'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.eff.ridge.Rd:6: Lost braces
     6 |  emph{Single Interior Knot} at the MSE Optimal m-Extent of Shrinkage. The
       |      ^
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ZigZagLogistic.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                   ^
checkRd: (-1) ZigZagLogistic.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                                 ^
checkRd: (-1) ZigZagLogistic.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{dataY}{Vector of length n containing {0, 1}-valued observations of the dependent variable y.}
       |                                            ^
checkRd: (-1) ciReg.Rd:10: Lost braces
    10 | \item{fit}{an object of class{lm}, i.e. the output from \code{\link{lm}}.}
       |                              ^
Specified C++14: please drop specification unless essential
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) sim_setup_preconfigured.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:31: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) sf_get_all_jobs_bulk.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_jobs_bulk.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_query_jobs_bulk.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_query_jobs_bulk.Rd:45-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_query_jobs_bulk.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) valid_metadata_list.Rd:10: Lost braces
    10 | code{list}; contains name and valid inputs for data types
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) binaryChoice.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:111: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:113: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:114: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
checkRd: (-1) ModelHMMR-class.Rd:37: Lost braces; missing escapes or markup?
    37 |         class {StatHMMR}).
       |               ^
Package suggested but not available for checking: ‘networkTomography’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) gen.ds.Rd:43-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gen.ds.Rd:50-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gen.ds.Rd:64-65: Lost braces
    64 |    \item{the dependence parameter \code{dep} or the vector of dependence parameters \code{dep}. When missing, these coefficients are obtained from independent standard uniform sampling.
       |         ^
checkRd: (-1) gen.ds.Rd:66: Lost braces
    66 |    \item{the list \code{asy} of asymmetric weights \eqn{\beta_{i,b}} for \eqn{b \in B}  and \eqn{i \in b}. When missing, these coefficients are obtained from independent standard uniform sampling followed by renormalization in order to satisfy the sum-to-one constraints.}
       |         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) OTC.Rd:42: Lost braces; missing escapes or markup?
    42 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
checkRd: (-1) OTC.Rd:83: Lost braces; missing escapes or markup?
    83 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
checkRd: (-1) OTHist.Rd:29: Lost braces; missing escapes or markup?
    29 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
checkRd: (-1) dOTC.Rd:72: Lost braces; missing escapes or markup?
    72 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) setData.ReducedRankRegressions.Rd:14-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setData.ReducedRankRegressions.Rd:17-18: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
License stub is invalid DCF.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) get.events.Rd:51: Lost braces
    51 |   code{\link[deSolve]{events}}
       |       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) scatterD3.Rd:209: Lost braces; missing escapes or markup?
   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       | ^
checkRd: (-1) scatterD3.Rd:209: Lost braces
   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       |                                              ^
checkRd: (-1) PermBiclust.beta.ks.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.beta.ks.Rd:30: Lost braces
    30 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
checkRd: (-1) PermBiclust.sigclust.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.sigclust.Rd:33: Lost braces
    33 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
checkRd: (-1) PermBiclust.sigclust_stop.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.sigclust_stop.Rd:36: Lost braces
    36 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_profile.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) schoRsch.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:45: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) reduce_dimensionality.Rd:19: Lost braces
    19 | \item{ndim}{the maximum dimension of the space which the data are to be represented in; must be in {1, 2, \ldots, n-1}.}
       |                                                                                                    ^
checkRd: (-1) ti_scorpius.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{distance_method}{A character string indicating which correlationcoefficient (or covariance) is to be computed. One of "pearson", "spearman" (default), or "cosine". Domain: {spearman, pearson, cosine}. Default: spearman. Format: character.}
       |                                                                                                                                                                                   ^
checkRd: (-1) ti_scorpius.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{smoother}{\code{principal_curve} parameter; choice of smoother. Domain: {smooth_spline, lowess, periodic_lowess}. Default: smooth_spline. Format: character.}
       |                                                                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
checkRd: (-1) scriptloc.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Get location of script in a fashion analagous to ${BASH_SOURCE[0]}}
       |                                                          ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘untitled_consensus_cluster’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                  ^
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                                         ^
checkRd: (-1) geom_flat_violin.Rd:7: Lost braces
     7 | url{https://gist.github.com/dgrtwo/eb7750e74997891d7c20}
       |    ^
checkRd: (-1) sda.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sdc_extabs.Rd:59: Lost braces
    59 | (including ]code{forcelist} variables) that can be used to form tables.}
       |                 ^
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
checkRd: (-1) msdpd.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hyperpar.Rd:17: Lost braces
    17 | \item{c}{denotes the expected range of eqn{f} .}
       |                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) seas.check.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:58: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) seedCCA.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{u}{numeric, maximum number of projections. The default is 10. This is used for \code{type="seed1"}, \code{type="seed2"} and {tyepe="pls"}.}
       |                                                                                                                                   ^
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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) convert2snafu.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) correct.changes.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) textcleaner.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) textcleaner.Rd:100-101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:116: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:119: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:130: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) append.dictionary.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:44-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:89-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:95-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NRW.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NRW.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.compareShiny.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.compareShiny.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.compareShiny.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PAVranking.Rd:77-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:80-82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:83-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sendmail_options.Rd:32-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:38-39: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) match_dataphy.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_dataphy.Rd:39-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_dataphy.Rd:42-44: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                               ^
checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                                                          ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                              ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                                                     ^
Found the following files/directories:
  ‘assocpointpair_result.csv’ ‘foundereffectfinder_result.csv’
  ‘getfreqs_result.csv’ ‘getfreqs_result.png’ ‘orPlot.pdf1_1.pdf’
  ‘orPlot.pdf2_1.pdf’ ‘orPlot.pdf3_1.pdf’ ‘orPlot.pdf4_1.pdf’
  ‘orPlot.pdf5_1.pdf’ ‘orPlot.pdf6_1.pdf’ ‘orPlot.pdf7_1.pdf’
  ‘orPlot.pdf8_1.pdf’ ‘q-values_result.csv’ ‘rewritetuple_result.csv’
  ‘tartan_plot.pdf’ ‘vispair_plot.pdf’ ‘vispairfeat_plot.pdf’
  ‘volcano_plot.pdf’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BPCells’
Packages suggested but not available for checking: 'BPCells', 'presto'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bisee.Rd:127: Lost braces
   127 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) hisee.Rd:101: Lost braces
   101 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) isee.Rd:116: Lost braces
   116 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) see.Rd:98: Lost braces
    98 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                   ^
checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) changept.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) changept.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) changept.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:32-33: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCOSA’
Package unavailable to check Rd xrefs: ‘rCOSA’
Package suggested but not available for checking: ‘hydromad’
checkRd: (-1) age_corr.Rd:15: Lost braces
    15 | \item{plot}{Should the results be plotted? (/code{TRUE/FALSE})}
       |                                                  ^
checkRd: (-1) age_corr.Rd:17: Lost braces
    17 | \item{agecorrection}{Correct for jumps in age (/code{TRUE}) or
       |                                                     ^
checkRd: (-1) age_corr.Rd:18: Lost braces
    18 | only for starting time (/code{FALSE})}
       |                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) shiftrPrepare.Rd:37: Lost braces
    37 |     See code{\link{shiftrPermBinary}} function and the respective example.
       |             ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) js_calls.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pickCheckboxNamesAndLabels.Rd:14: Lost braces
    14 | \item{choices}{link{pickCheckboxInput} choices list.}
       |                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) display.Rd:17: Lost braces; missing escapes or markup?
    17 | div which wraps your message to display it in the {position} corner of your shiny app.
       |                                                   ^
checkRd: (-1) info_value.Rd:15: Lost braces; missing escapes or markup?
    15 | div which wraps rendered value to display it in the {position} corner of your shiny app.
       |                                                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) shinyjs-defunct.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shinyjs-defunct.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shinyjs-defunct.Rd:20: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) store_googledrive.Rd:19: Lost braces; missing escapes or markup?
    19 | See the {gargle} package to manage authentication, and especially
       |         ^
checkRd: (-1) store_googledrive.Rd:20: Lost braces; missing escapes or markup?
    20 | \href{https://gargle.r-lib.org/articles/articles/managing-tokens-securely.html}{this vignette from {gargle} package} to manage the process.
       |                                                                                                    ^
checkRd: (-1) custom-labels.Rd:7: Lost braces; missing escapes or markup?
     7 | \title{Modify {shinymanager} labels to use custom text}
       |               ^
checkRd: (-1) use_language.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Use {shinymanager} labels}
       |            ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘uchardet’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘uchardet’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) shiny_pivot_table.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:64: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) addValidationSuffix.Rd:13: Lost braces; missing escapes or markup?
    13 | A string `"{tagId}-shinyreforms-validation"`.
       |            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
checkRd: (-1) add_class.Rd:18: Lost braces; missing escapes or markup?
    18 | Custom function for adding a CSS class used in {shinysurveys}.
       |                                                ^
checkRd: (-1) disable_element.Rd:16: Lost braces; missing escapes or markup?
    16 | Custom function for disabling an HTML element in {shinysurveys}.
       |                                                  ^
checkRd: (-1) enable_element.Rd:16: Lost braces; missing escapes or markup?
    16 | Custom function for disabling an HTML element in {shinysurveys}.
       |                                                  ^
checkRd: (-1) extendInputType.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{extension}{A shiny input type not natively supported by {shinysurveys}. See the examples section for more information.}
       |                                                               ^
checkRd: (-1) getSurveyData.Rd:15: Lost braces; missing escapes or markup?
    15 | default, and the built-in {shinysurveys} userID will be used.}
       |                           ^
checkRd: (-1) radioMatrixInput.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{...}{Additional arguments specific to {shinysurveys} required questions.}
       |                                             ^
checkRd: (-1) remove_class.Rd:18: Lost braces; missing escapes or markup?
    18 | Custom function for removing a CSS class used in {shinysurveys}.
       |                                                  ^
checkRd: (-1) toggle_element.Rd:18: Lost braces; missing escapes or markup?
    18 | Custom function for toggling enable/disable state of HTML element in {shinysurveys}.
       |                                                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) run_shinytitle_example.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) run_shinytitle_example.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MrBayes.Rd:24: Lost braces
    24 | \item{contype}{A character string; the type of consensus tree calculated from the posterior distribution of trees}{either "halfcompat" (majority-rule consensus tree) or "allcombat" (strict consensus tree)}
       |                                                                                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) shutterplot.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.'
       |                       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) pop.dist.Rd:41: Lost braces; missing escapes or markup?
    41 | where \emph{dist(i,j)} represents the distance between populations \emph{i} and \emph{j}, \emph{m} and \emph{n} are the number of sequences in populations \emph{i} and \emph{j}, respectively, and \emph{dist(H_{ki},H_{lj})} is the distance between the \emph{k-th} sequence found in population \emph{i} and the \emph{l-th} sequence found in population \emph{j}. 
       |                                                                                                                                                                                                                  ^
checkRd: (-1) pop.dist.Rd:41: Lost braces; missing escapes or markup?
    41 | where \emph{dist(i,j)} represents the distance between populations \emph{i} and \emph{j}, \emph{m} and \emph{n} are the number of sequences in populations \emph{i} and \emph{j}, respectively, and \emph{dist(H_{ki},H_{lj})} is the distance between the \emph{k-th} sequence found in population \emph{i} and the \emph{l-th} sequence found in population \emph{j}. 
       |                                                                                                                                                                                                                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) drr.Rd:36: Lost braces; missing escapes or markup?
    36 |   \code{drr} {is Rosin - Rammler probability density function}\cr
       |              ^
checkRd: (-1) drr.Rd:37: Lost braces; missing escapes or markup?
    37 |   \code{urr} {is Rosin - Rammler cumulative distribution function (CDF) representing undersize mass fraction}\cr
       |              ^
checkRd: (-1) drr.Rd:38: Lost braces
    38 |   \code{orr} {is Rosin - Rammler complementary CDF representing oversize mass fraction ie. relative remainder on the sieve with the mesh size \code{x}}\cr
       |              ^
Specified C++11: please drop specification unless essential
checkRd: (-1) add_k_mer_state.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) sig.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
Found the following files/directories:
  ‘ExportFigtree1.tre’
checkRd: (-1) siland.Rd:64: Lost braces; missing escapes or markup?
    64 | \item x_{l,i}, local variable l,
       |         ^
checkRd: (-1) siland.Rd:70: Lost braces; missing escapes or markup?
    70 | \item d_{r,i} the distance between the center of pixel r and the observation at site i.
       |         ^
checkRd: (-1) inlandwaters.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_Y_Binary_X.Rd:51: Lost braces
    51 |     \item \code{dist = "binomial"} is drawn from eqn{Bin(XB, XB(1-XB))}
       |                                                     ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) create_modelDF.Rd:25-38: Lost braces
    25 | convert_xlsx_to_csv<-function(xlsx_file){
       |                                         ^
checkRd: (-1) create_modelDF.Rd:33-36: Lost braces
    33 |   for (i in Sheetnames) {
       |                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
checkRd: (-1) internal.statistics.one.lm.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) internal.statistics.one.lm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
checkRd: (-1) coxsimSpline.Rd:93: Lost braces; missing escapes or markup?
    93 | {FD(h[i](t)) = (exp(g(x[j]) - g(x[l])) - 1) * 100}
       | ^
checkRd: (-1) simPH.Rd:16-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:20-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:25-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:34-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:50-53: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) SimDataDist-class.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SimDataDist-class.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) createData.Rd:7: Lost braces
     7 |         This function can be used to create data from a set of parameters created from \code{\link{draw}}, called a code{paramSet}. This function is used internally to create data, and is available publicly for accessibility and debugging.
       |                                                                                                                         ^
checkRd: (-1) exportData.Rd:7: Lost braces
     7 |         This function can be used to export data created from a set of parameters created from \code{\link{draw}}, called a code{paramSet}. This function can export data to be analyzed with either Mplus or LISREL.
       |                                                                                                                                 ^
Package suggested but not available for checking: ‘INLA’
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
checkRd: (-1) make_one_dataset.Rd:67: Lost braces; missing escapes or markup?
    67 |  \code{within.SD} to be extremely small (e.g., $1 * 10^{-7}$) and all corresponding correlations in matrix
       |                                                        ^
checkRd: (-1) add_bold.Rd:15: Lost braces; missing escapes or markup?
    15 | For example, in latex it would take "2" and output "{\\bf 2}"; in html
       |                                                     ^
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) sitar-package.Rd:27: Lost braces; missing escapes or markup?
    27 | individual curves, adjusted for {abcd} to lie on top of (i.e. be
       |                                 ^
checkRd: (-1) sitar.Rd:110: Lost braces; missing escapes or markup?
   110 | \code{\link{nlme}}) (default {nlmeControl(returnObject = TRUE)}).}
       |                              ^
checkRd: (-1) rawCCD.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{distr.type}{school district type (constructed for illustration purposes; (values={"A", "B", "C", "D"})).}
       |                                                                                          ^
checkRd: (-1) selectMatch.Rd:61: Lost braces; missing escapes or markup?
    61 | \item{replacementUnitsFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "replacementUnits.csv"}
       |                                                                    ^
checkRd: (-1) selectMatch.Rd:63: Lost braces; missing escapes or markup?
    63 | \item{subUnitTableFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "subUnitTable.csv"}
       |                                                                ^
checkRd: (-1) selectMatch.Rd:66: Lost braces; missing escapes or markup?
    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                  ^
checkRd: (-1) selectMatch.Rd:66: Lost braces; missing escapes or markup?
    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                                                                                  ^
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ss.cc.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ss.ci.Rd:26: Lost braces
    26 | \item{alpha}{The eqn{\\alpha} error used to compute the \eqn{100*(1-\\alpha)\%} confidence interval}
       |                     ^
checkRd: (-1) ss.rr.Rd:84: Lost braces; missing escapes or markup?
    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |     ^
checkRd: (-1) ss.rr.Rd:84: Lost braces; missing escapes or markup?
    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |                 ^
checkRd: (-1) ss.rr.Rd:87: Lost braces; missing escapes or markup?
    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                            ^
checkRd: (-1) ss.rr.Rd:87: Lost braces; missing escapes or markup?
    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                                        ^
Package which this enhances but not available for checking: ‘kmndirs’
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) outliers.hdts.Rd:44: Lost braces; missing escapes or markup?
    44 |   \item I.cov.rob - The matrix (V'GnV)^{-1} used to compute the statistics to detect the idiosyncratic outliers.
       |                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘captioner’
checkRd: (-1) nba_team_logo.Rd:22: Lost braces; missing escapes or markup?
    22 | https://i.cdn.turner.com/nba/nba/.element/img/4.0/global/logos/512x512/bg.white/svg/{team_short_name}.svg
       |                                                                                     ^
checkRd: (-1) fit_slim.Rd:24: Lost braces; missing escapes or markup?
    24 | sum(x' V^{-1} (y - x beta)) = 0 as the covariance V tends from V[, , 1] +
       |          ^
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) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
GNU make is a SystemRequirements.
checkRd: (-1) cities_lon_lat.Rd:6: Lost braces
     6 | A subset of world.cities{maps}. Extracted in order to shink number of dependencies. 
       |                         ^
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) trlong.Rd:17: Lost braces
    17 |     \item{\code{resp}}{a factor indicating the transport mode choice, and \code{B} denotes taking the bus, code{D} denotes driving one's own vehicle, \code{F} denotes getting a ride with a friend, \code{O} denotes other, and \code{W} denotes walking}
       |                                                                                                                ^
checkRd: (-1) smdocker_log.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:35-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                  ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                            ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                          ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                                    ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                              ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                        ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                      ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) SMMA.Rd:115: Lost braces
   115 |  is the empirical explained variance from \cite{Meinshausen and B{u}hlmann, 2015}.  See \cite{Lund et al., 2020} for more details and references.
       |                                                                  ^
checkRd: (-1) SMMA.Rd:170: Lost braces
   170 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
Specified C++11: please drop specification unless essential
checkRd: (-1) estimMk.Rd:44: Lost braces; missing escapes or markup?
    44 | estimMk returns the transition probability matrix of size (S^{k})xS (with S = length(E)) 
       |                                                              ^
Specified C++11: please drop specification unless essential
checkRd: (-1) getKernel.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getKernel.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smoof_function.Rd:10: Lost braces
    10 | or code{smoof_multi_objective_function}. Both single- and multi-objective functions share the following attributes.
       |        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) hoods2dsmooth.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dmeitsjer.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dsmooth.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) smoothie-package.Rd:42: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) smoothtail-package.Rd:63: Lost braces
    63 | Kaspar Ru{f}{i}bach (maintainer), \email{kaspar.rufibach@gmail.com} , \cr \url{http://www.kasparrufibach.ch}
       |          ^
checkRd: (-1) smoothtail-package.Rd:63: Lost braces
    63 | Kaspar Ru{f}{i}bach (maintainer), \email{kaspar.rufibach@gmail.com} , \cr \url{http://www.kasparrufibach.ch}
       |             ^
Problems with news in ‘NEWS.md’:
No news entries found.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
Found the following files/directories:
  ‘my_new_social_media_plot.png’
checkRd: (-1) SnakesAndLaddersGame.Rd:25: Lost braces; missing escapes or markup?
    25 | {Hector Haffenden} {haffendenh@cardiff.ac.uk}
       |                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                  ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                           ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                                      ^
checkRd: (-1) sk_GLS.Rd:40: Lost braces; missing escapes or markup?
    40 | Operations with V^{-1} are computed using the factorization \code{fac} (see \code{sk_var}), or
       |                   ^
checkRd: (-1) sk_LL.Rd:37: Lost braces; missing escapes or markup?
    37 | \code{quad_form} is z^T V^{-1} z, for the observed response vector z, which is constructed
       |                           ^
checkRd: (-1) sk_var.Rd:41: Lost braces; missing escapes or markup?
    41 | returns the quadratic form X^T V^{-1} X.
       |                                  ^
checkRd: (-1) sk_var.Rd:33: Lost braces; missing escapes or markup?
    33 | either matrix \code{V}, or X^T V^{-1} X, or a factorization ('chol' or 'eigen')
       |                                  ^
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) knockoffGenotypes.Rd:32: Lost braces; missing escapes or markup?
    32 | This function efficiently constructs group-knockoffs of {0,1,2} variables distributed
       |                                                         ^
checkRd: (-1) knockoffGenotypes.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{X}{a {0,1,2} matrix of size n-by-p containing the original variables.}
       |            ^
checkRd: (-1) knockoffGenotypes.Rd:29: Lost braces; missing escapes or markup?
    29 | A {0,1,2} matrix of size n-by-p containing the knockoff variables.
       |   ^
checkRd: (-1) maize.line.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maize.line.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maize.line.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maize.line.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) raw.data.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{call.rate}{\code{numeric}. Threshold for removing marker by missing genotype rate. SNP with \code{call rate} below threshold are removed from dataset. Must be between {0, 1}}
       |                                                                                                                                                                              ^
checkRd: (-1) raw.data.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{maf}{Threshold for removing SNP by minor allele frequency. Must be between {0, 1}}
       |                                                                                  ^
checkRd: (-1) plot.selm.Rd:101: Lost braces
   101 | data. Default value for code{which} is \code{2:4} if \code{p>1}, otherwise
       |                             ^
Found the following calls to attach():
File ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘.R_Test’
'LazyData' is specified without a 'data' directory
checkRd: (-1) map.active.Rd:82: Lost braces
    82 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.add.Rd:99: Lost braces
    99 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.csa.mca.Rd:35: Lost braces
    35 | \link{soc.csa}, \link{map.csa.all}, link{map.csa.mca.array}
       |                                         ^
checkRd: (-1) map.ctr.Rd:85: Lost braces
    85 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.ind.Rd:80: Lost braces
    80 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.mod.Rd:82: Lost braces
    82 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.sup.Rd:82: Lost braces
    82 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                          ^
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                                                        ^
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                                                                     ^
checkRd: (-1) s_soda_pred.Rd:8: Lost braces; missing escapes or markup?
     8 | S-SODA assumes within each slice the X vector follow multivariate normal distribution. This function predicts the response y by reverting the P(X | slice(y)) to P(slice(y) | X), and estimates the E(y|X) as sum_{h} E(y | slice(y)=h, X) P (slice(y)=h | X)
       |                                                                                                                                                                                                                   ^
checkRd: (-1) db_compact.Rd:41: Lost braces; missing escapes or markup?
    41 | database structure will be set to true. See GET /{db}. You can also obtain a list of
       |                                                  ^
Running examples in ‘soilassessment-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: depthharm
> ### Title: A function for harmonizing soil property between uniform depth
> ###   intervals in observation pits
> ### Aliases: depthharm
> 
> ### ** Examples
> 
> library(aqp)
This is aqp 2.1.0
> library(plyr)
> library(sp)

Attaching package: ‘sp’

The following objects are masked from ‘package:aqp’:

    coordinates, coordinates<-, proj4string, proj4string<-

> x=c(rep(2.12,4),rep(2.05,4))
> y=c(rep(9.34,4),rep(8.17,4))
> pit=c(rep(1,4),rep(2,4))
> depthcode=c(1,2,3,4,1,2,3,4)
> upper=c(0,18,25,35,0,12,33,50)
> lower=c(10,25,35,67,12,33,50,100)
> pH=c(6.7,5.5,5.1,6.7,6.4,5.8,5.3,5.0)
> df=data.frame(pit,x,y,upper,lower,depthcode,pH)
> lat=df$x;lon=df$y;id=df$pit;top=df$upper;
> bottom=df$lower;horizon=df$depthcode;Varn=df$pH
> 
> soildata <- join(data.frame(id, top, bottom, Varn, horizon),
+               data.frame(id, lat, lon), type='inner')
Joining by: id
> depths(soildata) <- id ~ top + bottom
> site(soildata) <- ~ lat + lon
> coordinates(soildata) <- ~ lat + lon
Error: unable to find an inherited method for function ‘coordinates<-’ for signature ‘object = "SoilProfileCollection"’
Execution halted
Error loading dataset 'gopheridge':
   Error in .requirePackage(package) : unable to find required package 'sp'
  
  Error loading dataset 'loafercreek':
   Error in .requirePackage(package) : unable to find required package 'sp'
  
  Error loading dataset 'mineralKing':
   Error in .requirePackage(package) : unable to find required package 'sp'
  
