Found the following significant warnings:
  duckdb/third_party/re2/re2/prog.h:153:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  duckdb/third_party/re2/re2/prog.h:431:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  duckdb/third_party/re2/re2/dfa.cc:124:25: warning: ISO C++ forbids flexible array member ‘next_’ [-Wpedantic]
  duckdb/third_party/re2/re2/onepass.cc:146:12: warning: ISO C++ forbids flexible array member ‘action’ [-Wpedantic]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/duckdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-25) 13.2.0’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'tibble', 'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'arrow', 'constructive', 'dbplyr', 'hms', 'lubridate', 'pillar',
  'purrr', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'ggmosaic', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'tidyverse', 'ggplot2', 'rstatix'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forcats', 'stringr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘igraph’

Packages suggested but not available for checking: 'testthat', 'dogesr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'tibble', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tab'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tsDyn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'mockery', 'readr', 'usethis', 'patrick', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘hglasso’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Seurat', 'dplyr', 'MAST'

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'purrr', 'ggplot2', 'readr', 'lubridate', 'imputeTS', 'greybox',
  'matlib', 'narray'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘drc’

Packages suggested but not available for checking:
  'eesim', 'ggplot2', 'dplyr', 'lubridate', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'simstandard', 'tidyr', 'ggplot2', 'tibble', 'patchwork',
  'stringr', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'googledrive', 'lubridate', 'tidyr', 'readr'

Packages suggested but not available for checking:
  'CoordinateCleaner', 'ggplot2', 'magick', 'testthat', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggforce', 'ggplot2', 'loo', 'patchwork', 'posterior', 'rstan',
  'tibble'

Packages suggested but not available for checking:
  'cmdstanr', 'dplyr', 'mice', 'testthat', 'tidyr'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'viridis', 'ari', 'gganimate'

Package suggested but not available for checking: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyverse', 'reshape2', 'tibble', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) predict.dynaTree.Rd:107: Lost braces
   107 |   For \code{coef} a new \R{XXc} field is created so as not to trample
       |                           ^
Package suggested but not available for checking: ‘readxl’
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'progress'

Packages suggested but not available for checking:
  'ggplot2', 'Hmisc', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dynutils', 'lmds', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'diffusionMap', 'igraph', 'lle', 'smacof'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DescTools', 'ggplot2', 'pec', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'dynutils', 'ggplot2', 'ggraph', 'ggrepel', 'GillespieSSA2',
  'igraph', 'lmds', 'patchwork', 'purrr', 'tibble', 'tidygraph',
  'tidyr', 'viridis'

Packages suggested but not available for checking:
  'dynwrap', 'Seurat', 'testthat'

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

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

Packages suggested but not available for checking:
  'devtools', 'usethis', 'testthat', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'plotly', 'dplyr', 'broom', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Produc.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:22: Lost braces in \itemize; meant \describe ?
Packages required but not available:
  'dplyr', 'dynutils', 'purrr', 'stringr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'reshape2', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'latex2exp', 'reshape2', 'mice', 'fda', 'car', 'tibble'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘DataCombine’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'stringr', 'tibble'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'babelwhale', 'dplyr', 'dynutils', 'dynparam', 'igraph', 'purrr',
  'readr', 'stringr', 'reshape2', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'dyndimred', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'gt', 'semPlot', 'stringr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DataCombine', 'ggplot2', 'accelerometry', 'hms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
GNU make is a SystemRequirements.
Running ‘eafplot.R’ [1s/1s]
  Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'shinyFiles', 'ggplot2', 'ggthemes', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) MHLS.Rd:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:55-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:75: Lost braces; missing escapes or markup?
    75 | From the initial values, \code{B0} and {S0}, \code{\link{MHLS}} draws \code{beta} and \code{subgrad} samples.
       |                                        ^
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'EpiEstim', 'epitrix', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'roxygen2', 'incidence', 'projections'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

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

Packages suggested but not available for checking: 'testthat', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggmap’

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'purrr', 'tidyr', 'dplyr', 'forcats', 'ggalluvial', 'ggplot2',
  'ggridges', 'recipes', 'stringr', 'tibble', 'progress'

Packages suggested but not available for checking:
  'testthat', 'nycflights13', 'vdiffr', 'pkgdown', 'workflows',
  'furrr', 'caret', 'parsnip', 'vip'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BDgraph', 'BGGM', 'dplyr', 'ggplot2', 'igraph', 'qgraph'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'vctrs', 'pillar', 'dplyr', 'tidyr', 'stringr'

Packages suggested but not available for checking: 'posterior', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘example_table1.csv’ ‘example_table1.txt’ ‘example_table2.csv’
  ‘example_table2.txt’ ‘example_table3.csv’ ‘example_table3.txt’
  ‘table1.csv’ ‘table2.csv’ ‘table2.txt’ ‘table3.txt’ ‘table4.txt’
Packages suggested but not available for checking:
  'RMariaDB', 'RPostgres', 'RSQLite', 'testthat'
Packages required but not available: 'rcompanion', 'FSA', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'annotate', 'diffcoexp', 'geneExpressionFromGEO', 'GEOquery',
  'jetset'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'plotly'

Packages suggested but not available for checking:
  'AnnotationDbi', 'org.Hs.eg.db', 'qvalue'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ArrayToNc.Rd:30-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ArrayToNc.Rd:39-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ArrayToNc.Rd:51-76: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘devtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'Hmisc', 'lubridate', 'readxl', 'stringr'

Packages suggested but not available for checking: 'testthat', 'readxlsb'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SSBtools', 'sdcTable'

Packages suggested but not available for checking: 'RegSDC', 'testthat'

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

Packages suggested but not available for checking:
  'DHARMa', 'glmmTMB', 'mockery', 'patchwork', 'testthat'

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

Package suggested but not available for checking: ‘randomcoloR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'readxl'

Package which this enhances but not available for checking: ‘gurobi’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘minimal_example.Rmd’ using rmarkdown
--- finished re-building ‘minimal_example.Rmd’

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

--- re-building ‘use_case_pilot_study.Rmd’ using rmarkdown

Quitting from lines 42-45 [import items] (use_case_pilot_study.Rmd)
Error: processing vignette 'use_case_pilot_study.Rmd' failed with diagnostics:
there is no package called 'readxl'
--- failed re-building ‘use_case_pilot_study.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘RSQLite’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'eatDB', 'haven', 'tibble', 'hms'

Packages suggested but not available for checking: 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.