  The dataset(s) may use package(s) not declared in Depends/Imports.
checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) solr_mlt.Rd:70: Lost braces; missing escapes or markup?
    70 | TermVector DEFAULT_FIELD_NAMES = new String[] {"contents"}
       |                                               ^
checkRd: (-1) solve_pH_from_AT.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:93: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) spe.Rd:101: Lost braces
   101 | code{spe} command; (4) \code{alpha} stores significance level as in
       |     ^
checkRd: (-1) load_sorvi_data.Rd:23: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
Unknown packages ‘persp3D’, ‘colkey’, ‘gm.prcomp’, ‘summary.gm.prcomp’, ‘plot.gm.prcomp’, ‘spectro’ in Rd xrefs
Package suggested but not available for checking: ‘gridlayout’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘NLMR’
Package suggested but not available for checking: ‘NLMR’
'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) sdf_unnest.Rd:20: Lost braces
    20 | \code{a1, a2, a3}, then code{sdf_explode(df, a)} will produce output with each record replicated
       |                             ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) counterfactual_yhat.Rd:47: Lost braces; missing escapes or markup?
    47 | We want the counterfactual Yhat_{g' <- G} |X=x,G=g (or alternatively
       |                                 ^
checkRd: (-1) counterfactual_yhat.Rd:48: Lost braces; missing escapes or markup?
    48 | Yhat_{g' <- G} |G=g).
       |      ^
checkRd: (-1) counterfactual_yhat.Rd:58: Lost braces; missing escapes or markup?
    58 | To estimate Y'=Yhat_{g' <- G} | G=g, we need to
       |                     ^
checkRd: (-1) counterfactual_yhat.Rd:65: Lost braces; missing escapes or markup?
    65 | To estimate Y'=Yhat_{g' <- G} |X=x, G=g, we need to
       |                     ^
checkRd: (-1) counterfactual_yhat.Rd:27: Lost braces; missing escapes or markup?
    27 | indices representing sample(s) from counterfactual  Yhat_{g' <- G} |X=x,G=g
       |                                                          ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
checkRd: (-1) Coord.to.Pointers.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{triangle=TRUE}{Input \code{rows} and {cols} represent lower
       |                                            ^
checkRd: (-1) Coord.to.Pointers.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{triangle=FALSE}{Input \code{rows} and {cols} represent a full
       |                                             ^
checkRd: (-1) cholsolveAQinvAT.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Solve the equation X = AQ^{-1}t(A) under permutations}
       |                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |    ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |             ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                      ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                   ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                            ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.sparsereg.Rd:22-23: Lost braces
    22 | \env{main1, main2, main3}{
       |                          ^
checkRd: (-1) plot.sparsereg.Rd:25-27: Lost braces
    25 | \env{xlabel}{
       |             ^
checkRd: (-1) plot.sparsereg.Rd:29-31: Lost braces
    29 | \env{plot.one}{
       |               ^
checkRd: (-1) summary.sparsereg.Rd:27-29: Lost braces
    27 | \env{interval}{
       |               ^
checkRd: (-1) summary.sparsereg.Rd:31-33: Lost braces
    31 | \env{ci}{
       |         ^
checkRd: (-1) summary.sparsereg.Rd:35-37: Lost braces
    35 | \env{order}{
       |            ^
checkRd: (-1) summary.sparsereg.Rd:39-41: Lost braces
    39 | \env{normal}{
       |             ^
checkRd: (-1) summary.sparsereg.Rd:43-45: Lost braces
    43 | \env{select}{
       |             ^
checkRd: (-1) summary.sparsereg.Rd:47-48: Lost braces
    47 | \env{printit}{
       |              ^
checkRd: (-1) summary.sparsereg.Rd:50-52: Lost braces
    50 | \env{stage}{
       |            ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) SpatialBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SpatialBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SpatialBSS-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SpatialBSS-package.Rd:28: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) distSG.Rd:40: Lost braces; missing escapes or markup?
    40 |   matrix and weight matrix (plus a matrix with {eID} identifiers
       |                                                ^
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', 'spatstat', 'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.univar',
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.sparse',
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
checkRd: (-1) NEWS.Rd:137: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘spDataLarge’
Package suggested but not available for checking: ‘rgeoda’
checkRd: (-1) findRef.Rd:39: Lost braces
    39 | Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemi\`{e}re F, Verschoren A, Goethals B, Laukens K. (2011) An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics. 2011 Oct 20;12:405.
       |                                                              ^
checkRd: (-1) hClustAlign.Rd:70: Lost braces
    70 | Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemi\`{e}re F, Verschoren A, Goethals B, Laukens K. (2011) An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics. 2011 Oct 20;12:405.
       |                                                              ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
checkRd: (-1) FitAkdParameters.Rd:23: Lost braces; missing escapes or markup?
    23 |       p(y|ens) = 1 / K * sum {dnorm(y, z.i, s)} \cr
       |                              ^
checkRd: (-1) australia.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) australia.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) australia.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) australia.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) australia.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) speech_recompiler.Rd:25: Lost braces; missing escapes or markup?
    25 | The default compilation is that of \ code {speech_build (., compiler = TRUE}).
       |                                           ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.neig’
Specified C++11: please drop specification unless essential
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
    61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc}, 
       |                                                   ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) adaptIntegrateSpherePolar.Rd:14: Lost braces
    14 | code{adaptIntegrateBallPolar()} will likely miss these abrupt changes and give
       |     ^
Found the following files/directories:
  ‘AlphaGA_3.txt’ ‘AlphaML_3.txt’ ‘BetaGA_3.txt’ ‘BetaML_3.txt’
  ‘Performance_GA_ML_ 3 .pdf’ ‘SPIGA_3Pmon.Pm_St1.pdf’
  ‘SPIGA_3Pmon.Pm_St2.pdf’ ‘SPI_AG_3.txt’ ‘SPI_ML_3.txt’
  ‘SPI_ML_3Pm_St1.pdf’ ‘SPI_ML_3Pm_St2.pdf’ ‘SPI_ML_3Pm_St3.pdf’
  ‘SPI_ML_3Pm_St4.pdf’ ‘SPI_PARAM_3.txt’ ‘SPI_PARAM_3Pm_St1.pdf’
  ‘SPI_PARAM_3Pm_St2.pdf’ ‘SPI_PARAM_3Pm_St3.pdf’
  ‘SPI_PARAM_3Pm_St4.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) speedtestdata.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ds_aat.Rd:16: Lost braces
    16 | \doi{10.1111/add.14071}{Boffo et al., 2018}. Participants were presented stimuli from a "test"
       |                        ^
checkRd: (-1) ds_gng.Rd:16: Lost braces
    16 | described in detail in \doi{10.1016/j.tate.2019.102887}{Hedge, Powell, and Sumner (2018)}. 
       |                                                        ^
checkRd: (-1) ds_iat.Rd:19: Lost braces
    19 | \doi{10.1016/j.tate.2019.102887}{Abacioglu and colleagues (2019)}. 
       |                                 ^
checkRd: (-1) ds_rapi.Rd:15: Lost braces
    15 | problems within the last year (\doi{https://doi.org/10.15288/jsa.1989.50.30}{White & Labouvie, 1989}).
       |                                                                             ^
checkRd: (-1) ds_sst.Rd:17: Lost braces
    17 | described in detail in \doi{10.1016/j.tate.2019.102887}{Hedge, Powell, and Sumner (2018)}. 
       |                                                        ^
checkRd: (-1) ds_vpt.Rd:22: Lost braces
    22 | \doi{10.1111/acer.12853}{(Pronk, Deursen, Beraha, Larsen, & Wiers, 2015)}.
       |                         ^
checkRd: (-1) splithalfr.Rd:15: Lost braces
    15 |   \item \code{vignette("rapi_sum")} Sum-score for data of the 23-item version of the Rutgers Alcohol Problem Index (\doi{https://doi.org/10.15288/jsa.1989.50.30}{White & Labouvie, 1989})
       |                                                                                                                                                                  ^
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
Package suggested but not available for checking: ‘antaresViz’
Unknown package ‘antaresViz’ in Rd xrefs
checkRd: (-1) gbmidwcv.Rd:118: Lost braces
   118 | rfcv{randomForest} and gbm
       |     ^
checkRd: (-1) gbmokgbmidwcv.Rd:108: Lost braces
   108 | variable and anisotropy parameters. see notes vgm{gstat} for details.
       |                                                  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) spnn-package.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spnn-package.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spnn-package.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spnn-package.Rd:18: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘taxize’
'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:
    updates of 10th May 2021
Specified C++11: please drop specification unless essential
checkRd: (-1) shpdata1.Rd:7: Lost braces
     7 | \format{An object of class /code{"list"}.}
       |                                 ^
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
checkRd: (-1) sncFun.01110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-C1 in insertRef{Streck.2020}{spsh} using eq 21 which can be used
       |                                            ^
checkRd: (-1) sncFun.01110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-C1 in insertRef{Streck.2020}{spsh} using eq 21 which can be used
       |                                                         ^
checkRd: (-1) sncFun.02110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-B in insertRef{Streck.2020}{spsh}
       |                                           ^
checkRd: (-1) sncFun.02110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-B in insertRef{Streck.2020}{spsh}
       |                                                        ^
checkRd: (-1) sncFun.04110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-A  in insertRef{Streck.2020}{spsh}
       |                                            ^
checkRd: (-1) sncFun.04110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-A  in insertRef{Streck.2020}{spsh}
       |                                                         ^
checkRd: (-1) impactspsur.Rd:42: Lost braces; missing escapes or markup?
    42 | and a matching \code{Qres} list attribute if {Q} was given.
       |                                              ^
checkRd: (-1) spsur3sls.Rd:158: Lost braces; missing escapes or markup?
   158 |   the matrix of regressors, of order \emph{(Nxp_{g})}. Moreover, 
       |                                                 ^
checkRd: (-1) spsurgs3sls.Rd:67: Lost braces; missing escapes or markup?
    67 | \item{het}{default {FALSE}: if {TRUE} uses the methods 
       |                    ^
checkRd: (-1) spsurgs3sls.Rd:67: Lost braces; missing escapes or markup?
    67 | \item{het}{default {FALSE}: if {TRUE} uses the methods 
       |                                ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) spsOption.Rd:29: Lost braces; missing escapes or markup?
    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                   ^
checkRd: (-1) spsOption.Rd:29: Lost braces; missing escapes or markup?
    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                              ^
checkRd: (-1) spsOption.Rd:29: Lost braces; missing escapes or markup?
    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                                             ^
checkRd: (-1) vol.m3.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vol.m3.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vol.m3.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sqldf.Rd:248: Lost braces
   248 | and code{port} arguments of sqldf.
       |         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{ - a small, positive scalar that determines when iterations 
       |               ^
checkRd: (-1) fpiter.Rd:60-61: Lost braces
    60 |     \code{maxiter}{ - an integer denoting the maximum limit on the number of 
       |                   ^
checkRd: (-1) fpiter.Rd:63-65: Lost braces
    63 |     \code{trace}{ - a logical variable denoting whether some of the intermediate 
       |                 ^
checkRd: (-1) fpiter.Rd:67-70: Lost braces
    67 |     \code{intermed}}{ - a logical variable denoting whether the intermediate 
       |                     ^
checkRd: (-1) squarem.Rd:134: Lost braces
   134 |       along with the corresponding log-likelihood value.  When the code{objfn} is not specified it will return the fixed-point residual instead of the objective function values. 
       |                                                                        ^
checkRd: (-1) squidR.Rd:83: Lost braces; missing escapes or markup?
    83 |   \item \code{X1_sto_shared} (default \code{TRUE}): {logical}; if \code{TRUE}, the stochastic environmental effect included in the environmental effect x1 will be shared between individuals. If \code{FALSE}, each individual will experience a different stochastic environmental effect x1 (i.e. a new stochastic environmental effect is generated for each individual).
       |                                                     ^
checkRd: (-1) plot.SRCS.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:56-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:77-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:87-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:143-144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:145: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:146-148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:149: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) ssaBSS-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sscor.Rd:33: Lost braces; missing escapes or markup?
    33 | Otherwise, if {pdim=TRUE}, the pxp SSCM is computed, and then from the SSCM an estimator of the correlation matrix, which is done by the function \code{\link{SSCM2Shape}}, see there for details.
       |               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) new.distance.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:35-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:30-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:38-40: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                   ^
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                              ^
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                                      ^
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) SRanalysis.Rd:100: Lost braces
   100 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
checkRd: (-1) StabilizedRegression.Rd:109: Lost braces
   109 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) stabsel_parameters.Rd:42: Lost braces
    42 |     always use code{"none"}.}
       |                    ^
checkRd: (-1) stabsel_stabsel.Rd:25: Lost braces
    25 |     always use code{"none"}.}
       |                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) stackExample.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stackExample.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stamppFst.Rd:20: Lost braces
    20 | \code{Fsts}{a matrix of pairwise Fst values between populations}
       |            ^
checkRd: (-1) stamppFst.Rd:21: Lost braces
    21 | \code{Pvalues}{a matrix of p-values for each of the pairwise Fst values containined in the 'Fsts' matrix}
       |               ^
checkRd: (-1) stamppFst.Rd:22: Lost braces
    22 | \code{Bootstraps}{a dataframe of each Fst value generated during Bootstrapping and the associated confidence intervals}
       |                  ^
checkRd: (-1) standardize.Rd:94: Lost braces; missing escapes or markup?
    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                ^
checkRd: (-1) standardize.Rd:94: Lost braces; missing escapes or markup?
    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                                           ^
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_fields.Rd:27: Lost braces
    27 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
checkRd: (-1) identify_form_fields.Rd:34: Lost braces
    34 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
checkRd: (-1) abs_parms.Rd:67: Lost braces; missing escapes or markup?
    67 |    \item $S_{275-295}$ slope between 275 and 295 nm calculated with nonlinear regression
       |             ^
checkRd: (-1) abs_parms.Rd:68: Lost braces; missing escapes or markup?
    68 |    \item $S_{350-400}$ slope between 350 and 400 nm calculated with nonlinear regression
       |             ^
checkRd: (-1) abs_parms.Rd:69: Lost braces; missing escapes or markup?
    69 |    \item $S_{300-700}$ slope between 275 and 295 nm calculated with nonlinear regression
       |             ^
checkRd: (-1) abs_parms.Rd:70: Lost braces; missing escapes or markup?
    70 |    \item SR slope ratio, calculated by $S_{275-295}$/$S_{350-400}$
       |                                           ^
checkRd: (-1) abs_parms.Rd:70: Lost braces; missing escapes or markup?
    70 |    \item SR slope ratio, calculated by $S_{275-295}$/$S_{350-400}$
       |                                                         ^
checkRd: (-1) abs_parms.Rd:71: Lost braces; missing escapes or markup?
    71 |    \item E2:E3 ratio $a_{250}$/$a_{365}$
       |                         ^
checkRd: (-1) abs_parms.Rd:71: Lost braces; missing escapes or markup?
    71 |    \item E2:E3 ratio $a_{250}$/$a_{365}$
       |                                   ^
checkRd: (-1) abs_parms.Rd:72: Lost braces; missing escapes or markup?
    72 |    \item E4:E6 ratio $a_{465}$/$a_{665}$
       |                         ^
checkRd: (-1) abs_parms.Rd:72: Lost braces; missing escapes or markup?
    72 |    \item E4:E6 ratio $a_{465}$/$a_{665}$
       |                                   ^
checkRd: (-1) abs_parms.Rd:73: Lost braces; missing escapes or markup?
    73 |    \item $a_{254}$ absorbance at 254 nm
       |             ^
checkRd: (-1) abs_parms.Rd:74: Lost braces; missing escapes or markup?
    74 |    \item $a_{300}$ absorbance at 300 nm
       |             ^
checkRd: (-1) stargazer.Rd:229: Lost braces
   229 |   \item{report}{a character string containing only elements of {\code{"v"}, \code{"c"}, \code{"s"},\code{"t"}, \code{"p"}, \code{"*"}} that determines whether, and in which order, variable names (\code{"v"}), coefficients (\code{"c"}), standard errors/confidence intervals (\code{"s"}), test statistics (\code{"t"}) and p-values (\code{"p"}) should be reported in regression tables. If one of the aforementioned letters is followed by an asterisk (\code{"*"}), significance stars will be reported next to the corresponding statistic.}
       |                                                                ^
checkRd: (-1) stargazer.Rd:246: Lost braces
   246 |   \item{table.placement}{a character string containing only elements of {\code{"h"}, \code{"t"},\code{"b"}, \code{"p"}, \code{"!"}, \code{"H"}} that determines the table placement in its LaTeX floating environment.}
       |                                                                         ^
Package suggested but not available for checking: ‘starsdata’
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) AutoPollution.Rd:16: Lost braces
    16 |     \code{Side} \tab {Side of vehicle: code{1}=right or \code{2}=left}\cr
       |                                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) statcan_data.Rd:22: Lost braces; missing escapes or markup?
    22 | \code{statcan_data()} function has 2 arguments to fulfill to get data: {tableNumber} & {lang}.
       |                                                                        ^
checkRd: (-1) statcan_data.Rd:22: Lost braces; missing escapes or markup?
    22 | \code{statcan_data()} function has 2 arguments to fulfill to get data: {tableNumber} & {lang}.
       |                                                                                        ^
checkRd: (-1) statcan_search.Rd:18: Lost braces; missing escapes or markup?
    18 | The \code{statcan_search()} function has 2 arguments to fulfill to find a database: {keywords} and {lang}.
       |                                                                                     ^
checkRd: (-1) statcan_search.Rd:18: Lost braces; missing escapes or markup?
    18 | The \code{statcan_search()} function has 2 arguments to fulfill to find a database: {keywords} and {lang}.
       |                                                                                                    ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: ‘networksis’
'LazyData' is specified without a 'data' directory
checkRd: (-1) sample2indp.pow.Rd:48: Lost braces
    48 | Pooled standard deviation= \code{sp} = sqrt{((n1 - 1) sigma1^2 +(n2 - 1) sigma2^2) / (n1 + n2 - 2)}
       |                                            ^
checkRd: (-1) rankSTB.Rd:31: Lost braces; missing escapes or markup?
    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                        ^
checkRd: (-1) rankSTB.Rd:31: Lost braces; missing escapes or markup?
    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                                                                  ^
checkRd: (-1) rankSTB.Rd:31: Lost braces; missing escapes or markup?
    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                                                                      ^
checkRd: (-1) stb.default.Rd:43: Lost braces
    43 | sampling from the standard normal distribution. Another example is defining func=function(n){rchisq(n=n, df=3, ncp=2)}
       |                                                                                             ^
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) keypoints.Rd:35-36: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:37-39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:40-44: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:45-48: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:49-50: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:63-65: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:66-67: Lost braces in \enumerate; meant \describe ?
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) STEPCAM_ABC.Rd:19: Lost braces
    19 |   \code{rows}{ every row corresponds to a different plot or community} \cr
       |              ^
checkRd: (-1) STEPCAM_ABC.Rd:20: Lost braces
    20 |   \code{columns}{ every column corresponds to a different species.} \cr
       |                 ^
checkRd: (-1) STEPCAM_ABC.Rd:25: Lost braces
    25 |   \code{rows}{ every row corresponds to a different species} \cr
       |              ^
checkRd: (-1) STEPCAM_ABC.Rd:26: Lost braces
    26 |   \code{columns}{ the first column contains the name of the species, every consecutive column corresponds to a different trait} \cr
       |                 ^
checkRd: (-1) plotSTEPCAM.Rd:16: Lost braces
    16 |             - \code{DA}{ a vector containing the posterior distribution for the parameter dispersal assembly} \cr
       |                        ^
checkRd: (-1) plotSTEPCAM.Rd:17: Lost braces
    17 |             - \code{HF}{ a vector containing the posterior distribution for the parameter habitat filtering} \cr
       |                        ^
checkRd: (-1) plotSTEPCAM.Rd:18: Lost braces
    18 |             - \code{LS}{ a vector containing the posterior distribution for the parameter limiting similarity} \cr
       |                        ^
checkRd: (-1) tuneParam.Rd:28: Lost braces; missing escapes or markup?
    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
checkRd: (-1) tuneParamCL2.Rd:28: Lost braces; missing escapes or markup?
    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) landmarkMatrixToList.Rd:10: Lost braces
    10 |   \item{semilandmark.pattern}{a regular expression pattern passed to \code{sub()} for identifying and grouping curve points. The default is landmark names ending in one or more numbers. To disable grouping, set to code{''}.}
       |                                                                                                                                                                                                                           ^
checkRd: (-1) docker_config_collection.Rd:11: Lost braces; missing escapes or markup?
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("config")}
       | ^
checkRd: (-1) docker_container.Rd:13: Lost braces
    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_container")}
       | ^
checkRd: (-1) docker_image_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("image")}
       | ^
checkRd: (-1) docker_plugin_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("plugin")}
       | ^
checkRd: (-1) docker_service_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("service")}
       | ^
checkRd: (-1) docker_task.Rd:13: Lost braces
    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_task")}
       | ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘corrviz.html’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rsgeo’
checkRd: (-1) powderymildew.Rd:14-16: Lost braces
    14 | \code{$demographic.coord}{
       |                          ^
checkRd: (-1) powderymildew.Rd:18-20: Lost braces
    18 | \code{$genetic.coord}{
       |                      ^
checkRd: (-1) powderymildew.Rd:22-24: Lost braces
    22 | \code{$demographic.measures}{
       |                             ^
checkRd: (-1) powderymildew.Rd:26-28: Lost braces
    26 | \code{$genetic.frequencies}{
       |                            ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘myNewStrat.R’
Package suggested but not available for checking: ‘StrathE2E2examples’
checkRd: (-1) StrathE2E2-package.Rd:70: Lost braces; missing escapes or markup?
    70 | {Basic model operations:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:79: Lost braces; missing escapes or markup?
    79 | {Parameter estimation:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:88: Lost braces; missing escapes or markup?
    88 | {Sensitivity and Monte Carlo analyses:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:98: Lost braces; missing escapes or markup?
    98 | {Compare model runs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:105: Lost braces; missing escapes or markup?
   105 | {Fishery yield analysis:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:111: Lost braces; missing escapes or markup?
   111 | {Visualize model inputs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:117: Lost braces; missing escapes or markup?
   117 | {Visualize model outputs:} \cr
       | ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) isle.Rd:38: Lost braces
    38 | \code{\link[streamDAG]{stream.order}}, \code{\link[igraph]{delete.vertices}}, code{\link[igraph]{add.vertices}}, code{\link[igraph]{add.edges}}
       |                                                                                   ^
checkRd: (-1) isle.Rd:38: Lost braces
    38 | \code{\link[streamDAG]{stream.order}}, \code{\link[igraph]{delete.vertices}}, code{\link[igraph]{add.vertices}}, code{\link[igraph]{add.edges}}
       |                                                                                                                      ^
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
checkRd: (-1) calculateStatistics.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{quant}{numeric quantile to calculate {0,1}, default 0.95.}
       |                                            ^
checkRd: (-1) cmss.Rd:21: Lost braces
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                        ^
checkRd: (-1) cmss.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                            ^
checkRd: (-1) cmss.Rd:21: Lost braces
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                        ^
checkRd: (-1) cmss.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) subdetect-package.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subdetect-package.Rd:12: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) P3C.Rd:18: Lost braces; missing escapes or markup?
    18 |  used for this will be 1.00*10^{-PoissonThreshold}.}
       |                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) fp19.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:12-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) suggests.Rd:14: Lost braces; missing escapes or markup?
    14 | {suggests} aims to make that workflow as minimal and painless as possible,
       | ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) sunburst.Rd:30: Lost braces; missing escapes or markup?
    30 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{csvdata}
       |                                ^
checkRd: (-1) sunburst.Rd:88: Lost braces; missing escapes or markup?
    88 | \item{jsondata}{\code{deprecated} use data argument instead; data in nested d3 JSON hierarchy with `{name:...,  children:[];}`}
       |                                                                                                     ^
checkRd: (-1) sund2b.Rd:22: Lost braces; missing escapes or markup?
    22 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{list}, \code{character},
       |                                ^
GNU make is a SystemRequirements.
checkRd: (-1) BiclustSet-class.Rd:19: Lost braces
    19 |     \item{\code{Number}:}{code{"numeric"}, number of biclusters in the set}
       |                               ^
Package suggested but not available for checking: ‘velocyto.R’
checkRd: (-1) plot.Rd:42: Lost braces; missing escapes or markup?
    42 |  \item{color.off}{color code; specifying the color for set(s) which are "{absent}" for an intersection.}
       |                                                                          ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘extraTrees’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) getFittedProbs.Rd:6-8: Lost braces
     6 | getFittedValues <- function(object) {
       |                                     ^
checkRd: (-1) getFittedProbs.Rd:14-16: Lost braces
    14 | getFittedValues <- function(object) {
       |                                     ^
'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: ‘INLA’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘gurobi’
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'
checkRd: (-1) tprob.Rd:138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:141: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:142: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:145: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:146: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coxph_mpl_dc.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{mpl_h0t}{MPL estimates of the baseline hazard for T, i.e. h_{0T}(x_i)}
       |                                                                   ^
checkRd: (-1) coxph_mpl_dc.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{mpl_h0c}{MPL estimates of the baseline hazard for C, i.e. h_{0C}(x_i)}
       |                                                                   ^
checkRd: (-1) coxph_mpl_dc.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{mpl_H0t}{MPL estimates of the baseline cumulative hazard for T, i.e. H_{0T}(x_i)}
       |                                                                              ^
checkRd: (-1) coxph_mpl_dc.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{mpl_H0c}{MPL estimates of the baseline cumulative hazard for C, i.e. H_{0c}(x_i)}
       |                                                                              ^
checkRd: (-1) coxph_mpl_dc.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{mpl_S0t}{MPL estimates of the baseline survival for T, i.e. S_{0T}(x_i)}
       |                                                                     ^
checkRd: (-1) coxph_mpl_dc.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{mpl_S0c}{MPL estimates of the baseline survival for C, i.e. S_{0C}(x_i)}
       |                                                                     ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) sf.Rd:66: Lost braces; missing escapes or markup?
    66 | A {data.table} which is stored as an attribute of
       |   ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) coxDT.Rd:76: Lost braces; missing escapes or markup?
    76 | The estimation procedure here is performed using coxph {survival} and inserting these estimated
       |                                                        ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) koInstall.Rd:24: Lost braces; missing escapes or markup?
    24 | set, svKomodo loads {svSocket}, starts the socket server listening to the
       |                     ^
checkRd: (-1) svKomodo-package.Rd:18: Lost braces; missing escapes or markup?
    18 | Komodo and (2) the present {svKomodo} R package that work hand in hand to
       |                            ^
checkRd: (-1) svKomodo-package.Rd:28: Lost braces; missing escapes or markup?
    28 | Nevertheless, the SciViews-K Komodo addin and the {svKomodo} R package
       |                                                   ^
checkRd: (-1) svKomodo-package.Rd:31: Lost braces; missing escapes or markup?
    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                          ^
checkRd: (-1) svKomodo-package.Rd:31: Lost braces; missing escapes or markup?
    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                                         ^
checkRd: (-1) svKomodo-package.Rd:37: Lost braces; missing escapes or markup?
    37 | Both SciViews-K and {svKomodo} should be considered archived items. I keep
       |                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) eff_n.Rd:32: Lost braces; missing escapes or markup?
    32 | \code{\link[survey:surveysummary]{survey::svymean()}} and related functions from the {survey}
       |                                                                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) swDsn.Rd:28: Lost braces
    28 | numeric (scalar or vector): Relative treatment effect upon crossing over from control. Note that this is not the treatment effect (the treatment effect is specified in the call to other functions such as \code{swPwr} or \code{swSim})!  If \code{tx.effect.frac} is set to a scalar with value of 1, the standard SW CRT treatment effect will be presumed. If code{tx.effect.frac} is set to a scalar with a fractional value between 0 and 1, then only the first time point upon crossing over from control will have fractional relative treatment effect; the remaining exposure times will have a relative treatment effect of 1. If a vector of fractional treatment effect is specified, each element of the vector corresponds to the (fractional) treatment effect upon crossing over from control; if the length of the vector is less than total number of exposure times, the remaining time points will have a relative treatment effect value of 1; if the length of the vector is greater than total number of time points after crossing over, not all elements of \code{tx.effect.frac} will be used. The default value is (scalar) 1.
       |                                                                                                                                                                                                                                                                                                                                                                        ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘swephRdata’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
'LazyData' is specified without a 'data' directory
checkRd: (-1) hyph.support.en.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hyph.support.en.Rd:20: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
checkRd: (-1) kRp.hyphen-methods.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kRp.hyphen-methods.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kRp.hyphen-methods.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kRp.hyphen-methods.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manage.hyph.pat.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manage.hyph.pat.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manage.hyph.pat.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manage.hyph.pat.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elliptical.ts.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{epsilon}{positive convergence tolerance \emph{e}; the iterations converge when |fit - fit_{old}|/|fit| < \emph{e}. Default is \emph{e=1e-04}.}
       |                                                                                                   ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘odeintr’
Specified C++11: please drop specification unless essential
checkRd: (-1) coord2dist.Rd:14: Lost braces; missing escapes or markup?
    14 | \code{n} x 4 matrix of coordinates consisting of {lat or y, lon or x} pairs for each each site
       |                                                  ^
checkRd: (-1) create_synthetic_example.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_synthetic_example.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_synthetic_example.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initial_estimates_example.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initial_estimates_example.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initial_estimates_example.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) robCov.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robCov.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robCov.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robCov.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) slice.Rd:28: Lost braces
    28 | before plotting {ex: \code{trans = c(s = "exp", d = "exp")}}/}
       |                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.csv’
'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
Running examples in ‘table.glue-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: format_big
> ### Title: Format values left of decimal
> ### Aliases: format_big
> 
> ### ** Examples
> 
> 
> big_x <- 1234567
> 
> rspec <- format_big(round_spec(), mark = '|', interval = 3)
> 
> table_value(big_x, rspec) # returns "1|234|567"
Error in glue_data(.x = NULL, ..., .sep = .sep, .envir = .envir, .open = .open,  : 
  is.environment(.envir) is not TRUE
Calls: table_value -> <Anonymous> -> glue_data -> stopifnot
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘default_rounder.Rmd’ using rmarkdown

Quitting from lines 53-58 [unnamed-chunk-4] (default_rounder.Rmd)
Error: processing vignette 'default_rounder.Rmd' failed with diagnostics:
is.environment(.envir) is not TRUE
--- failed re-building ‘default_rounder.Rmd’

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

Quitting from lines 64-82 [unnamed-chunk-3] (table_guide.Rmd)
Error: processing vignette 'table_guide.Rmd' failed with diagnostics:
ℹ In argument: `tbv_height = table_glue("{height_est} ({height_lwr} -
  {height_upr})")`.
ℹ In group 1: `sex = "female"`.
Caused by error:
! Failed to evaluate glue component {..f(height_est)}
Caused by error in `glue_data()`:
! is.environment(.envir) is not TRUE
--- failed re-building ‘table_guide.Rmd’

SUMMARY: processing the following files failed:
  ‘default_rounder.Rmd’ ‘table_guide.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) tabmulti.Rd:68: Lost braces
    68 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
checkRd: (-1) tabmulti.svy.Rd:67: Lost braces
    67 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) parse_logs.Rd:38: Lost braces
    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |   ^
checkRd: (-1) parse_logs.Rd:38: Lost braces
    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |                      ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SKPar.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) TAQ-functions.Rd:119: Lost braces
   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.
       |                                                                                   ^
checkRd: (-1) TAQ-package.Rd:59: Lost braces
    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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) mean_ci.Rd:24: Lost braces
    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
checkRd: (-1) median_ci.Rd:24: Lost braces
    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
    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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) windows/tk2reg.Rd:17: Escaped LaTeX specials: \_
checkRd: (-1) windows/tk2reg.Rd:18: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) windows/tk2reg.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) windows/tk2reg.Rd:52: Escaped LaTeX specials: \_ \_
checkRd: (-1) windows/tk2reg.Rd:53: Escaped LaTeX specials: \_ \_
checkRd: (-1) windows/tk2reg.Rd:57: Escaped LaTeX specials: \_ \_
checkRd: (-1) windows/tk2reg.Rd:58: Escaped LaTeX specials: \_ \_
checkRd: (-1) windows/tk2reg.Rd:60: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Dependence on R version ‘4.2.3’ not with patchlevel 0
Package which this enhances but not available for checking: ‘R2wd’
checkRd: (-1) crossEntropy.Rd:32: Lost braces
    32 | link{squaredError}
       |     ^
'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) sendChatAction.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:25: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) Tendril.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) MC_CRUDE.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) MC_IS.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) PROB_BASEVAR-class.Rd:14: Lost braces
    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
checkRd: (-1) PROB_DETVAR-class.Rd:14: Lost braces
    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
checkRd: (-1) SORM.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) SYS_LSF-class.Rd:16: Lost braces
    16 | \item{\code{func}}{prepared for objective functions like SYS_LSF$func <- function(x){return(x[1] + x[2])}}
       |                                                                                     ^
checkRd: (-1) lognormConstCVCI.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lognormConstCVCI.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lognormConstCVCI.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) permucycle.Rd:37: Lost braces; missing escapes or markup?
    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);}
       |   ^
checkRd: (-1) permucycle.Rd:39: Lost braces; missing escapes or markup?
    39 |  {The third row means  there is a cycle of length 1, with member  (2);}
       |  ^
checkRd: (-1) permucycle.Rd:40: Lost braces; missing escapes or markup?
    40 |  {The fourth row is redundant for this specific case.}
       |  ^
checkRd: (-1) permucycle.Rd:41: Lost braces; missing escapes or markup?
    41 |  {One can read from the output of permucycle() to obtain cycle notation (13)(2) of the permutation, and other information.}
       |  ^
checkRd: (-1) infer_Z.Rd:16: Lost braces; missing escapes or markup?
    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.}
       |                                                                                                                                                         ^
checkRd: (-1) sibp.Rd:26: Lost braces
    26 | It is recommended to use link{sibp_param_search} instead of this function to search over multiple configurations of the most important parameters.  So long as only the training data is used, the analyst can freely experimient with as many parameter configurations as he likes without corrupting his causal inferences.  Once a parameter configuration is chosen, the user can then use \link{sibp_amce} on the test set to estimate the average marginal component effect (AMCE) for each treatment.}
       |                              ^
checkRd: (-1) sibp.Rd:28: Lost braces; missing escapes or markup?
    28 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variational approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
checkRd: (-1) sibp_amce.Rd:19: Lost braces
    19 |   \item{sibp.amce}{The table returned by code{sibp_amce}.}
       |                                              ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) make.phrase.matrix.Rd:20: Lost braces
    20 |  \\tabular{rrrrr}{
       |           ^
checkRd: (-1) make.phrase.matrix.Rd:20-23: Lost braces
    20 |  \\tabular{rrrrr}{
       |                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) tfd_von_mises_fisher.Rd:63: Lost braces; missing escapes or markup?
    63 | NOTE: Currently only n in {2, 3, 4, 5} are supported. For n=5 some numerical
       |                           ^
checkRd: (-1) predict.tfunHDDC.Rd:31-39: Lost braces
    31 | The teigen family. Stat Comput 22:1021{1029. <doi.org/10.1007/
       |                                       ^
'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) shoulders.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) shoulders.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) shoulders.Rd:23: 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3dimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                    ^
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                           ^
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                                          ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
checkRd: (-1) single_imputation.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) single_imputation.Rd:23-27: Lost braces in \itemize; meant \describe ?
'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’
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
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’
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
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: ‘fwelnet’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘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
checkRd: (-1) coef.tridim_transformation.Rd:31: Lost braces
    31 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
checkRd: (-1) coef.tridim_transformation.Rd:32: Lost braces
    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
checkRd: (-1) coef.tridim_transformation.Rd:32: Lost braces; missing escapes or markup?
    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
checkRd: (-1) predict.tridim_transformation.Rd:24: Lost braces
    24 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
checkRd: (-1) predict.tridim_transformation.Rd:25: Lost braces
    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
checkRd: (-1) predict.tridim_transformation.Rd:25: Lost braces; missing escapes or markup?
    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
checkRd: (-1) variable_summary.Rd:18: Lost braces; missing escapes or markup?
    18 | data.frame with "{var_name}" column for the mean and
       |                  ^
checkRd: (-1) variable_summary.Rd:19: Lost braces; missing escapes or markup?
    19 | "{var_name}_{prob}" columns for each probability.
       |  ^
checkRd: (-1) variable_summary.Rd:19: Lost braces; missing escapes or markup?
    19 | "{var_name}_{prob}" columns for each probability.
       |             ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
checkRd: (-1) summary.armasubsets.Rd:16: Lost braces
    16 | \item{matrix.logical}{With matrix=TRUE, the matrix is logical TRUE/FALSE or string "*"/code{" "}}
       |                                                                                            ^
checkRd: (-1) tsBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diss.AR.LPC.CEPS.Rd:39: Lost braces; missing escapes or markup?
    39 | If \code{order.x} or {order.y} are \code{NULL}, their respective series will be fitted automatically using a AR model.
       |                      ^
checkRd: (-1) diss.AR.PIC.Rd:31: Lost braces; missing escapes or markup?
    31 | If \code{order.x} or {order.y} are \code{NULL}, their respective series will be fitted automatically using a AR model. If \code{permissive} is \code{TRUE} and no AR order is found automatically, an AR order of 1 will be imposed, if this case fails, then no order can be found and the function produces an error.
       |                      ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) example.database2.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database2.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database3.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database3.Rd:19: Lost braces in \itemize; meant \describe ?
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
'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}
       |            ^
'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
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
'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
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
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
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: \&
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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: \&
'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 ?
'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
'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
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘prepr’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) get_cid.Rd:58-59: Lost braces
    58 | <structure search> is assembled as "{\code{substructure} |
       |                                     ^
checkRd: (-1) get_cid.Rd:59-60: Lost braces
    59 | \code{superstructure} | \code{similarity} | \code{identity}} / {\code{smiles}
       |                                                                ^
checkRd: (-1) get_cid.Rd:70-71: Lost braces
    70 | "{\code{fastidentity} | \code{fastsimilarity_2d} | \code{fastsimilarity_3d} |
       |  ^
checkRd: (-1) get_cid.Rd:71-72: Lost braces
    71 | \code{fastsubstructure} | \code{fastsuperstructure}}/{\code{smiles} |
       |                                                      ^
Running examples in ‘webdav-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: webdav_download_file
> ### Title: Download a file from the WebDAV server
> ### Aliases: webdav_download_file
> 
> ### ** Examples
> 
> # Example usage with a public WebDAV server.
> library(magrittr)
> library(httr2)
> test_server <- "https://www.webdavserver.com/" %>%
+   request() %>%
+   req_retry(max_tries = 3, max_seconds = 4, backoff =  ~ 1) %>%
+   req_perform()
> 
> # Download a file from the WebDAV server
> if (class(test_server) != "try-error")
+   webdav_download_file(base_url = test_server$url,
+     file_path = "Project.pdf",
+     destination_path = tempdir(),
+     verbose = TRUE)
Base URL: https://www.webdavserver.com/Userca7b831
Downloading from: Project.pdf to: /home/hornik/tmp/scratch/RtmpvWEVvG/Project.pdf
Server Path: https://www.webdavserver.com/Userca7b831/Project.pdf
Local Destination Path: /home/hornik/tmp/scratch/RtmpvWEVvG/Project.pdf
Base URL: https://www.webdavserver.com/Userca7b831/Project.pdf
Username: Not provided
Request object created successfully.
No authentication added.
Error during the download process: Failed to perform HTTP request.
Error in value[[3L]](cond) : Failed to download resource.
Calls: webdav_download_file ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
checkRd: (-1) Session.Rd:146: Lost braces
   146 | sQuote{page load} timeout specifies a time to wait for the page loading
       |       ^
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_geo_box.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milakes.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:22: Lost braces in \itemize; meant \describe ?
'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 ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: ‘wmtsa’
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.
'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
Running examples in ‘Xplortext-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.LexChar
> ### Title: Plot LexChar objects
> ### Aliases: plot.LexChar
> ### Keywords: plot
> 
> ### ** Examples
> 
> data(open.question)
> res.TD<-TextData(open.question, var.text=c(9,10), var.agg="Gen_Edu", Fmin=10, Dmin=10,
+         remov.number=TRUE, stop.word.tm=TRUE)
> LD<-LexChar(res.TD,maxCharDoc = 0)
> plot(LD)
Error in `gtable_add_grob()`:
! `grobs` must be a single grob or a list of grobs, not a list.
Backtrace:
     ▆
  1. ├─base::plot(LD)
  2. └─Xplortext:::plot.LexChar(LD)
  3.   ├─base::suppressWarnings(...)
  4.   │ └─base::withCallingHandlers(...)
  5.   └─Xplortext (local) marrangeGrob2(grobs = pword, nrow = numr, ncol = numc, top = top)
  6.     ├─base::do.call(gridExtra::arrangeGrob, c(grobs[groups[[g]]], params))
  7.     └─gridExtra (local) `<fn>`(...)
  8.       └─gtable::gtable_add_grob(grobs = grobs)
  9.         └─gtable:::stop_input_type(grobs, "a single grob or a list of grobs")
 10.           └─rlang::abort(message, ..., call = call, arg = arg)
Execution halted
'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
checkRd: (-1) boot.yhat.Rd:3: Lost braces
     3 | \title{Bootstrap metrics produced from /code{calc.yhat}}
       |                                             ^
checkRd: (-1) boot.yhat.Rd:19: Lost braces
    19 |     Ouput of /code{lm}
       |                   ^
checkRd: (-1) boot.yhat.Rd:22: Lost braces
    22 |     Output of /code{calc.yhat}
       |                    ^
checkRd: (-1) booteval.yhat.rd:3: Lost braces
     3 | \title{Evaluate bootstrap metrics produced from /code{calc.yhat}}
       |                                                      ^
checkRd: (-1) booteval.yhat.rd:5: Lost braces
     5 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
checkRd: (-1) combCI.rd:26: Lost braces
    26 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
checkRd: (-1) commonality.rd:12: Lost braces
    12 |     Output from /code{aps}
       |                      ^
checkRd: (-1) dombin.rd:12: Lost braces
    12 |     Output from /code{dominance}
       |                      ^
checkRd: (-1) dominance.rd:12: Lost braces
    12 |     Output from /code{aps}
       |                      ^
checkRd: (-1) plotCI.yhat.rd:5: Lost braces
     5 |   This function plots CIs that have been produced from /code{booteval.yhat}.
       |                                                             ^
checkRd: (-1) plotCI.yhat.rd:32: Lost braces
    32 |   This function plots CIs that have been produced from /code{booteval.yhat}.   
       |                                                             ^
checkRd: (-1) plotCI.yhat.rd:35: Lost braces
    35 | This returns a plot of CIs that have been produced from /code{booteval.yhat}.
       |                                                              ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'RNRCS', 'metScanR', '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.
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:74: Escaped LaTeX specials: \_
checkRd: (-1) zid.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:182: Lost braces
   182 |   dQuote{tab-delimited text file} when you have done and close the spreadsheet
       |         ^
checkRd: (-1) in.zoom.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_ztable.Rd:75: Lost braces; missing escapes or markup?
    75 | must be NULL or contain only elements of {"h","t","b","p","!","H"}.}
       |                                          ^
checkRd: (-1) ztable_sub.Rd:78: Lost braces; missing escapes or markup?
    78 | must be NULL or contain only elements of {"h","t","b","p","!","H"}.
       |                                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘qpmadr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ranger', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'car', 'plyr', 'HH'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

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.
Package required but not available: ‘hdm’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'swfscMisc', 'geosphere', 'gtsummary', 'gstat', 'sf', 'tmap',
  'raster', 'rnaturalearth'

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
Packages required but not available: 'lme4', 'Rcpp', 'RcppArmadillo'

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

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: ‘Rcpp’
Packages required but not available: 'sparsegl', 'fda'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘devtools’
checkRd: (-1) bind_tweets.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bind_tweets.Rd:22: Lost braces in \itemize; meant \describe ?
Error(s) in re-building vignettes:
  ...
--- re-building ‘academictwitteR-auth.Rmd’ using rmarkdown
--- finished re-building ‘academictwitteR-auth.Rmd’

--- re-building ‘academictwitteR-batchcompliance.Rmd’ using rmarkdown
--- finished re-building ‘academictwitteR-batchcompliance.Rmd’

--- re-building ‘academictwitteR-build.Rmd’ using rmarkdown

Quitting from lines 33-35 [unnamed-chunk-3] (academictwitteR-build.Rmd)
Error: processing vignette 'academictwitteR-build.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘academictwitteR-build.Rmd’

--- re-building ‘academictwitteR-errors.Rmd’ using rmarkdown
--- finished re-building ‘academictwitteR-errors.Rmd’

--- re-building ‘academictwitteR-intro.Rmd’ using rmarkdown
--- finished re-building ‘academictwitteR-intro.Rmd’

--- re-building ‘academictwitteR-tidy.Rmd’ using rmarkdown
--- finished re-building ‘academictwitteR-tidy.Rmd’

SUMMARY: processing the following file failed:
  ‘academictwitteR-build.Rmd’

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

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

Package suggested but not available for checking: ‘pander’

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.
Package required but not available: ‘reldist’

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

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

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

Quitting from lines 96-100 [unnamed-chunk-4] (accessibility.Rmd)
Error: processing vignette 'accessibility.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building ‘accessibility.Rmd’

--- re-building ‘decay_functions.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/accessibility.Rcheck/vign_test/accessibility/vignettes/decay_functions_files/figure-html/unnamed-chunk-4-1.png
576x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 37528 bytes
Input file size = 37654 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 29970
  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 = 29970

Output IDAT size = 29970 bytes (7558 bytes decrease)
Output file size = 30048 bytes (7606 bytes = 20.20% decrease)

--- finished re-building ‘decay_functions.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'flextable', 'officedown', 'pagedown'
Packages required but not available: 'plyr', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘raster’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘OpenMx’

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

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

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘hunspell’

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

Package suggested but not available for checking: ‘spelling’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'HDCI', 'extraDistr', 'Rcpp', 'RcppArmadillo'

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
Skipping checking math rendering: package 'V8' unavailable
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'

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

Packages suggested but not available for checking:
  'gdistance', 'raster', 'sf', 'terra'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'flextable', 'golem', 'plyr', 'shiny', 'shinycssloaders',
  'shinydashboard', 'shinydashboardPlus', 'shinyFeedback', 'shinyjs'

Packages suggested but not available for checking: 'spelling', 'shinytest2'

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

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'hetGP', 'lhs', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘devtools’

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

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

Packages suggested but not available for checking: 'plyr', 'minqa'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'gt', 'recipes'

Package suggested but not available for checking: ‘shiny’

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.
Packages required but not available: 'RProtoBuf', 'RestRserve'

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: ‘caret’

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

Package suggested but not available for checking: ‘cubature’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

Package suggested but not available for checking: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) adana.Rd:25: Lost braces; missing escapes or markup?
    25 |   \item{gatype}{Type of GA. \itemize{\item{"gga": generational GA}  \item{"ssga": steady state GA} } {Default value is "gga"}}
       |                                                                                                      ^
checkRd: (-1) adana.Rd:26: Lost braces; missing escapes or markup?
    26 |   \item{objective}{Type of optimization. \itemize{\item{"min": minimization}  \item{"max": maximization} } {Default value is "max"}}
       |                                                                                                            ^
checkRd: (-1) adana.Rd:34: Lost braces; missing escapes or markup?
    34 |                  {Default value is "initbin"}}
       |                  ^
checkRd: (-1) adana.Rd:56: Lost braces; missing escapes or markup?
    56 |                \itemize{\item{"integer"}  \item{"real"} } {Default value is "real"}}
       |                                                           ^
checkRd: (-1) adana.Rd:185: Lost braces; missing escapes or markup?
   185 |     {Default value is "w"}
       |     ^
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘glmnet’

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

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

Packages suggested but not available for checking:
  'dqrng', 'parallelDist', 'reshape2'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘glmnet’
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}.
       |                                                                                                                                                                                                          ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ComICS', 'pcaMethods', 'ranger'

Packages suggested but not available for checking: 'DeconRNASeq', 'WGCNA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
Packages required but not available: 'Rcpp', 'triebeard'

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: 'fda', 'Rfast'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'DT', 'miniUI', 'shiny', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'miniUI', 'shinyFiles', 'DT'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'recipes', 'spelling'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(additive)
  Loading required package: mgcv
  Loading required package: nlme
  This is mgcv 1.9-1. For overview type 'help("mgcv-package")'.
  Loading required package: parsnip
  > 
  > library(recipes)
  Error in library(recipes) : there is no package called 'recipes'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘BugReports.Rmd’ using rmarkdown
--- finished re-building ‘BugReports.Rmd’

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

Quitting from lines 19-21 [unnamed-chunk-2] (GetStarted.Rmd)
Error: processing vignette 'GetStarted.Rmd' failed with diagnostics:
there is no package called 'recipes'
--- failed re-building ‘GetStarted.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘coneproj’

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

Packages suggested but not available for checking:
  'ade4TkGUI', 'adegraphics', 'adephylo', 'ape', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ade4', 'adegraphics'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ade4', 'ape', 'shiny', 'seqinr', 'reshape2'

Packages suggested but not available for checking:
  'adespatial', 'pegas', 'hierfstat', 'spdep', 'interp', 'poppr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ade4', 'latticeExtra'

Packages suggested but not available for checking: 'car', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ade4', 'adehabitatLT'

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ade4', 'adehabitatHR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ade4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ade4', 'phylobase', 'ape', 'adegenet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shinyBS', 'V8', 'shinyjs', 'shiny', 'shinyWidgets', 'DT'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ade4', 'adegraphics', 'adephylo', 'spdep', 'shiny'

Packages suggested but not available for checking: 'ape', 'betapart'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'Rcpp', 'anytime'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AdhereRViz’
checkRd: (-1) med.groups.Rd:20: Lost braces; missing escapes or markup?
    20 | medication groups using the construction \emph{"{NAME}"}.
       |                                                 ^
checkRd: (-1) med.groups.Rd:26: Lost braces; missing escapes or markup?
    26 | Another example is "NotVita" defined as "(!{Vitamines})", which selects all
       |                                            ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'shinyWidgets', 'shinyjs', 'V8', 'colourpicker'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘AICcmodavg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ade4', 'adegraphics', 'ape', 'phylobase', 'phytools'

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

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

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:
  'mice', 'pammtools', 'pec', 'prodlim', 'riskRegression'
Running examples in ‘adjustedCurves-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adjusted_curve_test
> ### Title: Test if there is a difference between two Confounder-Adjusted
> ###   Survival Curves or CIFs
> ### Aliases: adjusted_curve_test
> 
> ### ** Examples
> 
> library(adjustedCurves)
> library(survival)
> 
> #### Simple Survival Case with adjusted survival curves ####
> 
> # simulate some data as example
> set.seed(42)
> sim_dat <- sim_confounded_surv(n=50, max_t=1.2)
> sim_dat$group <- as.factor(sim_dat$group)
> 
> # estimate a cox-regression for the outcome
> cox_mod <- coxph(Surv(time, event) ~ x1 + x2 + x3 + x4 + x5 + x6 + group,
+                  data=sim_dat, x=TRUE)
> 
> # use it to estimate adjusted survival curves with bootstrapping
> adjsurv <- adjustedsurv(data=sim_dat,
+                         variable="group",
+                         ev_time="time",
+                         event="event",
+                         method="direct",
+                         outcome_model=cox_mod,
+                         conf_int=FALSE,
+                         bootstrap=TRUE,
+                         n_boot=10) # n_boot should be much higher in reality
Loading required namespace: riskRegression
Failed with error:  ‘there is no package called ‘riskRegression’’
Error in loadNamespace(x) : there is no package called ‘riskRegression’
Calls: adjustedsurv ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(adjustedCurves)
  > 
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > library(testthat)
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:dplyr':
  
      matches
  
  > library(vdiffr)
  > library(survival)
  > library(ggplot2)
  > library(Matching)
  Loading required package: MASS
  
  Attaching package: 'MASS'
  
  The following object is masked from 'package:dplyr':
  
      select
  
  ## 
  ##  Matching (Version 4.10-15, Build Date: 2024-10-14)
  ##  See https://www.jsekhon.com for additional documentation.
  ##  Please cite software as:
  ##   Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
  ##   Software with Automated Balance Optimization: The Matching package for R.''
  ##   Journal of Statistical Software, 42(7): 1-52. 
  ##
  
  > library(WeightIt)
  > library(prodlim)
  Error in library(prodlim) : there is no package called 'prodlim'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘sf’
'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)
Error in library(sf) : there is no package called ‘sf’
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. 
       |                                                                           ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'DT', 'spelling'
Packages suggested but not available for checking:
  'devtools', 'miniUI', 'spelling', 'DT'
Packages suggested but not available for checking:
  'devtools', 'miniUI', 'spelling'
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lintr’ ‘pharmaversesdtm’ ‘pkgdown’ ‘testthat’
A package should be listed in only one of these fields.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘DT’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'devtools', 'spelling'
Packages suggested but not available for checking:
  'devtools', 'DT', 'miniUI', 'spelling'
Package suggested but not available for checking: ‘QCA’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'cubature', 'Rcpp'

Packages suggested but not available for checking:
  'flexsurv', 'plyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rstan’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rpact’
Running ‘testthat.R’ [52s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(adoptr)
  
  Attaching package: 'adoptr'
  
  The following object is masked from 'package:testthat':
  
      expectation
  
  > 
  > test_check("adoptr")
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 375 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_BinomialDistribution.R:93:1'): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'rpact'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_BinomialDistribution.R:93:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_IntegralScores.R:8:1'): (code run outside of `test_that()`) ────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'rpact'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_IntegralScores.R:8:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_minimize.R:152:5'): Optimal group-sequential design is superior to standard gs design ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'rpact'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_minimize.R:152:5
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 375 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggrepel', 'multichull', 'qgraph'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ade4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'learnr', 'BayesFactor', 'car', 'effects', 'GGally', 'WRS2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinycssloaders', 'shinyjs', 'DT', 'ggpubr', 'survminer',
  'shinythemes', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'sf', 'terra', 'cnmap'

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: ‘qvalue’

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

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.
       |                                                                                                                                                                                                                                                                                              ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggvis', 'plotly'

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

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', 'np', 'plm', 'rugarch',
  'sampleSelection', 'systemfit'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'DescTools', 'ggmcmc', 'spelling'
Problems with news in ‘NEWS.md’:
No news entries found.
Error(s) in re-building vignettes:
  ...
--- re-building ‘af_logit_exponential.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/afdx.Rcheck/vign_test/afdx/vignettes/af_logit_exponential_files/figure-html/unnamed-chunk-7-1.png
2400x1800 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 117033 bytes
Input file size = 117279 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 112843
  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 = 112843

Output IDAT size = 112843 bytes (4190 bytes decrease)
Output file size = 112921 bytes (4358 bytes = 3.72% decrease)


Quitting from lines 198-219 [unnamed-chunk-8] (af_logit_exponential.Rmd)
Error: processing vignette 'af_logit_exponential.Rmd' failed with diagnostics:
there is no package called 'DescTools'
--- failed re-building ‘af_logit_exponential.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'lme4', 'pbkrtest', 'lmerTest', 'car', 'reshape2'

Packages suggested but not available for checking:
  'plyr', 'latticeExtra', 'mlmRev', 'MEMSS', 'effects', 'jtools',
  'ggpubr', 'ggpol', 'glmmTMB', 'brms', 'rstanarm', 'ez',
  'ggResidpanel'

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

Quitting from lines 54-100 [hex-logo] (affiner.Rmd)
Error: processing vignette 'affiner.Rmd' failed with diagnostics:
there is no package called 'gridpattern'
--- failed re-building ‘affiner.Rmd’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reshape2', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gstat', 'plyr', 'shiny', 'shinyjs', 'dbscan', 'mixtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'drgee', 'stdReg', 'ivtools'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'photobiology', 'rstpm2'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gsignal', 'Rcpp', 'GGIR', 'reticulate', 'shiny', 'read.gt3x',
  'RcppArmadillo'

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

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

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

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

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

Package suggested but not available for checking: ‘faraway’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plyr', 'spdep'

Packages suggested but not available for checking: 'INLA', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘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
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lme4’

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

Package suggested but not available for checking: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AER', 'car', 'desplot', 'effects', 'gge', 'gstat', 'HH',
  'latticeExtra', 'lme4', 'MCMCglmm', 'pbkrtest', 'qicharts',
  'reshape2', 'SpATS'
Packages required but not available: 'lmerTest', 'pbkrtest'

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

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

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

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

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

Package suggested but not available for checking: ‘DT’

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

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

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

Package suggested but not available for checking: ‘recipes’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘unmarked’

Packages suggested but not available for checking:
  'fields', 'raster', 'spdep'

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

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

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

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘flexsurv’

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

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

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

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: 'shiny', 'ALDEx2'

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

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

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', 'Rcpp', 'reshape2', 'reticulate', 'smotefamily',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'text2vec', 'tidytext', 'topicmodels', 'udpipe', 'quanteda', 'shiny',
  'shinyFiles', 'shinyWidgets', 'shinydashboard', 'shinyjs', 'readtext'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) aimPlot.Rd:39: Lost braces; missing escapes or markup?
    39 |  \item \code{Variable} {1st column: The various aims to be completed}
       |                        ^
checkRd: (-1) aimPlot.Rd:40: Lost braces; missing escapes or markup?
    40 |  \item \code{Percentage} {2nd column: The percentage of completeness}
       |                          ^
Package suggested but not available for checking: ‘tinysnapshot’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘tmle’
Running examples in ‘AIPW-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AIPW_tmle
> ### Title: Augmented Inverse Probability Weighting (AIPW) uses tmle or
> ###   tmle3 as inputs
> ### Aliases: AIPW_tmle
> 
> ### ** Examples
> 
> vec <- function() sample(0:1,100,replace = TRUE)
> df <- data.frame(replicate(4,vec()))
> names(df) <- c("A","Y","W1","W2")
> 
> ## From tmle
> library(tmle)
Error in library(tmle) : there is no package called ‘tmle’
Execution halted
Running ‘testthat.R’ [14s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(AIPW)
  > 
  > test_check("AIPW")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 167 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-tmle_support.R:12:3'): AIPW_tmle class: tmle ───────────────────
  Error in `tmle(Y = df$Y, A = df$A, W = df[, 3:4], Q.SL.library = "SL.glm", 
      g.SL.library = "SL.glm", family = "binomial")`: could not find function "tmle"
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 167 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'leaflet', 'sf'

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'caRamel', 'FME', 'ggmcmc', 'Rmalschains', 'GGally'
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 'Rmalschains'
--- 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 'FME'
--- 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
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'shinyjs'

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:
  'leaflet', 'MazamaCoreUtils', 'MazamaRollUtils', 'MazamaTimeSeries'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) get_airnow_area.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{parameters}{Parameter(s) to return data for. Choices are PM_{2.5}
       |                                                                   ^
Package suggested but not available for checking: ‘vcr’
Running ‘testthat.R’ [1s/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)
  > library(air)
  > 
  > test_check("air")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/air.Rcheck/tests/testthat/helper-vcr.R"
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("air")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_helpers(".", env)
    7. │           └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at tests/testthat/helper-vcr.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘stuve.pdf’
Package required but not available: ‘mirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘SuperGauss’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggraph', 'ggforce', 'textstem', 'tidytext', 'ggwordcloud', 'tidyfst'

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. 
       |                          ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

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
       |                             ^
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ape', 'Rcpp', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sf', 'censable', 'geomander', 'redist', 'redistmetrics', 'tinytiger'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘EEM’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘devtools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown

Quitting from lines 44-58 [package_management] (Introduction.Rmd)
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
Package devtools is required but not installed. Please install it using install.packages(" devtools ").
--- 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: 'sf', 'stars', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘reshape2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘html_vignette.Rmd’ using rmarkdown

Quitting from lines 21-69 [setup] (html_vignette.Rmd)
Error: processing vignette 'html_vignette.Rmd' failed with diagnostics:
there is no package called 'reshape2'
--- failed re-building ‘html_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggpubr', 'univariateML'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'caret', 'seqinr', 'reshape2', 'bio3d'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcpp', 'RcppEigen', 'rstan'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘mirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘pedigree’
Packages required but not available: 'BiodiversityR', 'adegenet'

Packages suggested but not available for checking:
  'poppr', 'GGally', 'ggforce', 'ggrepel', 'gganimate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RNOmni', 'SKAT', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
checkRd: (-1) allestimates.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allestimates.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allestimates.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allestimates.Rd:28: Lost braces in \itemize; meant \describe ?
Packages required but not available: 'plyr', 'reshape2', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DT’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'devtools', 'reshape2'
Package required but not available: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dlookr', 'ggmosaic', 'ranger', 'glmnet'

Package suggested but not available for checking: ‘mice’

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

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

Packages suggested but not available for checking: 'bife', 'car'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'pedigree', 'Rcpp', 'reshape'

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

Package suggested but not available for checking: ‘alphahull’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘reticulate’

Packages suggested but not available for checking:
  'listviewer', 'pryr', 'V8'

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

Packages suggested but not available for checking: 'servr', 'spelling'

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 required but not available: ‘cubature’

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

Packages suggested but not available for checking:
  'ggmap', 'raster', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sf', 'sftime', 'terra', 'exactextractr', 'stars', 'nhdplusTools',
  'collapse'

Packages suggested but not available for checking:
  'lwgeom', 'devtools', 'tigris', 'spelling'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
checkRd: (-1) convertCoord.Rd:32: Lost braces
    32 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) convertCoord.individual.Rd:33: Lost braces
    33 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) getCoord.Rd:39: Lost braces
    39 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) getCoord.individual.Rd:39: Lost braces
    39 | here{https://lbs.amap.com/faq/account/key/72}}
       |     ^
checkRd: (-1) getLocation.Rd:60: Lost braces; missing escapes or markup?
    60 | {https://lbs.amap.com/faq/account/key/72}}
       | ^
checkRd: (-1) getLocation.individual.Rd:60: Lost braces
    60 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘shiny’
Packages suggested but not available for checking:
  'fields', 'RefManageR', 'sf', 'terra'
Error(s) in re-building vignettes:
  ...
--- re-building ‘AMAPVox.Rmd’ using rmarkdown
--- finished re-building ‘AMAPVox.Rmd’

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

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

Quitting from lines 30-33 [unnamed-chunk-2] (Publications.Rmd)
Error: processing vignette 'Publications.Rmd' failed with diagnostics:
there is no package called 'RefManageR'
--- failed re-building ‘Publications.Rmd’

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

--- re-building ‘amapvox-gui.Rmd’ using rmarkdown
--- finished re-building ‘amapvox-gui.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Package required but not available: ‘Rcpp’

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

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

Packages suggested but not available for checking: 'pander', 'qpdf'

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

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', 'reshape2'

Package suggested but not available for checking: ‘pander’

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

Packages suggested but not available for checking:
  'shiny', 'shinyBS', 'AICcmodavg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'MplusAutomation', 'reshape2', 'plyr', 'devtools'

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
Packages required but not available: 'devtools', 'ranger', 'shiny'

Packages suggested but not available for checking:
  'DT', 'pander', 'shinythemes', 'spelling'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) AmpliconDuo-package.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:40-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:43-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:53-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:56-58: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘tsibble’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ctmm', 'sf', 'sfheaders', 'terra'

Packages suggested but not available for checking:
  'adehabitatLT', 'ggraph', 'geosphere', 'leaflet', 'moveHMM', 'units'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'DESeq2', 'ggrepel', 'plyr'

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.
Package required but not available: ‘princurve’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'reshape2', 'shiny'
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggpubr', 'Seurat'

Package suggested but not available for checking: ‘Signac’

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: \~
Packages required but not available: 'glmnet', 'selectiveInference'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'raster', 'nabor'

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.
Packages required but not available: 'shiny', 'sf', 'plyr'

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:
  'tidytext', 'dbscan', 'apcluster', 'ggraph', 'ranger'

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

Packages suggested but not available for checking:
  'shiny', 'pryr', 'V8', 'servr'

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

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

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

Packages suggested but not available for checking:
  'gistr', 'shiny', 'devtools'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'animation', 'sf', 'crawl', 'ggmap'

Package suggested but not available for checking: ‘terra’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aniview
> ### Title: Animate an element when it comes into view
> ### Aliases: aniview
> 
> ### ** Examples
> 
> library(shiny)
Error in library(shiny) : there is no package called ‘shiny’
Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘TruncatedNormal’

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

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

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

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

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

Packages suggested but not available for checking:
  'sf', 'terra', 'keys', 'colourpicker', 'spelling'

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.
Package required but not available: ‘superb’

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

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

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

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

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

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', 'plyr'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gganimate’
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 ''gganimate'' is required. Please install it.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘caret’

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

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

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

Package suggested but not available for checking: ‘survey’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘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 ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'GGally', 'bayesplot', 'RcppArmadillo'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

Package suggested but not available for checking: ‘units’

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

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

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

Packages suggested but not available for checking:
  'glmnet', 'SurvMetrics', 'units'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'DT', 'shiny', 'shinydashboardPlus', 'shinydashboard', 'Rcpp',
  'rstan', 'rstantools', 'BayesFactor', 'car', 'reshape',
  'shinycssloaders', 'waiter', 'RcppEigen', 'StanHeaders'

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

Packages suggested but not available for checking: 'sf', 'spelling'

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

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

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

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

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

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

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

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

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

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

Packages suggested but not available for checking:
  'Spectrum', 'clusterProfiler', 'gprofiler2', 'DOSE'

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

Package suggested but not available for checking: ‘phangorn’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'kmer', 'Rcpp'

Packages suggested but not available for checking: 'ape', 'qpdf'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'episensr', 'shiny', 'golem', 'shinymaterial', 'shinyjs', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shinyBS', 'DT', 'plotly', 'shiny', 'shinythemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pROC’
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 'pROC'
--- failed re-building ‘aplore3-examples.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ggtree’
Package suggested but not available for checking: ‘ggtree’
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} 
       |                                                                           ^
Package required but not available: ‘flextable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ape', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gyro', 'Rcpp', 'RcppCGAL', 'RcppEigen'

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

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

Package suggested but not available for checking: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘proxyC’

Packages suggested but not available for checking:
  'isotree', 'recipes', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', '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
Packages required but not available:
  'DT', 'shiny', 'shinythemes', 'sortable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘optmatch’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen', 'RcppCGAL'

Package suggested but not available for checking: ‘transport’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BayesianTools', 'chirps', 'daymetr', 'listviewer', 'metrica',
  'nasapower', 'sensitivity', 'sf'
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 suggested but not available for checking: 'survey', 'srvyr'
Packages required but not available: 'openair', 'loa', 'ggtext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ape', 'sf', 'latticeExtra', 'tactile', 'compositions',
  'sharpshootR', 'markovchain', 'Gmedian', 'plyr'
Package required but not available: ‘terra’

Packages suggested but not available for checking: 'ggrepel', 'learnr'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: createGrid
> ### Title: Create a Grid grid covering a given geographic zone.
> ### Aliases: createGrid
> 
> ### ** Examples
> 
> 
> data("BarcelonaPop")
> BarcelonaPop.INSPIRE_GRID<-createGrid(BarcelonaPop)
Error in loadNamespace(x) : there is no package called ‘sf’
Calls: createGrid ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘plyr’

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

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

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: 'qqplotr', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sf’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'arcgisutils', 'jsonify', 'RcppSimdJson', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'arcgisutils', 'arcpbf', 'jsonify', 'RcppSimdJson', 'sf', 'terra'

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

Packages suggested but not available for checking:
  'arcgisbinding', 'collapse', 'jsonify'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ArchaeoData', 'tinysnapshot'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'plotly', 'cxhull', 'reshape2', 'shiny', 'shinythemes'

Package suggested but not available for checking: ‘SEAHORS’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘geometry’

Package suggested but not available for checking: ‘TDA’

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

Packages suggested but not available for checking: 'vcr', 'webmockr'

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.
Package required but not available: ‘flock’

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

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

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

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

Package suggested but not available for checking: ‘sf’

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

Package suggested but not available for checking: ‘magick’

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

Packages suggested but not available for checking: 'sf', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qCBA’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ghql’

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

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.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'ontologics', 'rmapshaper'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinydashboard', 'shinyBS', 'shinyjs'

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

Package suggested but not available for checking: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ranger’

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

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

Packages suggested but not available for checking:
  'colourpicker', 'shiny', 's2', 'sf', 'shinyBS'

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

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

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

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'hommel', 'RNifti', 'plyr'

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

Package suggested but not available for checking: ‘spelling’

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.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘xaringan’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'rugarch', 'tensorflow', 'keras', 'reticulate'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Q.iid
> ### Title: Precision matrix for a IID process
> ### Aliases: Q.iid r.iid
> 
> ### ** Examples
> 
> require("leaflet")
Loading required package: leaflet
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘leaflet’
> require("sp")
Loading required package: sp
> 
> # simulate iid data and attach to spatial polygons data frame
> US.df@data$data <- c(r.iid(1, M=nrow(US.graph), sigma=1))
> 
> # color palette of data
> pal <- colorNumeric(palette="YlGnBu", domain=US.df@data$data)
Error in colorNumeric(palette = "YlGnBu", domain = US.df@data$data) : 
  could not find function "colorNumeric"
Execution halted
Package required but not available: ‘lme4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'alphashape3d', 'compositions', 'geometry', 'Morpho', 'Rvcg'

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

Package suggested but not available for checking: ‘RSocrata’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'shiny', 'plyr', 'reshape2'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘reticulate’
Packages suggested but not available for checking: 'pander', 'pROC'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘miniUI’

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

Packages suggested but not available for checking:
  'pander', 'lmerTest', 'phia', 'DescTools'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'arulesCBA', 'arulesViz'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggraph', 'DT', 'plotly'

Packages suggested but not available for checking: 'shiny', 'shinythemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lutz', 'parzer', 'sf', 'spsurvey', 'units'

Package suggested but not available for checking: ‘soundecology’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'magick', 'V8'

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

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spdep’
Packages required but not available:
  'alphahull', 'alphashape3d', 'Rvcg', 'TDA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'mixsqp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'miniUI', 'shiny', 'shinycssloaders', 'spelling'
Packages required but not available: 'llama', 'plyr', 'reshape2'

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_network
> ### Title: Calculating Weighted Network
> ### Aliases: get_network
> 
> ### ** Examples
> 
> 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
> 
> ## test if one predicts the other via a mantel test (must be loaded externally)
> library(ape)
Error in library(ape) : there is no package called ‘ape’
Execution halted
Package suggested but not available for checking: ‘sem’
Packages required but not available: 'splines2', 'Rcpp'

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

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

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

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: 'factoextra', 'superheat'

Packages suggested but not available for checking: 'spelling', 'V8'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘shiny’
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                    ^
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                                                                                                                 ^
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                                                                                                                          ^
'LazyData' is specified without a 'data' directory
Package required but not available: ‘np’

Packages suggested but not available for checking: 'AER', 'faraway'

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

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

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
       |                                                  ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'caret', 'reshape2'

Package suggested but not available for checking: ‘klaR’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'dfdr'

Package suggested but not available for checking: ‘RcppXPtrUtils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'nanotime', 'onion', 'Rcpp'

Packages suggested but not available for checking:
  'asteRiskData', 'plotly', 'ggmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘fields’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘smacof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plyr', 'reshape2', 'DescTools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'terra', 'gstat', 'sf', 'Rcpp'

Package suggested but not available for checking: ‘rtop’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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]}
       |                                           ^
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  're2', 'binsegRcpp', 'LOPART'
Packages required but not available: 'leaflet', 'shiny'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package suggested but not available for checking: ‘trtf’
Packages suggested but not available for checking:
  'ggraph', 'magick', 'webshot2'
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'arm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) audioSample.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) audioSample.Rd:21: Lost braces in \itemize; meant \describe ?
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’

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

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

Package suggested but not available for checking: ‘spelling’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘V8’

Package suggested but not available for checking: ‘spelling’

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

Package suggested but not available for checking: ‘pander’

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

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

Package suggested but not available for checking: ‘ggrepel’

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.
Package required but not available: ‘MBESS’

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

Package suggested but not available for checking: ‘sf’

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

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

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: 'caret', 'minerva'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) get_candidate_covariates.Rd:50: Lost braces
    50 | \item \code{covars_data}   {The \code{data.frame} that is filtered out of \code{df} with only the selected \code{covars}}. The values of the
       |                            ^
checkRd: (-1) get_candidate_covariates.Rd:53: Lost braces
    53 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
checkRd: (-1) get_prioritised_covariates.Rd:40: Lost braces
    40 | \item \code{multiplicative_bias}{The absolute log of the multiplicative bias term for each of the auto-selected prioritised covariates}
       |                                 ^
checkRd: (-1) get_recurrence_covariates.Rd:34: Lost braces
    34 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
Package required but not available: ‘shiny’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spam', 'fields', 'LatticeKrig', 'Rcpp', 'RSpectra', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'DESeq2', 'ggrepel', 'GSVA', 'openxlsx', 'reshape2'

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

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

Package suggested but not available for checking: ‘gear’

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

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

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

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

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

VignetteBuilder package required for checking but not installed: ‘quarto’

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

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

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.
Packages required but not available: 'plyr', 'seqinr', 'ade4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'echarts4r', 'quanteda', 'quanteda.textstats'

Package suggested but not available for checking: ‘spelling’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mice', 'flextable', 'tidycmprsk', 'pammtools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) noauto_scorecard.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{fit}{See glm {stats}.}
       |                    ^
checkRd: (-1) noauto_scorecard2.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{fit}{See glm {stats}.}
       |                    ^
Packages required but not available:
  'tableone', 'pROC', 'car', 'coxed', 'plotly', 'survminer'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'jtools', 'recipes', 'tune', 'presenter', 'recosystem',
  'Ckmeans.1d.dp'

Packages suggested but not available for checking:
  'flextable', 'glmnet', 'ggstance', 'ranger'

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', 'ggrepel', 'kalmanfilter'

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'prophet', 'forecast', 'RcppRoll', 'shiny', 'shinycssloaders',
  'plotly'

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

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

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

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

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.
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
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘ggrepel’
Packages required but not available:
  'ape', 'phytools', 'tidytree', 'TreeTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available:
  'kohonen', 'shiny', 'rclipboard', 'DT', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘terra’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'httpuv', 'shiny', 'shinyjs'
Packages suggested but not available for checking: 'plumber', 'RestRserve'
Package suggested but not available for checking: ‘odbc’
checkRd: (-1) cosmos_mongo.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{host}{For \code{cosmos_mongo_endpoint}, the URL of the Cosmos DB MongoDB endpoint. Usually of the form "https://{account-name}.mongo.cosmos.azure.com:443/".}
       |                                                                                                                       ^
Packages required but not available:
  'reticulate', 'plyr', 'DT', 'servr', 'shiny', 'shinycssloaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘httpuv’
Packages required but not available:
  'nlmixr2', 'nlmixr2est', 'nonmem2rx', 'monolix2rx', 'qs', 'rxode2',
  'Rcpp', 'RcppArmadillo', 'RcppEigen'

Packages suggested but not available for checking:
  'lixoftConnectors', 'spelling', 'units'

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

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

Packages suggested but not available for checking:
  'ape', 'nLTT', 'spelling'

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

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.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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

Packages suggested but not available for checking:
  'pander', 'fields', 'pcalg'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘V8’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'bayesplot', 'ggrepel', 'StanHeaders',
  'RcppEigen'

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

Package suggested but not available for checking: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘C50’

Packages suggested but not available for checking: 'recipes', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'pdftools', 'spelling'
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘openxlsx’

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

Packages suggested but not available for checking:
  'spelling', 'knitcitations', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'DESeq2', 'Ckmeans.1d.dp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ade4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'multidplyr', 'RcppEigen',
  'StanHeaders'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppDist'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'fields', 'interp', 'BayesX', 'sf', 'spdep', 'keras', 'splines2',
  'sdPrior', 'glmnet', 'scoringRules', 'tensorflow'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'animation', 'leaflet', 'plotly', 'raster', 'Rcpp', 'RSpectra',
  'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘mice’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fdpbandsdata’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘madshapR’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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: 'rfPermute', 'swfscMisc'

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

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 required but not available: 'DT', 'miniUI', 'shiny'

Package suggested but not available for checking: ‘shinytest’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'BART', 'fdm2id'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘terra’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lme4', 'tmle', 'stan4bart'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggiraph', 'ggraph', 'tidybayes', 'tidytreatment', 'BART'

Package suggested but not available for checking: ‘ggforce’

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

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

Package suggested but not available for checking: ‘Rraven’

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

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

Packages suggested but not available for checking:
  'ggrepel', 'qs', 'reshape2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) bd_collect.Rd:30: Lost braces; missing escapes or markup?
    30 | the {dplyr}'s verbs and thus use it in local memory completely.
       |     ^
checkRd: (-1) bd_write.Rd:52: Lost braces; missing escapes or markup?
    52 | Writes a remote table to disk that was called via {bdplyr}.
       |                                                   ^
checkRd: (-1) bdplyr.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Compatibility with {dplyr} verbs without using SQL language}
       |                           ^
Package suggested but not available for checking: ‘coneproj’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'sf', 'slippymath', 'terra', 'stars', 'magick'

Packages suggested but not available for checking:
  'raster', 'mapview', 'mapedit'

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
Package required but not available: ‘do’

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'listviewer', 'openxlsx', 'flextable', 'shiny'
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Earlier versions
checkRd: (-1) BasicTable.Rd:659: Lost braces; missing escapes or markup?
   659 | `function(v, cell) { if(isTRUE(v>0.8)) return("green") }`.\cr
       |                    ^
checkRd: (-1) TableStyle.Rd:151: Lost braces; missing escapes or markup?
   151 | The CSS style rule, e.g. { text-align: center; color: red; }
       |                          ^
checkRd: (-1) TableStyle.Rd:172: Lost braces; missing escapes or markup?
   172 | The CSS style rule, e.g. cell { text-align: center; color: red; }
       |                               ^
checkRd: (-1) TableStyles.Rd:209: Lost braces; missing escapes or markup?
   209 | The CSS style rule, e.g. { text-align: center; color: red; }
       |                          ^
checkRd: (-1) TableStyles.Rd:232: Lost braces; missing escapes or markup?
   232 | The CSS style rule, e.g. cell { text-align: center; color: red; }
       |                               ^
Running examples in ‘basictabler-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TableOpenXlsxRenderer
> ### Title: R6 class that renders a table into an Excel worksheet.
> ### Aliases: TableOpenXlsxRenderer
> 
> ### ** Examples
> 
> # This class is for internal use only.  It is
> # created only by the BasicTable class when rendering to Excel.
> library(basictabler)
> tbl <- qtbl(data.frame(a=1:2, b=3:4))
> library(openxlsx)
Error in library(openxlsx) : there is no package called ‘openxlsx’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘v01-introduction.Rmd’ using rmarkdown
--- finished re-building ‘v01-introduction.Rmd’

--- re-building ‘v02-workingwithcells.Rmd’ using rmarkdown
--- finished re-building ‘v02-workingwithcells.Rmd’

--- re-building ‘v03-outputs.Rmd’ using rmarkdown

Quitting from lines 127-145 [unnamed-chunk-4] (v03-outputs.Rmd)
Error: processing vignette 'v03-outputs.Rmd' failed with diagnostics:
there is no package called 'flextable'
--- failed re-building ‘v03-outputs.Rmd’

--- re-building ‘v04-styling.Rmd’ using rmarkdown
--- finished re-building ‘v04-styling.Rmd’

--- re-building ‘v05-findingandformatting.Rmd’ using rmarkdown
--- finished re-building ‘v05-findingandformatting.Rmd’

--- re-building ‘v06-shiny.Rmd’ using rmarkdown
--- finished re-building ‘v06-shiny.Rmd’

--- re-building ‘v07-excelexport.Rmd’ using rmarkdown
--- finished re-building ‘v07-excelexport.Rmd’

SUMMARY: processing the following file failed:
  ‘v03-outputs.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) nfiMetrics.Rd:23: Lost braces
    23 | code{(4)} the number of
       |     ^
Package required but not available: ‘rmcfs’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'GGally', 'faraway'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘plyr’
checkRd: (-1) ExperimentJob.Rd:14: Lost braces
    14 |   \item{\code{algo.id} [\code{character(1)}]:}{algo.id}{Algorithm ID.}
       |                                                        ^
checkRd: (-1) getAlgorithmIds.Rd:13: Lost braces
    13 | \item{ids}{[code{integer}]\cr
       |                 ^
checkRd: (-1) getProblemIds.Rd:13: Lost braces
    13 | \item{ids}{[code{integer}]\cr
       |                 ^
checkRd: (-1) makeExperimentRegistry.Rd:28: Lost braces
    28 | Default is dQuote{<name of registry>_files} in current working directory.}
       |                  ^
Packages required but not available:
  'shiny', 'shinyWidgets', 'shinydashboard', 'DT', 'spsComps',
  'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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: ‘ranger’
checkRd: (-1) JobCollection.Rd:41: Lost braces
    41 |  \item{namespaces}{code{character} with required packages to load via \code{\link[base]{requireNamespace}}.}
       |                        ^
checkRd: (-1) addAlgorithm.Rd:31: Lost braces
    31 | Algorithms are functions which get the code{data} part as well as the problem instance (the return value of the
       |                                            ^
Running ‘testthat.R’ [31s/59s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(batchtools)
  > 
  > test_check("batchtools")
  ### [bt]: Setting seed to 29402 ...
  ### [bt]: Setting seed to 3080 ...
  ### [bt]: Setting seed to 3082 ...
  ### [bt]: Setting seed to 3081 ...
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 1452 ]
  
  ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test_ClusterFunctionsSSH.R:4:3', 'test_memory.R:4:3',
    'test_sweepRegistry.R:37:3'
  • Test requires killJobs (2): 'test_killJobs.R:3:3', 'test_waitForJobs.R:14:3'
  • Test requires listJobsRunning (1): 'test_findJobs.R:79:3'
  • manual test (1): 'test_manual.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_estimateRuntimes.R:20:3'): estimateRuntimes ────────────────────
  Error in `estimateRuntimes(tab, reg = reg)`: Please install package 'ranger' for runtime estimation
  Backtrace:
      ▆
   1. └─batchtools::estimateRuntimes(tab, reg = reg) at test_estimateRuntimes.R:20:3
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 1452 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘batchtools.Rmd’ using rmarkdown

Quitting from lines 383-389 [unnamed-chunk-23] (batchtools.Rmd)
Error: processing vignette 'batchtools.Rmd' failed with diagnostics:
there is no package called 'ranger'
--- failed re-building ‘batchtools.Rmd’

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

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

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

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

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

Package suggested but not available for checking: ‘INLA’

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

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 required but not available: 'reshape2', 'ggExtra'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'reshape', 'rstan', 'rstantools', 'mcmcse', 'StanHeaders',
  'RcppEigen'

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

Package suggested but not available for checking: ‘plumber’

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.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘forecast’

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: ‘MTS’

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 ?
Skipping checking math rendering: package 'V8' unavailable
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plyr’

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

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

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.
Package required but not available: ‘bayesDP’

Package suggested but not available for checking: ‘devtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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: \$
Skipping checking math rendering: package 'V8' unavailable
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}.}
       |                                                                    ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'reshape2', 'rstantools', 'rstan', 'RcppEigen', 'StanHeaders'

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

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
Packages required but not available:
  'oro.nifti', 'neurobase', 'Rcpp', 'RcppArmadillo', 'RcppDist'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'stars', 'terra', 'tmap', 'RcppArmadillo'

Package suggested but not available for checking: ‘RcppArmadillo’

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

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

Packages suggested but not available for checking: 'arm', 'lme4'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ciftiTools', 'excursions', 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking:
  'geometry', 'INLA', 'rdist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bayesplot', 'forecast', 'Rcpp', 'rstan', 'rstantools',
  'StanHeaders', 'prophet', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bayesplot', 'Rcpp', 'rstan', 'rstantools', 'geometry', 'RcppEigen',
  'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

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}.}
       |                                                            ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'AquaticLifeHistory', 'bayesplot', 'Rcpp', 'rstan', 'rstantools',
  'tidybayes', 'RcppEigen', 'StanHeaders'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reshape2', 'nse'

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

Packages suggested but not available for checking: 'clinDR', 'spelling'

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:
  'heatmaply', 'plotly', 'rintrojs', 'shiny', 'shinyAce',
  'shinydashboard', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rstan', 'ggpubr', 'lhs', 'Rcpp', 'reshape', 'rstantools',
  'RcppEigen', 'StanHeaders'

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

Packages suggested but not available for checking:
  'devtools', 'recipes', 'rstan', 'spelling'

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

Package suggested but not available for checking: ‘webshot2’

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

Packages suggested but not available for checking: 'lhs', 'sensitivity'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'factorstochvol', 'Rcpp', 'stochvol', 'RcppArmadillo'

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

Packages suggested but not available for checking: 'mcmcse', 'rstan'

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

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

Package suggested but not available for checking: ‘wpp2015’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

Quitting from lines 44-47 [unnamed-chunk-2] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'rstanarm'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'FastGP', 'Rcpp', 'RcppArmadillo'

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.}
       |                                    ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'shiny', 'leaflet', 'sf', 'RcppArmadillo'

Packages suggested but not available for checking:
  'spelling', 'ggforce', 'RcppArmadillo', 'shinythemes', 'DT',
  'datamods'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘brms’

Package suggested but not available for checking: ‘rstan’

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

Packages suggested but not available for checking:
  'shiny', 'cyjShiny', 'qtlnet'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape2’

Packages suggested but not available for checking:
  'rstan', 'rstanarm', 'rstantools', 'shinystan'

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

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

Package suggested but not available for checking: ‘wpp2015’

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

Package suggested but not available for checking: ‘bayesplot’

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

Package suggested but not available for checking: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'RcppEigen', 'RcppNumerical'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'forecast', 'scoringRules'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘pgdraw’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'reshape', 'plyr', 'RcppArmadillo', 'RcppDist'

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

Package suggested but not available for checking: ‘spelling’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstanarm', 'groupdata2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘splines2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'lme4', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'BDgraph', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'GGally', 'riskRegression', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'BayesFactor', 'bayesplot', 'blavaan', 'brms', 'collapse', 'gamm4',
  'ggdist', 'glmmTMB', 'lme4', 'marginaleffects', 'mediation',
  'ordbetareg', 'RcppEigen', 'rstan', 'rstanarm'
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'rworldmap', 'wpp2015', 'sf'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘extraDistr’

Packages suggested but not available for checking: '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 ?
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'faraway', 'hdi'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'rstan', 'StanHeaders', 'bayesplot', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'BDgraph', 'ess', 'RcppArmadillo', 'RcppEigen'

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

Package suggested but not available for checking: ‘spdep’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

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

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

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

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.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'pander', 'plyr'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'Rcpp', 'RcppAnnoy', 'reticulate', 'Rtsne', 'Seurat',
  'SeuratObject', 'uwot'

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

Package suggested but not available for checking: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 ?
Packages required but not available:
  'Rcpp', 'rstan', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'emdbook', 'AICcmodavg'
Note: skipping ‘quasi.Rnw’ due to unavailable dependencies: 'AICcmodavg'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'mvnfast', 'greybox', 'glmnet'

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘glmnet’
Error(s) in re-building vignettes:
  ...
--- re-building ‘bcaboot.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bcaboot.Rcheck/vign_test/bcaboot/vignettes/bcaboot_files/figure-html/unnamed-chunk-7-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 73718 bytes
Input file size = 73892 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 60031
  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 = 60031

Output IDAT size = 60031 bytes (13687 bytes decrease)
Output file size = 60109 bytes (13783 bytes = 18.65% decrease)


Quitting from lines 127-131 [unnamed-chunk-8] (bcaboot.Rmd)
Error: processing vignette 'bcaboot.Rmd' failed with diagnostics:
Please install glmnet package for this vignette.
--- failed re-building ‘bcaboot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
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:
  'lme4', 'mixAK', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'joineRML', 'survminer'

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
       |                                                                                                   ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘gRbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'crul', 'leaflet', 'leaflet.extras', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘fabiabreast.txt’
Packages required but not available: 'MCMCvis', 'reshape2', 'rstan'

Package suggested but not available for checking: ‘plotly’

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

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

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

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

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

Packages suggested but not available for checking:
  'lwgeom', 'raster', 'terra', 'stars'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Running ‘spelling.R’ [0s/0s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available:
  'CoordinateCleaner', 'DT', 'qs', 'rnaturalearth', 'sf'

Package suggested but not available for checking: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinyBS', 'shinydashboard', 'shinyjs', 'shinyFiles'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘pROC’

Packages suggested but not available for checking: 'ssgraph', 'huge'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'shinyBS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'cld2', 'tuber'
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘dump.txt’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘cvCovEst’
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
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘DWreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'DT', 'plyr', 'devtools'

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

Package suggested but not available for checking: ‘spelling’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'StanHeaders', 'RcppEigen'

Packages suggested but not available for checking:
  'shiny', 'pander', 'shinythemes', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'shiny', 'shinydashboard', 'httpuv', 'Rcpp', 'plyr'

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

Packages suggested but not available for checking: 'spelling', 'tracerer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘beast_plot_toy.pdf’
Packages required but not available: 'ggdist', 'mixtools'

Package suggested but not available for checking: ‘spelling’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘emdbook’

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

Package suggested but not available for checking: ‘webshot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CoordinateCleaner', 'ggspatial', 'openxlsx', 'rnaturalearth', 'sf'

Packages suggested but not available for checking:
  'bdc', 'devtools', 'emld', 'galah', 'leaflet', 'plotly', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘marginaleffects’
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

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

Package suggested but not available for checking: ‘openxlsx’

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

Package suggested but not available for checking: ‘openxlsx’

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

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

Packages suggested but not available for checking:
  'raster', 'rasterVis', 'stars', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'extraDistr', 'LambertW', 'Rcpp', 'rstan', 'rstantools', 'RcppEigen',
  'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_datatable_past
> ### Title: Interactive table of results
> ### Aliases: get_datatable_past
> 
> ### ** Examples
> 
> ## Need the DT package
> ## View all results for prog test
> get_datatable_past("prog")
Error: Install DT package to use datatable
Execution halted
Packages suggested but not available for checking: 'DT', 'RcppZiggurat'
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'tidybayes', 'RcppEigen',
  'StanHeaders'

Package suggested but not available for checking: ‘bayesplot’

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 ?
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) hill.Rd:39: Lost braces; missing escapes or markup?
    39 | \code{a} in {0, 1, 2} (see details))}
       |             ^
checkRd: (-1) read_ambi.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_ambi.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rstantools', 'rstan', 'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: ‘StanHeaders’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'gstat', 'ade4', 'leaflet', 'leaflet.extras'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'belg', 'comat', 'Rcpp', 'terra', 'landscapemetrics', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'glmnet', 'RcppEigen'

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinythemes', 'shinydashboard', 'shinyWidgets', 'shinyBS',
  'shinyjs', 'DT'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'mice', 'Amelia'
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
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ape', 'geometry', 'picante'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'car', 'quarto'

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Malformed Title field: should not end in a period.
Package required but not available: ‘Rcpp’

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

Package suggested but not available for checking: ‘devtools’

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: ‘Rcpp’

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

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

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

Packages suggested but not available for checking: 'stlplus', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'spelling'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'lme4', 'extraDistr', 'QRM'

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

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

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

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

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

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

Packages suggested but not available for checking: 'lme4', 'SKAT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'BFpack', 'GGally', 'mvnfast', 'reshape', 'Rcpp', 'RcppArmadillo',
  'RcppDist'

Packages suggested but not available for checking: 'networktools', 'mice'

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

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'EasyMx', 'OpenMx'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘car’

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

Package suggested but not available for checking: ‘qgraph’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bayesm', 'Rcpp', 'stochvol', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'oro.nifti', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'shiny', 'shinydashboard', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘humaniformat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bibliometrix’
Packages required but not available:
  'DT', 'ggrepel', 'plotly', 'openxlsx', 'rscopus', 'shiny', 'tidytext'

Package suggested but not available for checking: ‘shinycssloaders’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rcrossref’

Package suggested but not available for checking: ‘devtools’

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

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'fields', 'DAAG', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'pcalg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘crypto2’
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 'crypto2'
--- failed re-building ‘bidask.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
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}.
       |                                                                                                                                                                                                                                                                                  ^
Packages required but not available:
  'ape', 'sf', 'fasterize', 'raster', 'terra'

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

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

Package suggested but not available for checking: ‘alpaca’

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

Packages suggested but not available for checking: 'survey', 'TAM'

Packages which this enhances but not available for checking:
  'intsvy', 'LSAmitR'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ffbase’
Packages required but not available: 'sf', 'spatialreg', 'spdep'

Packages suggested but not available for checking: 'INLA', 'tmap'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fields’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'bigmemory', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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’.
Package required but not available: ‘plotly’

Packages suggested but not available for checking: 'shiny', 'DT'

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

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

Packages suggested but not available for checking: 'optmatch', 'rrelaxiv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Packages which this enhances but not available for checking:
  'biganalytics', 'bigtabulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘bigmemory’
Package required but not available: ‘flock’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘SKAT’
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. }
       |                                                                                                                                                                                                        ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘check-vs-SKAT-2.Rmd’ using rmarkdown

Quitting from lines 13-16 [unnamed-chunk-1] (check-vs-SKAT-2.Rmd)
Error: processing vignette 'check-vs-SKAT-2.Rmd' failed with diagnostics:
there is no package called 'SKAT'
--- failed re-building ‘check-vs-SKAT-2.Rmd’

--- re-building ‘matrix-free.Rmd’ using rmarkdown
--- finished re-building ‘matrix-free.Rmd’

--- re-building ‘skat-proj.Rmd’ using rmarkdown
--- finished re-building ‘skat-proj.Rmd’

SUMMARY: processing the following file failed:
  ‘check-vs-SKAT-2.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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

Package suggested but not available for checking: ‘spelling’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bigstatsr', 'bigparallelr', 'bigsparser', 'bigreadr', 'bigutilsr',
  'Rcpp', 'runonce', 'RcppArmadillo', 'roptim'

Packages suggested but not available for checking:
  'gaston', 'pcadapt', 'RSpectra', 'spelling'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'bigparallelr', 'Rcpp', 'RSpectra', 'RcppArmadillo'

Packages suggested but not available for checking:
  'bigmemory', 'bigreadr', 'glmnet', 'ModelMetrics', 'plotly',
  'spelling'

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

Package suggested but not available for checking: ‘devtools’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bigparallelr', 'nabor', 'Rcpp', 'RSpectra'

Packages suggested but not available for checking: 'Gmedian', 'spelling'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ade4', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape2’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘gsDesign’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘semver’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
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 ?
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppEigen'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_jenksbreaks
> ### Title: Create Jenks breaks
> ### Aliases: create_jenksbreaks
> 
> ### ** Examples
> 
> jenks_breaks <- create_breaks(1:10, method="jenks")
Error in create_jenksbreaks(x, control = control) : 
  Please install BAMMtools: install.packages('BAMMtools')
Calls: create_breaks -> create_jenksbreaks
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(binst)
  > 
  > test_check("binst")
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 18 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_jenks.R:4:3'): jenks breaks ────────────────────────────────────
  Error in `create_jenksbreaks(x, control = control)`: Please install BAMMtools: install.packages('BAMMtools')
  Backtrace:
      ▆
   1. └─binst::create_breaks(1:10, method = "jenks") at test_jenks.R:4:3
   2.   └─binst::create_jenksbreaks(x, control = control)
  ── Error ('test_jenks.R:11:3'): jenks breaks for iris ──────────────────────────
  Error in `create_jenksbreaks(x, control = control)`: Please install BAMMtools: install.packages('BAMMtools')
  Backtrace:
      ▆
   1. └─binst::create_breaks(iris$Sepal.Length, method = "jenks") at test_jenks.R:11:3
   2.   └─binst::create_jenksbreaks(x, control = control)
  ── Error ('test_jenks.R:17:3'): jenks breaks has control params correctly passed ──
  Error in `create_jenksbreaks(x, control = control)`: Please install BAMMtools: install.packages('BAMMtools')
  Backtrace:
      ▆
   1. └─binst::create_breaks(1:10, method = "jenks", control = list(k = 3)) at test_jenks.R:17:3
   2.   └─binst::create_jenksbreaks(x, control = control)
  ── Error ('test_jenks.R:22:3'): jenks breaks has control params correctly passed when k is not in it ──
  Error in `create_jenksbreaks(x, control = control)`: Please install BAMMtools: install.packages('BAMMtools')
  Backtrace:
      ▆
   1. └─binst::create_breaks(1:10, method = "jenks", control = list(subset = NULL)) at test_jenks.R:22:3
   2.   └─binst::create_jenksbreaks(x, control = control)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 18 ]
  Error: Test failures
  Execution halted
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

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

Packages suggested but not available for checking: 'bigmemory', 'msa'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcmdr’

Packages suggested but not available for checking:
  'car', 'effects', 'dismo', 'raster', 'terra', 'maxlike', 'glmnet',
  'geosphere', 'ENMeval', 'red', 'maxnet', 'sf', 'blockCV', 'envirem',
  'concaveman'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mixtools', 'shiny', 'shinydashboard', 'shinyWidgets', 'golem'

Package suggested but not available for checking: ‘pander’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ringApply.Rd:9: Lost braces; missing escapes or markup?
     9 |   \item{lv}{{numeric} position, or {character} name, of an
       |                                    ^
Skipping checking math rendering: package 'V8' unavailable
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
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'FME', 'lamW'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘FME’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'WGCNA', 'caret', 'ggpubr', 'ggstatsplot', 'jiebaR', 'mlr3verse',
  'uwot', 'ggforce', 'ggnetwork'

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

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

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

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

Package suggested but not available for checking: ‘geodata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking:
  'asreml', 'ARTool', 'lme4', 'sommer'
Packages required but not available: 'terra', 'reshape', 'reshape2', 'pROC'

Packages suggested but not available for checking:
  'maxnet', 'car', 'caret', 'dismo', 'ENMeval', 'raster', 'ggpubr',
  'tidyterra', 'ggtext'

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

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:
  'kohonen', 'imagerExtra', 'GPareto'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fields', 'lutz', 'raster', 'sf', 'suntools'

Packages suggested but not available for checking:
  'ggspatial', 'prettymapr', 'vol2birdR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'bipartite', 'dbscan', 'fastkmedoids', 'sf', 'Rcpp'

Packages suggested but not available for checking: 'ade4', 'rnaturalearth'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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}.
       |                                                                                                                                                                              ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'energy', 'fda.usc', 'parallelDist', 'osqp', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'devtools', 'glmnet', 'plsRcox', 'pROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'car', 'bshazard', 'rstpm2', 'Epi'
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
Package required but not available: ‘learnr’

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'afex', 'MCMCglmm', 'openxlsx', 'plyr', 'reportRmd', 'rstatix'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'soilphysics', 'SpatialEpi'
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘bipartite’
Running examples in ‘bipartiteD3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Matrix2DF
> ### Title: Convert a bipartite-style matrix to dataframe
> ### Aliases: Matrix2DF
> 
> ### ** Examples
> 
> 
> data(Safariland, package='bipartite')
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘bipartite’
Calls: data -> find.package
Execution halted
Note: skipping ‘bipartiteD3_Intro.Rmd’ due to unavailable dependencies:
  'bipartite'
Package required but not available: ‘Rcpp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dclone', 'mice', 'micemd', 'miceadds'
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 suggested but not available for checking:
  'caret', 'geometry', 'ggrepel'
Running examples in ‘biplotEZ-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alpha.bags
> ### Title: Create alpha bags
> ### Aliases: alpha.bags
> 
> ### ** Examples
> 
> biplot (iris[,1:4]) |> PCA(group.aes=iris[,5]) |> alpha.bags(alpha=0.95) |> plot()
Computing 0.95 -bag for setosa 
Error in loadNamespace(x) : there is no package called ‘geometry’
Calls: plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: ‘wru’

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

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

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: ‘sf’
Running examples in ‘biscale-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bi_scale_color
> ### Title: Apply Bivariate Color to ggplot Object
> ### Aliases: bi_scale_color
> 
> ### ** Examples
> 
> # load dependencies
> library(ggplot2)
> 
> # add breaks, 3x3
> data <- bi_class(stl_race_income, x = pctWhite, y = medInc, style = "quantile", dim = 3)
> 
> # create map
> plot <- ggplot() +
+   geom_sf(data = data, aes(color = bi_class), size = 2, show.legend = FALSE) +
+   bi_scale_color(pal = "GrPink", dim = 3)
Error in loadNamespace(x) : there is no package called ‘sf’
Calls: geom_sf ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘devtools’

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

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

Package suggested but not available for checking: ‘spam’

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

Package suggested but not available for checking: ‘fields’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MarkerBasedDecomposition
> ### Title: Performs marker-based decomposition of bulk expression using
> ###   marker genes
> ### Aliases: MarkerBasedDecomposition
> 
> ### ** Examples
> 
> library(Biobase)
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> sim.data <- SimulateData(n.ind=10, n.genes=100, n.cells=100,
+                          cell.types=c("Neurons", "Astrocytes", "Microglia"),
+                          avg.props=c(.5, .3, .2))
Error in loadNamespace(x) : there is no package called ‘plyr’
Calls: SimulateData ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BisqueRNA)
  > 
  > test_check("BisqueRNA")
  [ FAIL 1 | WARN 9 | SKIP 0 | PASS 51 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_sim.R:6:3'): Simulation provides output ────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'plyr'
  Backtrace:
      ▆
   1. ├─BisqueRNA::SimulateData(3, 3, 2, c("a", "b"), c(0.5, 0.5)) at test_sim.R:6:3
   2. │ └─base::sapply(1:n.cells, function(x) SimulateBarcode(x, ind, barcode.length))
   3. │   └─base::lapply(X = X, FUN = FUN, ...)
   4. │     └─BisqueRNA (local) FUN(X[[i]], ...)
   5. │       └─BisqueRNA:::SimulateBarcode(x, ind, barcode.length)
   6. └─base::loadNamespace(x)
   7.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8.     └─base (local) withOneRestart(expr, restarts[[1L]])
   9.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 9 | SKIP 0 | PASS 51 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bisque.Rmd’ using rmarkdown

Quitting from lines 67-74 [simulate] (bisque.Rmd)
Error: processing vignette 'bisque.Rmd' failed with diagnostics:
there is no package called 'plyr'
--- failed re-building ‘bisque.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'rstantools', 'Rcpp', 'rstan', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘tidyquant’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'gridpattern', 'magick'
Packages required but not available:
  'terra', 'caper', 'picante', 'ape', 'betapart', 'CommEcol'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rfast’

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

Package suggested but not available for checking: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘mrfDepth’
Packages required but not available: 'fields', 'Rcpp'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘RQuantLib’
Package required but not available: ‘DHARMa’

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.
Package required but not available: ‘fields’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'geometry', 'spaMM', 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking: 'minqa', 'lbfgsb3c'

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

Packages suggested but not available for checking: 'geodata', 'tidyterra'

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

Quitting from lines 116-119 [unnamed-chunk-5] (introduction_to_blaise.Rmd)
Error: processing vignette 'introduction_to_blaise.Rmd' failed with diagnostics:
there is no package called 'LaF'
--- failed re-building ‘introduction_to_blaise.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ggExtra’
Package required but not available: ‘RSpectra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘openxlsx’
Running ‘testthat.R’ [21s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(blastula)
  > 
  > test_check("blastula")
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 150 ]
  
  ══ Skipped tests (10) ══════════════════════════════════════════════════════════
  • On CRAN (10): 'test-add_cta_button.R:10:3', 'test-blocks.R:6:3',
    'test-blocks.R:25:3', 'test-blocks.R:54:3', 'test-helper_fcns.R:15:3',
    'test-integration.R:105:3', 'test-render_blocks.R:6:3',
    'test-render_blocks.R:14:3', 'test-render_blocks.R:29:3',
    'test-render_blocks.R:76:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-mime.R:155:7'): excel attachment ───────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'openxlsx'
  Backtrace:
      ▆
   1. ├─withr::with_tempfile(...) at test-mime.R:151:3
   2. │ └─base::eval(substitute(code), envir = env)
   3. │   └─base::eval(substitute(code), envir = env)
   4. └─base::loadNamespace(x) at test-mime.R:155:7
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 150 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'bayesplot', 'StanHeaders',
  'RcppEigen'

Package suggested but not available for checking: ‘cmdstanr’

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

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

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

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

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’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'rtkore', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'Rcpp'

Packages suggested but not available for checking:
  'terra', 'automap', 'shiny', 'tmap', 'biomod2', 'gstat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'glmnet', 'glmnetcr', 'pryr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'DT', 'shinybusy', 'shinyjs', 'shinythemes'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'collapse', 'ks'

Packages suggested but not available for checking:
  'devtools', 'questionr', 'reldist'

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

Packages suggested but not available for checking: 'miniUI', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'car', 'Rcpp'

Package suggested but not available for checking: ‘xplorerr’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'caret'

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Amelia', 'sem'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'forecast', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'edstan', 'RcppEigen', 'StanHeaders'

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

Package suggested but not available for checking: ‘plm’

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:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

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

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

Packages suggested but not available for checking: 'cmdstanr', 'tidybayes'

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
Packages required but not available: 'fields', 'multicool'

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

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'spTimer', 'rstan', 'rstantools', 'CARBayes', 'CARBayesST',
  'spTDyn', 'inlabru', 'ggpubr', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'INLA', 'extraDistr', 'ggrepel', 'sf', 'ggspatial', 'interp',
  'magick'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'gRain', 'gRbase'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'gRbase', 'gRain'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'gRain', 'gRbase', 'qgraph', 'reshape2'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'GreedyEPL', 'BNPmix'
checkRd: (-1) MvInv.Rd:23-35: Lost braces
    23 | function(eps, u = 0.5, alpha = 1, kappa = 1, gama = 1 / 2, N = 3001) {
       |                                                                      ^
checkRd: (-1) dt_.Rd:19-21: Lost braces
    19 | function(x, df, mean, sd) {
       |                           ^
Running examples in ‘BNPdensity-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MixPY1
> ### Title: Pitman-Yor process mixture of Type I
> ### Aliases: MixPY1
> 
> ### ** Examples
> 
> # Data
> data(acidity)
> x <- acidity
> # Fitting the model under default specifications
> out <- MixPY1(x)
Error: Package "BNPmix" is needed for this function to work. Please install it.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'ggpubr', 'RcppArmadillo', 'RcppDist'

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

Package suggested but not available for checking: ‘popkin’

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

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

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

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

Package suggested but not available for checking: ‘np’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qgraph’
Packages required but not available: 'shiny', '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}} }
       |                                             ^
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘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 'reshape2'
--- 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: 'ranger', 'opera'

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

Packages suggested but not available for checking:
  'adiposerefdata', 'musclerefdata'

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 ?
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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>
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

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

Package suggested but not available for checking: ‘openxlsx’

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:
  'brms', 'glmnet', 'Rcpp', 'splines2', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'aorsf', 'tune'
Packages required but not available: 'Rcpp', 'RcppNumerical', 'RcppEigen'

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'miniUI', 'servr', 'shiny'
Package required but not available: ‘pryr’

Packages suggested but not available for checking: 'flow', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

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

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'IsingFit', 'qgraph', 'IsingSampler', 'mgm', 'NetworkToolbox',
  'networktools'

Packages suggested but not available for checking:
  'GGMncv', 'BDgraph', 'graphicalVAR', 'relaimpo', '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', 'gt', 'flextable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘qvalue’
Package unavailable to check Rd xrefs: ‘qvalue’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
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
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'npboottprm', 'shiny', 'shinyjs', 'shinythemes'

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

Package suggested but not available for checking: ‘mvabund’

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

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

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

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

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

Package suggested but not available for checking: ‘devtools’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘imager’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘latticeExtra’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rhino', 'shiny', 'spelling'
Packages required but not available: 'DT', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'devtools', 'shiny'
Package required but not available: ‘httpuv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'mcmcse', 'Rcpp', 'fabMix', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'spelling'
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘qpdf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp_sv.Rd:75: Lost braces; missing escapes or markup?
    75 | $$SV = sqrt(sum(x_{i+1} - x_i)^2/n-1)$$
       |                   ^
checkRd: (-1) bp_sv.Rd:80: Lost braces; missing escapes or markup?
    80 | $$SD = sqrt(sum(x_{i+1} - xbar)^2/n-1)$$
       |                   ^
checkRd: (-1) sv.Rd:78: Lost braces; missing escapes or markup?
    78 | $$SV = sqrt(sum(x_{i+1} - x_i)^2/n-1)$$
       |                   ^
checkRd: (-1) sv.Rd:82: Lost braces; missing escapes or markup?
    82 | $$SD = sqrt(sum(x_{i+1} - xbar)^2/n-1)$$
       |                   ^
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: ‘spelling’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'geojsonio', 'raster', 'rgbif', 'rnaturalearth', 'sf'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘V8’
Package required but not available: ‘reticulate’

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

Package suggested but not available for checking: ‘DT’

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 required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'devtools', 'hunspell', 'quarto'

Packages suggested but not available for checking: 'rstatix', 'spelling'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ade4', 'car', 'ggrepel', 'mediation', 'oro.nifti'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'CCA', 'brainR', 'oro.nifti'

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

Package suggested but not available for checking: ‘servr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘QCA’

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

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

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

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

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

Package suggested but not available for checking: ‘devtools’

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

Package suggested but not available for checking: ‘spelling’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'caret', 'ranger'
Packages required but not available: 'plyr', 'Rcpp'

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

Package suggested but not available for checking: ‘breathteststan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'breathtestcore', 'StanHeaders',
  'RcppEigen'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
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 ?
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'DT', 'shiny'
Package suggested but not available for checking: ‘reshape2’
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
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'shinydashboard', 'plotly'

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'Rcpp', 'RcppEigen', 'BayesFactor', 'rstan', 'rstanarm'
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘splines2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'brms', 'Rcpp', 'RcppArmadillo'

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

Packages suggested but not available for checking:
  'fst', 'gt', 'gtsummary', 'mmrm', 'Rcpp', 'RcppEigen', 'rstan',
  'StanHeaders'

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

Packages suggested but not available for checking:
  'cmdstanr', 'projpred', 'priorsense', 'shinystan', 'splines2',
  'rtdists', 'extraDistr', 'mice', 'spdep', 'lme4', 'MCMCglmm', 'ape',
  'arm', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘cubature’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Cyclops’

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

Packages suggested but not available for checking: 'mice', 'plyr'

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

Packages suggested but not available for checking:
  'gghighlight', 'lme4', 'spelling', 'tsibbledata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages suggested but not available for checking:
  'brms', 'effects', 'fixest', 'glmmTMB', 'gt', 'gtsummary', 'lme4',
  'marginaleffects', 'mice', 'mmrm', 'multgee', 'plm', 'rstanarm',
  'spelling', 'survey', 'tidycmprsk'
Running examples in ‘broom.helpers-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: model_get_n
> ### Title: Get the number of observations
> ### Aliases: model_get_n model_get_n.default model_get_n.glm
> ###   model_get_n.glmerMod model_get_n.multinom model_get_n.LORgee
> ###   model_get_n.coxph model_get_n.survreg model_get_n.model_fit
> ###   model_get_n.tidycrr
> 
> ### ** Examples
> 
> lm(hp ~ mpg + factor(cyl) + disp:hp, mtcars) |>
+   model_get_n()
# A tibble: 6 × 2
  term         n_obs
  <chr>        <dbl>
1 (Intercept)     32
2 mpg             32
3 factor(cyl)6     7
4 factor(cyl)8    14
5 hp:disp         32
6 factor(cyl)4    11
> 
> mod <- glm(
+   response ~ stage * grade + trt,
+   gtsummary::trial,
+   family = binomial,
+   contrasts = list(stage = contr.sum, grade = contr.treatment(3, 2), trt = "contr.SAS")
+ )
Error in loadNamespace(x) : there is no package called ‘gtsummary’
Calls: glm ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tidy.Rmd’ using rmarkdown

Quitting from lines 33-46 [setup] (tidy.Rmd)
Error: processing vignette 'tidy.Rmd' failed with diagnostics:
there is no package called 'gtsummary'
--- failed re-building ‘tidy.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'brms', 'dotwhisker', 'glmmADMB', 'glmmTMB', 'lmerTest', 'lme4',
  'MCMCglmm', 'mediation', 'pander', 'pbkrtest', 'rstan', 'rstanarm',
  'rstantools', 'TMB'
Packages suggested but not available for checking:
  'AER', 'car', 'caret', 'drc', 'epiR', 'fixest', 'glmnet',
  'glmnetUtils', 'interp', 'joineRML', 'ks', 'lme4', 'mediation',
  'plm', 'spdep', 'spatialreg', 'spelling', 'survey', 'systemfit'
Package suggested but not available for checking: ‘spelling’
Running ‘spelling.R’ [0s/0s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package required but not available: ‘httpuv’

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:
  'plyr', 'afex', 'mediation', 'interactions', 'jtools', 'lmerTest'

Packages suggested but not available for checking:
  'openxlsx', 'ggtext', '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'.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘torch’

Packages suggested but not available for checking: 'recipes', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'blavaan', 'blme', 'rstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'fresh', 'waiter', 'httpuv'

Packages suggested but not available for checking: 'golem', 'DT'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘webshot2’

Packages suggested but not available for checking:
  'shiny', 'reactable.extras'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Epi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘webshot2’
Package suggested but not available for checking: ‘shiny’
Package required but not available: ‘ggpubr’

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

Packages suggested but not available for checking:
  'bayesplot', 'collapse', 'jtools', 'extraDistr', 'spelling', 'ggtext'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: run_with_themer
> ### Title: Theme customization UI
> ### Aliases: run_with_themer bs_themer
> 
> ### ** Examples
> 
> library(shiny)
Error in library(shiny) : there is no package called ‘shiny’
Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘mixtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘C50’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'glmnet', 'neurobase', 'oro.nifti', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BayesFactor', 'mvnfast', 'RSpectra', 'plyr', 'ks', 'ggmcmc', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bs_accordion_sidebar
> ### Title: Accordion-sidebar panel-group
> ### Aliases: bs_accordion_sidebar use_bs_accordion_sidebar
> ###   bs_append.bsplus_accordion_sidebar
> ###   bs_set_opts.bsplus_accordion_sidebar
> 
> ### ** Examples
> 
> bs_accordion_sidebar(id = "meet_the_beatles") %>%
+   bs_append(
+     title_side = "John Lennon",
+     content_side = "Rhythm guitar, vocals",
+     content_main = "Dear Prudence"
+   ) %>%
+   bs_append(
+     title_side = "Paul McCartney",
+     content_side = "Bass guitar, vocals",
+     content_main = "Blackbird"
+   )
Error in loadNamespace(x) : there is no package called ‘shiny’
Calls: %>% ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bsplus)
  > 
  > test_check("bsplus")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 75 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-accordion_sidebar.R:4:1'): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `library("shiny")`: there is no package called 'shiny'
  Backtrace:
      ▆
   1. └─base::library("shiny") at test-accordion_sidebar.R:4:1
  ── Error ('test-shiny.R:3:1'): (code run outside of `test_that()`) ─────────────
  Error: Shiny needed for this function to work. Please install it.
  Backtrace:
      ▆
   1. └─bsplus::shiny_iconlink() at test-shiny.R:3:1
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 75 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘stochvol’
Running examples in ‘bsreg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bm
> ### Title: Fit a Bayesian model
> ### Aliases: bm bm.formula bm.bm blm bslx bsar bsem bsdm bsdem bsv
> 
> ### ** Examples
> 
> N <- 100L
> beta <- 1:5
> X <- matrix(rnorm(N * 5), N, 5)
> y <- X %*% beta + rnorm(N)
> 
> bm(y ~ X, n_burn = 100, n_draw = 100)
Error: Package 'stochvol' required for this method.
Execution halted
Package required but not available: ‘fICA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bayesplot', 'diagis', 'Rcpp', 'ramcmc', 'RcppArmadillo', 'sitmo'

Packages suggested but not available for checking: 'ramcmc', 'sde', 'sitmo'

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.
Packages required but not available: 'SpatialBSS', 'rSPDE'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'hdi', 'pROC'
Note: skipping ‘pros.Rnw’ due to unavailable dependencies: 'pROC'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘extraDistr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'gt', 'gtsummary', 'reshape', 'spam'

Package suggested but not available for checking: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'DT', 'shiny', 'shinyjqui'
Packages required but not available: 'RcppArmadillo', 'bsvars', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppTN', 'stochvol', 'RcppArmadillo'

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

Package suggested but not available for checking: ‘gsynth’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mapsf', 'Rcpp', 'sf', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘fastglm’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

Package suggested but not available for checking: ‘udpipe’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggforce', 'plyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'bayesm'

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

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
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'plyr', 'RcppArmadillo'

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

Packages suggested but not available for checking:
  'gamm4', 'glmertree', 'glmmTMB', 'lmerTest', 'pbkrtest'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'gprofiler2', 'DESeq2', 'ggrepel', 'shinyWidgets',
  'shinyjqui', 'ggforce', 'noisyr', 'GENIE3', 'DT', 'shinyjs',
  'shinyLP', 'UpSetR'

Package suggested but not available for checking: ‘shinythemes’

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

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

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

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

Packages suggested but not available for checking:
  'DescTools', 'energy', 'linkspotter', 'minerva'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'car', 'rsq'
Error(s) in re-building vignettes:
  ...
--- re-building ‘bumbl.Rmd’ using rmarkdown

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

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'caret', 'embed', 'keras', 'luz', 'recipes', 'stacks', 'tensorflow',
  'torch', 'torchvision', 'uwot'
Packages required but not available: 'shiny', 'miniUI'

Package suggested but not available for checking: ‘edeaR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bupaR', 'edeaR', 'processcheckR', 'processmapR'

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: 'plyr', 'reshape2'

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

Package suggested but not available for checking: ‘devtools’

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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘shiny’
checkRd: (-1) depreciation-class.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) depreciation-class.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) depreciation-class.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) depreciation-class.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loan-class.Rd:46-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loan-class.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loan-class.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model2df-methods.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model2df-methods.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model2df-methods.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model2df-methods.Rd:38-39: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking:
  'C50', 'caret', 'ClusterR', 'ddalpha', 'flexsurv', 'ipred', 'klaR',
  'nestedmodels', 'ranger', 'recipes', 'RSpectra', 'xrf'
Packages required but not available:
  'Rcpp', 'prodlim', 'riskRegression', 'RcppArmadillo'

Package suggested but not available for checking: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'RcppEigen', 'RcppNumerical'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

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

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: ‘Rcpp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plyr', 'ranger'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Seurat', 'reshape2'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CADF_to_migration_model
> ### Title: CADF_to_migration_model converts CADF data to migration model
> ###   data
> ### Aliases: CADF_to_migration_model
> 
> ### ** Examples
> 
> tmatrix <- CADF_to_migration_model(cadf.data.sample)
Error in loadNamespace(x) : there is no package called ‘markovchain’
Calls: CADF_to_migration_model ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘dynlm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'Seurat', 'DescTools', 'ProFAST', 'ggrepel', 'scater',
  'ade4', 'RcppArmadillo'

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

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', 'ggrepel', 'RcmdrMisc', 'reshape2'

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

Quitting from lines 51-53 [unnamed-chunk-1] (Adapting_Algorithm_for_CAISEr.Rmd)
Error: processing vignette 'Adapting_Algorithm_for_CAISEr.Rmd' failed with diagnostics:
there is no package called 'smoof'
--- failed re-building ‘Adapting_Algorithm_for_CAISEr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ape', 'heatmaply', 'plotly', 'DT'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘cubature’

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

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

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

Package suggested but not available for checking: ‘ranger’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'minqa', 'lbfgsb3c'

Package suggested but not available for checking: ‘ibm’

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

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

Package suggested but not available for checking: ‘ReGenesees’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘cubature’

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

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

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

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

Package suggested but not available for checking: ‘spelling’

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

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

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

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

Package suggested but not available for checking: ‘sctransform’

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

Package suggested but not available for checking: ‘devtools’

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

Packages suggested but not available for checking:
  'devtools', 'mrgsolve', 'rxode2'

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

Packages suggested but not available for checking:
  'DT', 'leaflet', 'magick', 'mapview', 'overlap', 'plotly',
  'reshape2', 'ritis', 'shiny', 'shinydashboard', 'tesseract',
  'taxize', 'terra', 'units', 'unmarked'

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

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

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

Package suggested but not available for checking: ‘picante’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'leaflet', 'mapdeck', 'sf', 'geojsonsf', 'lwgeom'
Packages required but not available: 'plyr', 'BoutrosLab.plotting.general'

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

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

Packages suggested but not available for checking:
  'DT', 'pander', 'shinythemes', 'spelling'

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

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

Packages suggested but not available for checking:
  'Seurat', 'scater', 'batchelor', 'scran'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'DT'
Packages required but not available: 'propagate', 'qtl2', 'qtl2convert'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'shinyjs', 'shinyWidgets', 'shinyjqui', 'plotly',
  'rintrojs', 'shinycssloaders', 'DT'

Packages suggested but not available for checking:
  'shinydashboard', 'shinydashboardPlus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reticulate’

Packages suggested but not available for checking:
  'Ryacas', 'magick', 'pdftools', 'qpdf'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'CARBayesdata', 'GGally', 'glmnet', 'mapview', 'sf', 'spam',
  'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'CARBayesdata', 'GGally', 'leaflet', 'sf', 'spam', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'httpuv', 'magick', 'RSelenium', 'wdman'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'shinydashboard'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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: \$
Skipping checking math rendering: package 'V8' unavailable
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
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘qpdf’

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

Package suggested but not available for checking: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages suggested but not available for checking:
  'car', 'lme4', 'spelling', 'survey'
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggrepel’

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

Packages suggested but not available for checking:
  'glmnet', 'klaR', 'spelling'

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

Package suggested but not available for checking: ‘Cubist’

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

Packages suggested but not available for checking:
  'BradleyTerry2', 'Cubist', 'ipred', 'klaR', 'subselect', 'themis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) build_for_cran.Rd:13: Lost braces
    13 | The exit status code{R CMD build}, invisibly.
       |                     ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

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', 'survey'

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

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

Package suggested but not available for checking: ‘cartography’

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

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

Package suggested but not available for checking: ‘lwgeom’

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

Packages suggested but not available for checking:
  'rnaturalearth', 'rnaturalearthhires'

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

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

Packages suggested but not available for checking:
  'lwgeom', 'SpatialPosition'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'ranger', 'pryr', 'RcppArmadillo'

Package suggested but not available for checking: ‘RcppArmadillo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘glmnet’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘extraDistr’

Package suggested but not available for checking: ‘glmnet’

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

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

Package suggested but not available for checking: ‘pROC’

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

Package suggested but not available for checking: ‘GGally’

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

Package suggested but not available for checking: ‘ape’

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

Packages suggested but not available for checking:
  'geodata', 'mapview', 'stars', 'rnaturalearth', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
Running examples in ‘cat2cat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary_c2c
> ### Title: Adjusted summary for linear regression when based on replicated
> ###   dataset
> ### Aliases: summary_c2c
> 
> ### ** Examples
> 
> data("occup_small", package = "cat2cat")
> data("trans", package = "cat2cat")
> 
> occup_old <- occup_small[occup_small$year == 2008, ]
> occup_new <- occup_small[occup_small$year == 2010, ]
> 
> occup_2 <- cat2cat(
+   data = list(
+     old = occup_old,
+     new = occup_new,
+     cat_var = "code",
+     time_var = "year"
+   ),
+   mappings = list(trans = trans, direction = "backward"),
+   ml = list(
+     data = occup_new,
+     cat_var = "code",
+     method = "knn",
+     features = c("age", "sex", "edu", "exp", "parttime", "salary"),
+     args = list(k = 10)
+   )
+ )
Error in delayed_package_load("caret", sprintf("Please install %s package to use the %s model in the cat2cat function.",  : 
  Please install caret package to use the knn model in the cat2cat function.
Calls: cat2cat -> cat2cat_ml -> validate_ml -> delayed_package_load
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cat2cat.Rmd’ using rmarkdown

Quitting from lines 95-120 [unnamed-chunk-2] (cat2cat.Rmd)
Error: processing vignette 'cat2cat.Rmd' failed with diagnostics:
Please install caret package to use the knn model in the cat2cat function.
--- 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: 'mapSpain', 'sf', 'terra'

Packages suggested but not available for checking:
  'slippymath', 'tidyterra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'Ecdat', 'lme4', 'glmnet', 'penalized'
Note: skipping ‘multinomial-travel.Rnw’ due to unavailable dependencies:
  'Ecdat'
Note: skipping ‘random-knee2.Rnw’ due to unavailable dependencies: 'lme4'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ade4', 'ape', 'rasterVis', 'hypervolume', 'FD', 'geometry'

Packages suggested but not available for checking:
  'entropart', 'picante', 'mice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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.
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 ?
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'marginaleffects', 'ggpubr', 'Epi', 'lme4'
Running examples in ‘catregs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compare.margins
> ### Title: Compares two marginal effects (MEMs or AMEs). Estimate of
> ###   uncertainty is from a simulated draw from a normal distribution.
> ### Aliases: compare.margins
> 
> ### ** Examples
> 
> data("essUK")
> m1 <- glm(safe ~ religious + minority*female + age,data=essUK,family="binomial")
> des<-margins.des(m1,expand.grid(minority=c(0,1),female=c(0,1)))
> des
  minority female religious      age
1        0      0  3.602404 53.14563
2        1      0  3.602404 53.14563
3        0      1  3.602404 53.14563
4        1      1  3.602404 53.14563
> ma1<-suppressWarnings(as.data.frame(marginaleffects::avg_slopes(m1,
+ variables="female",newdata=data.frame(minority=0,religious=3.6024,age=53.146))))
Error in loadNamespace(x) : there is no package called ‘marginaleffects’
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

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

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'Rcpp', 'RcppArmadillo', 'RcppGSL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rfast', 'Rfast2'

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

Packages suggested but not available for checking: 'spelling', 'geiger'

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

Package suggested but not available for checking: ‘extraDistr’

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

Package suggested but not available for checking: ‘ks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggalt', 'modEvA', 'naniar', 'DT', 'hrbrthemes', 'summarytools'
Packages required but not available: 'CBPS', 'PSweight', 'spelling'

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.
Package required but not available: ‘survey’

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'wCorr', 'Rcpp', 'Ecume'

Package suggested but not available for checking: ‘ranger’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CBPS', 'lbfgsb3c', 'osqp', 'Rcpp', 'torch', 'RcppEigen'

Packages suggested but not available for checking:
  'reticulate', 'rkeops', 'V8'

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'dagitty', 'rstan', 'rstantools', 'ggdag', 'RcppArmadillo',
  'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'DeclareDesign', 'bayesplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ranger', 'np', 'hdm', 'glmnet', 'grf'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'metap', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'hypergeo2', 'Rcpp'

Package suggested but not available for checking: ‘extraDistr’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'MatchIt', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'sf'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'terra', 'lwgeom'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rfast’

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

Packages suggested but not available for checking:
  'countcolors', 'devtools', 'DT'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'diceR', 'plyr'

Package suggested but not available for checking: ‘spelling’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ufs’

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

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

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

Package suggested but not available for checking: ‘nnTensor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘hotcold.csv’
Packages required but not available:
  'plotly', 'shiny', 'bs4Dash', 'fresh', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ddpcr', 'RcppArmadillo', 'RcppDist', 'RcppNumerical',
  'RcppEigen'

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

Package suggested but not available for checking: ‘CDM’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘caret’

Package suggested but not available for checking: ‘ranger’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'odbc', 'DatabaseConnector', 'pool'
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'BIFIEsurvey', 'miceadds'

Packages which this enhances but not available for checking:
  'dina', 'GDINA', 'mirt', 'rrum'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plotly', 'freqparcoord', 'partools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'geojsonsf', 'lutz', 'sf', 'terra'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘mixtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sdcHierarchies', 'sdcTable', 'ptable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'Seurat', 'DESeq2', 'RcppAnnoy', 'SeuratObject'
Running examples in ‘cellpypes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: find_knn
> ### Title: Find approximate k-nearest neighbors
> ### Aliases: find_knn
> 
> ### ** Examples
> 
>   # Imagine we have 30 cells and 100 features:
>  fmat <- matrix(rnorm(3000), ncol=30)
>  nn <- find_knn(fmat,k=15)
Error in find_knn(fmat, k = 15) : 
  requireNamespace("RcppAnnoy", quietly = TRUE) is not TRUE
Calls: find_knn -> stopifnot
Execution halted
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'wordspace', 'RSpectra', 'uwot'
Running ‘testthat.R’ [8s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(celltrackR)
  > 
  > test_check("celltrackR")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 322 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'testImmuneMapIntegration.R:20:2'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('testClusterFunctions.R:8:1'): (code run outside of `test_that()`) ───
  <packageNotFoundError/error/condition>
  Error in `packageVersion("irlba")`: there is no package called 'irlba'
  Backtrace:
      ▆
   1. └─utils::packageVersion("irlba") at testClusterFunctions.R:8:1
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 322 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reshape2', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'robustHD', 'rospca', 'GSE'

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

Package suggested but not available for checking: ‘Amelia’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'icenReg', 'condSURV', 'RcppEigen'

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'MomTrunc', 'tlrmvnmvt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘chilemapas’
Package suggested but not available for checking: ‘geobr’
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Package required but not available: ‘prodlim’

Packages suggested but not available for checking:
  'aorsf', 'flexsurv', 'glmnet', 'ipred', 'pec'

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

Package suggested but not available for checking: ‘AER’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggrepel’
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
       |         ^
checkRd: (-1) call_api_once.Rd:36: Lost braces
    36 | A code{data.frame} with the requested variables at the requested
       |       ^
'LazyData' is specified without a 'data' directory
Packages required but not available: 'sf', 'sfnetworks'

Packages suggested but not available for checking: 'smoothr', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) centroid.Rd:22: Lost braces; missing escapes or markup?
    22 | Centroid value C_{cen}(v) for node v defined as:
       |                  ^
checkRd: (-1) clusterrank.Rd:23: Lost braces; missing escapes or markup?
    23 | where the term f(c_{i}) accounts for the effect of i's local clustering and the term '+1' results from the contribution of \eqn{j}{j} itself. \cr
       |                    ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'shinythemes'

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

Package suggested but not available for checking: ‘tidycensus’

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

Package suggested but not available for checking: ‘compareGroups’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘gravity’
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spelling’
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: 'terra', 'slippymath', 'vapour'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CBPS', 'twang', 'Rcpp', 'glmnet', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'plotly', 'reshape', 'shiny', 'shinyjs', 'shinyWidgets',
  'shinymaterial', 'shinyjqui', 'sortable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shinyAce', 'shinymeta', 'colourpicker', 'DT', 'plotly', 'shiny',
  'shinycssloaders', 'shinyjs', 'shinyWidgets', 'shinyjqui', 'sortable'

Package suggested but not available for checking: ‘xpose’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Problems with news in ‘NEWS.md’:
No news entries found.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘ggiraph’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major refactoring of the code
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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: 'sf', 'terra', 'geosphere'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘jsonvalidate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dagitty’
Running ‘testthat.R’ [5s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cfid)
  > 
  > test_check("cfid")
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 203 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-graphs.R:200:3'): dagitty sanity ───────────────────────────────
  Error: Package `dagitty` is not available.
  Backtrace:
      ▆
   1. └─cfid::export_graph(g, "dagitty") at test-graphs.R:200:3
   2.   └─cfid:::stopifnot_(...)
   3.     └─cfid:::stop_(message)
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 203 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plyr', 'osmdata', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'osqp', 'cgam', 'gratia', 'coneproj', 'TruncatedNormal'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

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

Packages suggested but not available for checking:
  'hrbrthemes', 'productplots'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) comparisonsTable.cgOneFactorFit.Rd:47: Lost braces
    47 |         call (see {\dots } section below.)
       |                   ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'systemfit', 'cplm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
       |                                          ^
Packages required but not available:
  'glmnet', 'ks', 'Rcpp', 'RcppArmadillo'

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

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: 'ChannelAttribution', 'shiny'

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

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

Package suggested but not available for checking: ‘lax’

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: 'ipaddress', 'spelling'
Error(s) in re-building vignettes:
  ...
--- re-building ‘charlatan.Rmd’ using rmarkdown
--- finished re-building ‘charlatan.Rmd’

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

--- re-building ‘creating-realistic-data.Rmd’ using rmarkdown

Quitting from lines 219-235 [unnamed-chunk-7] (creating-realistic-data.Rmd)
Error: processing vignette 'creating-realistic-data.Rmd' failed with diagnostics:
Please install ipaddress
--- failed re-building ‘creating-realistic-data.Rmd’

SUMMARY: processing the following file failed:
  ‘creating-realistic-data.Rmd’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) cql.Rd:28: Lost braces; missing escapes or markup?
    28 | {X} \code{<x_var>, <(x_facet)>}: \tab\tab\tab\tab  X-axis variable. May include a second categorical\cr
       | ^
checkRd: (-1) cql.Rd:30: Lost braces; missing escapes or markup?
    30 | {Y} \code{<y_var>}: \tab\tab\tab\tab Y-axis variable. *Not used for \code{hist}.\cr
       | ^
checkRd: (-1) cql.Rd:38: Lost braces; missing escapes or markup?
    38 | {Y_label} \code{'<ylab>'}: \tab\tab\tab\tab  Y-axis custom label. Defaults to <y_var>\cr
       | ^
checkRd: (-1) cql.Rd:39: Lost braces; missing escapes or markup?
    39 | {Legend} \code{'<legend>'}: \tab\tab\tab\tab  Legend custom label. Defaults to <x_category>\cr
       | ^
checkRd: (-1) cql.Rd:40: Lost braces; missing escapes or markup?
    40 | {Colorset} \code{'<clist>'}: \tab\tab\tab\tab  Custom set of colors for <x_category> levels.\cr
       | ^
checkRd: (-1) cql.Rd:42: Lost braces; missing escapes or markup?
    42 | {AggFunc} \code{'<func>'}: \tab\tab\tab\tab Summary function for \code{bar} type.\cr
       | ^
checkRd: (-1) cql.Rd:45: Lost braces; missing escapes or markup?
    45 | {Fit} \code{'<show_se>'}: \tab\tab\tab\tab Valid types: \code{true|false}. Fit quadratic line.\cr
       | ^
checkRd: (-1) cql.Rd:47: Lost braces; missing escapes or markup?
    47 | {ConfInt} \code{'<interval>'}: \tab\tab\tab\tab  Show error bars. Value is confidence interval value. E.g. '.95'
       | ^
'LazyData' is specified without a 'data' directory
Package required but not available: ‘pdftools’

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

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

Package suggested but not available for checking: ‘shinytest2’

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

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: ‘spelling’
Package suggested but not available for checking: ‘quarto’
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"}.
       |                                                                               ^
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package suggested but not available for checking: ‘darts’
Packages required but not available:
  'spinifex', 'plotly', 'shiny', 'shinythemes', 'shinycssloaders', 'DT'

Package suggested but not available for checking: ‘gganimate’

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

Package suggested but not available for checking: ‘ggpmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'fmcsR', 'ChemmineR', 'hillR', 'ape', 'GUniFrac', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ChemoSpecUtils’

Packages suggested but not available for checking:
  'mlrMBO', 'smoof', 'lhs', 'RcppRoll'

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

Packages suggested but not available for checking:
  'js', 'speaq', 'hyperSpec'

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

Packages suggested but not available for checking:
  'ChemoSpec', 'ChemoSpec2D'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'GenomicInteractions', 'Gviz', 'countreg'
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘survey’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘chillR’
Packages required but not available:
  'fields', 'metR', 'plyr', 'raster', 'Rcpp', 'reshape2'

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

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

Package suggested but not available for checking: ‘car’

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

Packages suggested but not available for checking: 'drc', 'spelling'

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

Packages suggested but not available for checking: 'climatrends', 'vcr'

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

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

Package suggested but not available for checking: ‘cmdstanr’

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.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘bayesm’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'elevatr', 'geosphere', 'tanaka', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rfast2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'acs', 'ggmap', 'tigris', 'tidycensus'

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

Package suggested but not available for checking: ‘spatialwarnings’

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

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

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

Packages suggested but not available for checking: 'entab', 'mzR'

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

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

Packages suggested but not available for checking:
  'devtools', 'flexdashboard', 'pagedown', 'xaringan'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggraph’

Packages suggested but not available for checking:
  'clustree', 'plotly', 'Seurat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'RNifti', 'Rfast', 'plotly', 'neurobase', 'oro.nifti', 'servr'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) ec.datalag.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{prepares Dy y_1 Dy_1 ... Dy_{nlag-1} for estimation}
       |                                    ^
checkRd: (-1) ec.datalag.Rd:15: Lost braces
    15 | ymat contains the folloiwing columns {Dy y_1 Dy_1 ... Dy_{nlag-1}}
       |                                      ^
checkRd: (-1) ec.datalag.Rd:15: Lost braces; missing escapes or markup?
    15 | ymat contains the folloiwing columns {Dy y_1 Dy_1 ... Dy_{nlag-1}}
       |                                                          ^
checkRd: (-1) lagn.Rd:21: Lost braces; missing escapes or markup?
    21 |              REM: alternative to "lead-lag" {dplyr} which applies to vector y
       |                                             ^
Package required but not available: ‘oro.nifti’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'oro.nifti', 'RNifti'

Packages suggested but not available for checking:
  'ggpubr', 'manipulateWidget', 'webshot2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ChIPseeker', 'DESeq2', 'fgsea', 'ggrepel'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'FactoMineR', 'factoextra', 'GGally', 'Rtsne', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘BAMBI’
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(circhelp)
  Loading required package: data.table
  Loading required package: ggplot2
  > library(circular)
  
  Attaching package: 'circular'
  
  The following objects are masked from 'package:stats':
  
      sd, var
  
  > library(BAMBI)
  Error in library(BAMBI) : there is no package called 'BAMBI'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘vcr’
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘spelling’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RInside', 'RcppArmadillo'

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.
       |            ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'OptCirClust', 'Rcpp'

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

Package suggested but not available for checking: ‘ggrepel’

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

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
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘MESS’

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

Packages suggested but not available for checking: 'vcr', 'webmockr'

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: ‘plotly’

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.
Packages required but not available: 'torch', 'torchvision', 'lme4'

Packages suggested but not available for checking:
  'spelling', 'plotly', 'ggraph'

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

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

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
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘feather’
Running ‘testthat.R’ [10s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(civis)
  > 
  > test_check("civis")
  [ FAIL 1 | WARN 5 | SKIP 0 | PASS 1058 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_civis_ml.R:585:3'): newer CivisML versions use feather ─────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'feather'
  Backtrace:
      ▆
   1. ├─civis:::stash_local_dataframe(x, temp_id)
   2. └─base::loadNamespace(x)
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 5 | SKIP 0 | PASS 1058 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'AER', 'kcmeans'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘BART’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survey', 'DT', 'shiny', 'shinyjs'

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

Package suggested but not available for checking: ‘sf’

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘FRAPO’
Skipping checking math rendering: package 'V8' unavailable
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
Packages required but not available: 'marginaleffects', 'mvnfast'

Packages suggested but not available for checking:
  'MatchIt', 'Amelia', 'survey', 'estimatr', 'fixest', 'logistf',
  'AER', 'ivreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'caret'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘units’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘cellWise’

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

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

Packages suggested but not available for checking: 'readtext', 'cld3'

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

Package suggested but not available for checking: ‘cld2’

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: ‘spelling’
checkRd: (-1) clean.Rd:136: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:141: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:142: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘sf’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Packages suggested but not available for checking: 'devtools', 'rasciidoc'

VignetteBuilder package required for checking but not installed: ‘rasciidoc’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'gganimate', 'ggtext', 'transformr', 'imputeTestbench', 'imputeTS',
  'shiny'

Packages suggested but not available for checking: 'timetk', 'spelling'

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 required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sf', 'raster', 'reshape2', 'plyr', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘seqHMM’
Packages required but not available: 'reshape2', 'plyr'

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

Package suggested but not available for checking: ‘onion’

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

Packages suggested but not available for checking: 'spelling', 'pander'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'gganimate', 'mapSpain', 'sf', 'terra'
Package required but not available: ‘terra’

Package suggested but not available for checking: ‘rangeBuilder’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MHisopleths
> ### Title: Isopleths on a months-hours diagram
> ### Aliases: MHisopleths
> ### Keywords: hplot
> 
> ### ** Examples
> 
> data(climatol_data)
> MHisopleths(AWS_1year,'Temp',title='Mean temperature (C) -- My airport, 2002')
Error in MHisopleths(AWS_1year, "Temp", title = "Mean temperature (C) -- My airport, 2002") : 
  This function requires the package fields.
Please, install it and re-run the function
Execution halted
Package required but not available: ‘nasapower’

Packages suggested but not available for checking:
  'ag5Tools', 'chirps', 'sf'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'rts', 'raster', 'terra'

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

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

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

Packages suggested but not available for checking:
  'climatrends', 'gosset', 'nasapower', 'sf', 'PlackettLuce'

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

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

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

Packages suggested but not available for checking:
  'inTextSummaryTable', 'patientProfilesVis', 'DT'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'BayesFactor', 'lme4'

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

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.
Skipping checking math rendering: package 'V8' unavailable
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},
       |                                                                 ^
Package required but not available: ‘reticulate’

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

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

Packages suggested but not available for checking:
  'plotly', 'pander', 'flextable'

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

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

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

Package suggested but not available for checking: ‘apc’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: ‘car’

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: 'ggrepel', 'dbscan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘tfruns’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) cb_participant_count.Rd:13: Lost braces
    13 | \item{query}{A phenotype query defined using the code{\link{phenotype}} function and logic operators (see example below)}
       |                                                      ^
checkRd: (-1) phenotype.Rd:10: Lost braces
    10 | \item{id}{A single phenotype id. Possible phenotyoes can be explored using the code{\link{cb_search_phenotypes}} function}
       |                                                                                    ^
Package required but not available: ‘car’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) clr.Rd:24: Lost braces
    24 | the sense that its Karhunen-Lo\`{e}ve decomposition has qx terms only.}
       |                                 ^
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'mlmRev', 'AER', 'plm', 'lme4', 'ivreg'
Skipping checking math rendering: package 'V8' unavailable
Package which this enhances but not available for checking: ‘ape’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'crul', 'devtools'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘tableone’

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
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plotly', 'clusterSim'

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

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

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

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: 'Rcpp', 'aricode'

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

Packages suggested but not available for checking: 'dbscan', 'Seurat'

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

Package suggested but not available for checking: ‘ClustVarLV’

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

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

Package suggested but not available for checking: ‘plotly’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘apcluster’

Package suggested but not available for checking: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘clusterhap_reports’
Packages required but not available:
  'Rcpp', 'Ckmeans.1d.dp', 'RcppArmadillo'

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

Packages suggested but not available for checking:
  'DT', 'shinyalert', 'shinyFiles', 'shinyjs', 'shinythemes',
  'shinyWidgets', 'shinycssloaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mice', 'micemd', 'knockoff', 'glmnet', 'ClusterR', 'FactoMineR',
  'diceR', 'NPBayesImputeCat', 'Rfast', 'reshape2', 'Rcpp',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'VIM', 'missMDA', 'clustrd'

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

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

Package suggested but not available for checking: ‘devtools’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'OpenImageR', 'FD'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ade4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘spdep’

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

Packages suggested but not available for checking: 'ggExtra', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘procs’

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.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'BiDAG', 'pcalg'

Packages suggested but not available for checking:
  'ggraph', 'ggpubr', 'reshape2', 'car', 'ks'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'rARPACK', 'GGally', 'plyr', 'ggrepel'

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

Packages suggested but not available for checking: 'Seurat', 'spelling'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fmesher', 'lme4', 'MoEClust', 'sf', 'TMB', 'RcppEigen'

Packages suggested but not available for checking:
  'GGally', 'ggspatial', 'giscoR', 'inlabru', 'mvnfast', 'sdmTMB'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘kohonen’
Note: skipping ‘clValid.Rnw’ due to unavailable dependencies: 'kohonen'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppGSL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘smoof’

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

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}
       |                     ^
Package required but not available: ‘reshape2’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Ryacas0’

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', 'imager'

Packages suggested but not available for checking: 'DT', 'magick'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CMF.from.model.matrices
> ### Title: Create a CMF model object from fitted matrices
> ### Aliases: CMF.from.model.matrices
> 
> ### ** Examples
> 
> ### Example 'adopting' a model from 'recosystem'
> library(cmfrec)
> library(recosystem)
Error in library(recosystem) : there is no package called ‘recosystem’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cmfrec_vignette.Rmd’ using rmarkdown

Quitting from lines 108-116 [unnamed-chunk-2] (cmfrec_vignette.Rmd)
Error: processing vignette 'cmfrec_vignette.Rmd' failed with diagnostics:
there is no package called 'MatrixExtra'
--- failed re-building ‘cmfrec_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'GFM', 'Rcpp', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'survey', 'robCompositions'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
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
       |                                  ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘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: \#
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘ggpubr’
Running examples in ‘cmpsR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cmps_segment_plot
> ### Title: Plot the selected basis segment and its cross-correlation curve
> ###   at all scales based on the results of CMPS algorithm
> ### Aliases: cmps_segment_plot
> 
> ### ** Examples
> 
> library(cmpsR)
> library(ggpubr)
Error in library(ggpubr) : there is no package called ‘ggpubr’
Execution halted
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'fields', 'raster', 'trend'

Packages suggested but not available for checking:
  'cmsaf', 'cmsafvis', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cmsafops', 'cmsafvis', 'colourpicker', 'raster', 'shiny',
  'shinyFiles', 'shinyjs', 'shinythemes', 'shinyWidgets'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cmsafops', 'fields', 'raster', 'sf', 'rasterVis'

Packages suggested but not available for checking:
  'animation', 'rnaturalearth', 'spelling'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'censReg', '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
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

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

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

Packages suggested but not available for checking:
  'frscore', 'causalHyperGraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
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
       |                                                                       ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fields’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

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

Packages suggested but not available for checking:
  'HiCseg', 'plotly', 'InteractionSet', 'shinythemes',
  'shinycssloaders', 'DT', 'heatmaply', 'shinyjs'

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

Packages suggested but not available for checking: 'PopGenome', 'phyclust'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'fields', 'sfheaders'

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

Package suggested but not available for checking: ‘disttree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'MatchIt', 'twang', 'twangContinuous', 'optmatch', 'CBPS',
  'designmatch', 'optweight', 'mice', 'MatchThem', 'cem', 'caret'
Running examples in ‘cobalt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bal.tab.optmatch
> ### Title: Balance Statistics for 'optmatch' Objects
> ### Aliases: bal.tab.optmatch
> 
> ### ** Examples
> 
> ## Don't show: 
> if (requireNamespace("ebal", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ data("lalonde", package = "cobalt")
+ 
+ lalonde$prop.score <- glm(treat ~ age + educ + race + 
+                               married + nodegree + re74 + re75, 
+                           data = lalonde, family = binomial)$fitted.values
+ pm <- optmatch::pairmatch(treat ~ prop.score, data = lalonde)
+ 
+ ## Using formula and data; LHS of formula not required
+ bal.tab(pm, formula = ~ age + educ + race +
+             married + nodegree + re74 + re75,
+         data = lalonde)
+ 
+ ## Using covs
+ covs <- subset(lalonde, select = -c(re78, treat))
+ bal.tab(pm, covs = covs)
+ ## Don't show: 
+ }) # examplesIf
> data("lalonde", package = "cobalt")
> lalonde$prop.score <- glm(treat ~ age + educ + race + married + nodegree + 
+     re74 + re75, data = lalonde, family = binomial)$fitted.values
> pm <- optmatch::pairmatch(treat ~ prop.score, data = lalonde)
Error in loadNamespace(x) : there is no package called ‘optmatch’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'caret', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinythemes', 'ggtern', 'DT'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘rkward’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package which this enhances but not available for checking: ‘rkward’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'glmnet', 'plyr', 'pROC', 'ggpubr', 'survminer'

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

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

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

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 ?
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘compositions’

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

Packages suggested but not available for checking:
  'DT', 'shinytest', 'lme4', 'shiny', 'miniUI', 'ufs', 'rosetta',
  'GGally'

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

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.
Package suggested but not available for checking: ‘Rcpp’
Packages suggested but not available for checking:
  'odbc', 'spelling', 'gt', 'flextable'
Packages required but not available: 'crul', 'urltools'

Packages suggested but not available for checking: 'jsonld', 'jsonvalidate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bvpSolve’
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'imputeTS', 'tensorflow', 'keras', 'narray', 'philentropy', 'greybox'

Package suggested but not available for checking: ‘reticulate’

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

Package suggested but not available for checking: ‘wTO’

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

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'reshape2', 'devtools'
Package required but not available: ‘openxlsx’

Package suggested but not available for checking: ‘spelling’

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

Package suggested but not available for checking: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'shinydashboard', 'shinyjs'

Package suggested but not available for checking: ‘shinytest2’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
Problems with news in ‘NEWS.md’:
No news entries found.
Packages required but not available: 'shiny', 'shinyjs', 'paws'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘DatabaseConnector’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Packages suggested but not available for checking:
  'flextable', 'ggpubr', 'gt', 'odbc', 'plotly', 'spelling'
Packages suggested but not available for checking: 'odbc', 'gt', 'ggpubr'
Package required but not available: ‘DatabaseConnector’

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

Package suggested but not available for checking: ‘Eunomia’

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

Package suggested but not available for checking: ‘DT’

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

Package suggested but not available for checking: ‘odbc’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘openxlsx’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘cubature’

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

Packages suggested but not available for checking:
  'fastverse', 'plm', 'fixest', 'RcppArmadillo', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘shiny’
Packages suggested but not available for checking:
  'devtools', 'DT', 'servr'
Packages suggested but not available for checking: 'ranger', 'spelling'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'fda', 'spam'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'car', 'coloc'

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

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

Packages suggested but not available for checking:
  'shinytest', 'devtools', 'shinyBS'

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

Packages suggested but not available for checking: 'leaflet', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reshape2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘colorBlindness.Rmd’ using rmarkdown

Quitting from lines 21-27 [unnamed-chunk-1] (colorBlindness.Rmd)
Error: processing vignette 'colorBlindness.Rmd' failed with diagnostics:
there is no package called 'reshape2'
--- failed re-building ‘colorBlindness.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ape', 'plotly', 'qpdf'

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

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

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

Packages suggested but not available for checking:
  'sf', 'rnaturalearth', 'tigris'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
Packages required but not available: 'dqrng', 'ggrepel', 'ggalt', 'plotly'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'shinyjs'
Skipping checking math rendering: package 'V8' unavailable
Package which this enhances but not available for checking: ‘plyr’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

Package suggested but not available for checking: ‘spelling’

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

Package suggested but not available for checking: ‘shinydisconnect’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'shiny', 'shinyjs', 'plotly'
Packages required but not available: 'Rfast', 'Rfast2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Unexported object imported by a ':::' call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
Package required but not available: ‘clusterSim’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) xsimplex.Rd:6: Lost braces; missing escapes or markup?
     6 |              Generates all points on a {p,n} simplex lattice (i.e. a p-part
       |                                        ^
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘pROC’

Package suggested but not available for checking: ‘Seurat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘SAMBA’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
Packages required but not available: 'ranger', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'reshape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'splines2', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'RcppEigen', 'RcppNumerical'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'rncl', 'ape', 'picante', 'adespatial', 'betapart'

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.
Package required but not available: ‘DatabaseConnector’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'GGally', 'useful', 'reshape2', 'plyr', 'RcppArmadillo'

Package suggested but not available for checking: ‘qpdf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'pcalg', 'InvariantCausalPrediction', 'glmnet', 'backShift', 'CAM',
  'huge'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'HardyWeinberg', 'flextable', 'PMCMRplus'

Packages suggested but not available for checking:
  'shiny', 'shinyBS', 'shinyjs', 'shinyjqui', 'shinythemes',
  'shinyWidgets', 'shinydashboardPlus', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Package suggested but not available for checking: ‘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 required but not available: 'GauPro', 'mixopt', 'plyr'

Packages suggested but not available for checking:
  'GGally', 'ggpubr', 'ContourFunctions', 'lhs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) glass.Rd:10: Lost braces
    10 | \item{item}{factor}{200 levels - which item the measurements came from}
       |                    ^
checkRd: (-1) glass.Rd:11-12: Lost braces
    11 | \item{fragment}{factor}{4 levels - which of the four fragments from each item the observations were made
       |                        ^
checkRd: (-1) glass.Rd:13: Lost braces
    13 | \item{logNaO}{numeric}{log of sodium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:14: Lost braces
    14 | \item{logMgO}{numeric}{log of magnesium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:15: Lost braces
    15 | \item{logAlO}{numeric}{log of aluminium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:16: Lost braces
    16 | \item{logSiO}{numeric}{log of silicon concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:17: Lost braces
    17 | \item{logKO}{numeric}{log of potassium concentration to oxygen concentration}
       |                      ^
checkRd: (-1) glass.Rd:18: Lost braces
    18 | \item{logCaO}{numeric}{log of calcium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:19: Lost braces
    19 | \item{logFeO}{numeric}{log of iron concentration to oxygen concentration}
       |                       ^
Packages required but not available: 'Rcpp', 'bio3d', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

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: ‘factoextra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Benchmarking', 'spdep', 'nonparaeff', 'np', 'FactoMineR', 'GWmodel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggforce', 'reshape2'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'greybox', 'legion', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'higlasso', 'glmnet', 'bkmr', 'qgcomp', 'gWQS', 'pROC', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'plyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'plyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Boruta', 'Compositional', 'ranger', 'Rfast', 'Rfast2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bigstatsr', 'energy', 'glmnet', 'mixture', 'mvhtests', 'regda',
  'Rfast', 'Rfast2', 'Rnanoflann'

Package suggested but not available for checking: ‘bigparallelr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Compositional', 'MultivariateRandomForest', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bayesm’

Package suggested but not available for checking: ‘energy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Ternary’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ape’

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'V8', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'Rvcg'

Package suggested but not available for checking: ‘rmarchingcubes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘trackeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
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
       |                                ^
Packages required but not available: 'glmnet', 'wdm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

Packages suggested but not available for checking: 'promises', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘RPtests’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BayesFactor', 'shiny'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘np’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘shinytest2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'plyr'

Packages suggested but not available for checking:
  'hdrcde', 'keras', 'ks', 'C50', 'BART', 'caret', 'glmnet',
  'glmnetUtils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'hdrcde'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'terra', 'sf', 'blockCV', 'ranger'
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction_to_confcons.Rmd’ using rmarkdown

Quitting from lines 65-71 [unnamed-chunk-3] (introduction_to_confcons.Rmd)
Error: processing vignette 'introduction_to_confcons.Rmd' failed with diagnostics:
there is no package called 'terra'
--- failed re-building ‘introduction_to_confcons.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction_to_confcons.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘cellWise’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

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: ‘spelling’
Package required but not available: ‘RcppTOML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lme4’

Packages suggested but not available for checking:
  'robustlmm', 'robustvarComp', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'miniUI', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstantools’

Packages suggested but not available for checking: 'rstanarm', 'brms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fda', '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: 'glmnet', 'hrbrthemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘penalized’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘caret’

Package suggested but not available for checking: ‘FeatureTerminatoR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fst’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘Ternary’

Packages suggested but not available for checking:
  'ape', 'phangorn', 'Quartet', 'TreeSearch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘miceadds’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggrepel', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'sf', 'Rcpp', 'fixest', 'lwgeom', 's2', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinydashboard', 'waiter', 'shinyWidgets', 'summarytools',
  'openxlsx', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'spelling', 'webshot2'
Packages required but not available:
  'rmgarch', 'rugarch', 'glmnet', 'riskParityPortfolio', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘webmockr’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(connectwidgets)
  > 
  > test_check("connectwidgets")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/connectwidgets.Rcheck/tests/testthat/setup.R"
  Caused by error in `library()`:
  ! there is no package called 'webmockr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("connectwidgets")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library(webmockr) at tests/testthat/setup.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggrepel', 'leidenAlg', 'N2R', 'reshape2', 'Rtsne', 'sccore', 'Rcpp',
  'RcppArmadillo', 'RcppEigen'

Packages suggested but not available for checking:
  'conosPanel', 'DESeq2', 'p2data', 'pagoda2', 'plyr', 'rmumps',
  'Seurat', 'shinycssloaders', 'uwot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggrepel', 'Rcpp', 'zlib'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Packages suggested but not available for checking:
  'ggrepel', 'plotly', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GGally', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinydashboard'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘coneproj’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Univranks.Rd:69: Lost braces; missing escapes or markup?
    69 | To obtain the preference rankings from the paired comparisons the procedure has been the following: the first row of the raw data is [1  3  2   1   2   1  1  2  1   1   1   2   1    1   2]. London is preferred to Paris, St. Gallen, Barcelona Stockholm (LP, LM, LSg, LB and LSt are always equal to 1), and there is no preference between London and Milan (they are tied); Milan is preferred to Paris (PM = 2), St. Gallen, Barcelona and Stockholm; and so on. The first ordering is then <{L M} Sg St B P> corresponding to a ranking [1,5,1,2,4,3], where the columns indicate L  P  M Sg  B St.  
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ^
Packages required but not available:
  'forecast', 'FME', 'GA', 'adaptMCMC', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'units', 'quantities'
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘sf’

Package suggested but not available for checking: ‘spdep’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'DiagrammeRsvg', 'sf'
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'StanHeaders', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'mixture', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'quanteda', 'text2vec', 'reshape2'

Package suggested but not available for checking: ‘hunspell’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'geometry', 'Rcpp', 'reshape', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lhs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘interp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'orthoDr', 'AER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘riskRegression’

Packages suggested but not available for checking:
  'pammtools', 'gganimate', 'transformr', 'plotly', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'pryr', 'extraDistr', 'SHELF', 'shiny'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'eurostat', 'ggpubr', 'leaflet'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tm', 'topicmodels', 'word2vec', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'miniUI', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'geiger', 'magick', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fields', 'StatMatch'

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: 'plyr', 'reshape'

Package suggested but not available for checking: ‘cooccur’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘urltools’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'httpuv', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'pROC', 'plyr', 'ClustGeo', 'RcppArmadillo'

Packages suggested but not available for checking: 'ggtree', 'imager'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'cubature', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geometry’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'geosphere', 'rgbif', 'rnaturalearth', 'terra'

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RcppSimdJson’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lmomco’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mcmcse', 'Rcpp', 'spam', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘copBasic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

Packages suggested but not available for checking:
  'fitbitViz', 'tmap', 'leaflet', 'leafgl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'leaflet', 'sf'

Package suggested but not available for checking: ‘stars’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'coloc', 'ggrepel', 'RcppArmadillo'

Package suggested but not available for checking: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pcaMethods', 'CVXR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cordillera', 'smacofx', 'smacof', 'analogue', 'crs', 'minqa'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rvinecopulib’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'copBasic', 'flexsurv', 'icenReg', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘vines’

Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rvinecopulib’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'lcopula', 'mev', 'rugarch'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rvinecopulib’

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.
Package suggested but not available for checking: ‘energy’
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'energy''

Quitting from lines 89-100 [unnamed-chunk-3] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
You need to install R package energy.
--- 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: 'ape', 'seqinr', 'kmer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rtsne’
Error(s) in re-building vignettes:
  ...
--- re-building ‘coranking.Rmd’ using rmarkdown

Quitting from lines 13-30 [setup] (coranking.Rmd)
Error: processing vignette 'coranking.Rmd' failed with diagnostics:
there is no package called 'Rtsne'
--- failed re-building ‘coranking.Rmd’

SUMMARY: processing the following file failed:
  ‘coranking.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘dbscan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'vcfR', 'adegenet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'oro.dicom', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘StatMatch’
Running ‘test.R’ [90s/86s]
Running the tests in ‘tests/test.R’ failed.
Complete output:
  > library(testthat)
  > library(mockr)
  
  Attaching package: 'mockr'
  
  The following objects are masked from 'package:testthat':
  
      local_mock, with_mock
  
  > library(corehunter)
  Loading required package: rJava
  > 
  > test_check("corehunter")
  [ FAIL 2 | WARN 17 | SKIP 0 | PASS 2369 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('testData.R:562:3'): read phenotype data from file ───────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'StatMatch'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at testData.R:562:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('testData.R:605:5'): create phenotype data from data frame ───────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'StatMatch'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(gd(df), gd2(df)) at testData.R:640:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─corehunter (local) gd(df)
   5. └─base::loadNamespace(x) at testData.R:605:5
   6.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   7.     └─base (local) withOneRestart(expr, restarts[[1L]])
   8.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 17 | SKIP 0 | PASS 2369 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
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.
       |                  ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SRS', 'ggrepel', 'plotly', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
Running examples in ‘coreSim-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: b_sim
> ### Title: Simulate coefficients from a GLM by making draws from the
> ###   multivariate normal distribution
> ### Aliases: b_sim
> 
> ### ** Examples
> 
> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(coreSim)
  > library(car)
  Error in library(car) : there is no package called 'car'
  Execution halted
Packages required but not available: 'ape', 'phangorn', 'phytools'

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: ‘Rdisop’
Running examples in ‘CorMID-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CalcTheoreticalMDV
> ### Title: CalcTheoreticalMDV.
> ### Aliases: CalcTheoreticalMDV
> 
> ### ** Examples
> 
> # standard distribution matrix
> fml <- "C5H6Si1"
> CalcTheoreticalMDV(fml = fml)
         M+0        M+1        M+2
M0 0.8748246 0.09235479 0.03282065
M1 0.0000000 0.91344742 0.08655258
M2 0.0000000 0.00000000 1.00000000
> 
> # extend to more columns (number of measured ions) if required
> CalcTheoreticalMDV(fml = fml, nmz = 4)
         M+0        M+1        M+2         M+3         M+4
M0 0.8733741 0.09220166 0.03276623 0.001657999 0.000000000
M1 0.0000000 0.88280182 0.08364880 0.032215212 0.001334166
M2 0.0000000 0.00000000 0.89323821 0.074976662 0.031785127
M3 0.0000000 0.00000000 0.00000000 0.931860228 0.068139772
M4 0.0000000 0.00000000 0.00000000 0.000000000 1.000000000
> 
> # limit to a smaller number of biological carbon (i.e. if compounds are silylated)
> CalcTheoreticalMDV(fml = fml, nmz = 4, nbio = 2)
         M+0        M+1        M+2         M+3         M+4
M0 0.8733741 0.09220166 0.03276623 0.001657999 0.000000000
M1 0.0000000 0.88280182 0.08364880 0.032215212 0.001334166
M2 0.0000000 0.00000000 0.89323821 0.074976662 0.031785127
> CalcTheoreticalMDV(fml = fml, nmz = 4, nbio = 2, algo="Rdisop")
Error in verify_suggested("Rdisop") : 
  The use of this function requires packageRdisop. Please install.
Calls: CalcTheoreticalMDV -> verify_suggested
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘phyloseq’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ranger', 'SpatialTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'palasso'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_policy_scores.Rd:63: Lost braces
    63 | \code{low_estimate}\\code{high_estimate} columns. The \code{SD_estimate} column has the standard deviation of the
       |                          ^
Running examples in ‘CoronaNetR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_event
> ### Title: Access CoronaNet Event Data API
> ### Aliases: get_event
> 
> ### ** Examples
> 
> # Grab all data for Saudi Arabia from first 4 months of pandemic
> 
> saudi_data <- get_event(countries = "Saudi Arabia", type = "All",
+ type_sub_cat = "All", from = "2019-12-31", to = "2020-04-30")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Could not resolve host: postgrest-588174062.us-east-2.elb.amazonaws.com
Calls: get_event ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown

Quitting from lines 55-56 [unnamed-chunk-1] (Introduction.Rmd)
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
Could not resolve host: postgrest-588174062.us-east-2.elb.amazonaws.com
--- 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: 'plyr', 'gganimate', '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: 'DT', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'later', 'promises', 'reticulate'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'padr', 'plyr', 're2', 'shiny', 'shinydashboard', 'shinyjs',
  'shinyWidgets'

Package suggested but not available for checking: ‘shinytest2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'wordcloud', 'Rcpp', 'udpipe', 'quanteda', 'tokenbrowser',
  'RNewsflow', 'rsyntax'

Packages suggested but not available for checking: 'tm', 'topicmodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'mmand'

Package suggested but not available for checking: ‘profr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘xcms’
Packages required but not available: 'recipes', 'plotly', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BayesFactor', 'energy', 'ggraph', 'gt', 'lme4', 'rstanarm', 'wdm',
  'WRS2', 'openxlsx2'
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ranger', 'spelling'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(corrgrapher)
  > 
  > test_check("corrgrapher")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/corrgrapher.Rcheck/tests/testthat/setup.R"
  Caused by error in `library()`:
  ! there is no package called 'ranger'
  Backtrace:
       ▆
    1. ├─testthat::test_check("corrgrapher")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library(ranger) at tests/testthat/setup.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘qpdf’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'gganimate', 'ggraph', 'GGally', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'forecast', 'hts'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggcorrplot', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'bayesplot', 'reshape2', 'RcppArmadillo', 'RcppDist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘cosinor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
Package required but not available: ‘animation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'OpenMx', 'ctsem', 'MBESS', 'openxlsx', '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 required but not available: ‘lamW’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Package required but not available: ‘StatMatch’

Packages suggested but not available for checking:
  'GGally', 'trtf', 'keras', 'mlt', 'tidymodels', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'DT', 'pander', 'reshape2', 'shinythemes', 'shinycssloaders',
  'shinyWidgets', 'spelling'

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 suggested but not available for checking:
  'RSpectra', 'rdist', 'Seurat'
Running examples in ‘countland-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Cluster
> ### Title: Perform spectral clustering on dot products.
> ### Aliases: Cluster
> 
> ### ** Examples
> 
> gold_path <- system.file("testdata", package = "countland", mustWork = TRUE)
> gold.data <- Seurat::Read10X(data.dir = gold_path)
Error in loadNamespace(x) : there is no package called ‘Seurat’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘compositions’

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:
  'Rcpp', 'flexsurv', 'car', 'standardize', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'altdoc', 'eurostat'
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'FastGP', 'spikeSlabGAM', 'splines2', 'Rcpp', 'TruncatedNormal',
  'RcppArmadillo'

Package suggested but not available for checking: ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘simstudy’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

Package suggested but not available for checking: ‘TMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'V8', 'gstat'

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'plyr', 'qgraph'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'glmnet', 'Rcpp', 'reshape2', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'colourpicker', 'shiny'

Packages suggested but not available for checking:
  'shinyjs', 'shinymeta', 'mrgsolve', 'GGally', 'ggrepel', 'ggstance',
  'plotly', 'shinyAce', 'Rcpp', 'ggdist', 'ggpmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'autothresholdr', 'mgc', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tokenizers’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'plotly', 'shiny', 'shinydashboard', 'shinycssloaders', 'DT'

Package suggested but not available for checking: ‘devtools’

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.
Package required but not available: ‘sf’

Packages suggested but not available for checking:
  'ggrepel', 'leaflet', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DT’
Error(s) in re-building vignettes:
  ...
--- re-building ‘covid19dbcand.Rmd’ using rmarkdown

Quitting from lines 70-71 [unnamed-chunk-7] (covid19dbcand.Rmd)
Error: processing vignette 'covid19dbcand.Rmd' failed with diagnostics:
there is no package called 'DT'
--- failed re-building ‘covid19dbcand.Rmd’

SUMMARY: processing the following file failed:
  ‘covid19dbcand.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'EpiEstim', 'gt'

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: 'devtools', 'mapview', 'plotly', 'sf'

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.
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

Packages suggested but not available for checking:
  'convey', 'SIPDIBGE', 'srvyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'seqinr', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'EpiEstim', 'ggtext'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘DT’
Running ‘testthat.R’ [79s/115s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ops <- options("crayon.enabled" = FALSE, warn = 1)
  > library(testthat)
  > library("covr")
  > 
  > # Skip tests on Solaris as gcc is not in the PATH and I do not have an easy way
  > # to mimic the CRAN build environment
  > if (!tolower(Sys.info()[["sysname"]]) == "sunos") {
  +   Sys.setenv("R_TESTS" = "")
  +   test_check("covr")
  + }
  [ FAIL 2 | WARN 0 | SKIP 10 | PASS 298 ]
  
  ══ Skipped tests (10) ══════════════════════════════════════════════════════════
  • On CRAN (9): 'test-Compiled.R:3:3', 'test-Compiled.R:36:3',
    'test-Compiled.R:49:3', 'test-Compiled.R:65:3', 'test-Compiled.R:81:3',
    'test-Compiled.R:89:3', 'test-record_tests.R:167:3',
    'test-tally_coverage.R:2:3', 'test-utils.R:46:3'
  • getRversion() >= "4.0.0" is TRUE (1): 'test-utils.R:37:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-gitlab.R:8:3'): gitlab ───────────────────────────────────────
  `gitlab(coverage = cov)` threw an error.
  Message: The `DT` and `htmltools` packages must be installed to use `covr::report()`
  Class:   simpleError/error/condition
  Backtrace:
      ▆
   1. ├─testthat::expect_error(gitlab(coverage = cov), NA) at test-gitlab.R:8:3
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─covr::gitlab(coverage = cov)
   7.   └─covr::report(coverage, file = out_file, browse = FALSE)
  ── Failure ('test-gitlab.R:10:3'): gitlab ──────────────────────────────────────
  file.exists("TestS4/public/coverage.html") is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 2 | WARN 0 | SKIP 10 | PASS 298 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘np’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rvinecopulib’

Package suggested but not available for checking: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'SHT', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘magick’
Package required but not available: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mediation’

Package suggested but not available for checking: ‘bindrcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'caret', 'ggrepel', 'ggpubr', 'glmnet', 'mixOmics', 'survcomp',
  'survminer'

Packages suggested but not available for checking:
  'nsROC', 'smoothROCtime', 'ggforce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'MESS', 'qvalue'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dbscan', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘mvnfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘knockoff’

Packages suggested but not available for checking:
  'BEST', 'ranger', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'minqa', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'crops', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rcpp’
Package required but not available: ‘pdftools’

Packages suggested but not available for checking: 'magick', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'V8'

Packages suggested but not available for checking:
  'shinyAce', 'shinybusy', 'shinyFiles', 'shinyjqui', 'shinyWidgets'

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.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'ggpubr', 'qwraps2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'Rfast', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'survey', 'srvyr', 'usmap'
Packages required but not available: 'Rcpp', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plm’

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 required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'wordcloud', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinyjs', 'miniUI', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'NMF', 'recommenderlab'
Packages required but not available: 'Rcpp', 'sf', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘scoringRules’

Package suggested but not available for checking: ‘quarto’

VignetteBuilder package required for checking but not installed: ‘quarto’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fastglm', 'Rcpp', 'ggpubr', 'lme4', 'reshape2', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘shiny’
Package required but not available: ‘glmnet’

Packages suggested but not available for checking: 'grf', 'BART'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'crew', 'paws.common', 'paws.compute', 'paws.management'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘crew’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'later', 'promises'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘udpipe’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'gghighlight', 'ggtext'
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'osfr', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gt’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'shiny', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'keras', 'reticulate'

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.
Package required but not available: ‘ggforce’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggpmisc', 'ggpubr', 'ggrepel', 'sccore', 'sparseMatrixStats'

Packages suggested but not available for checking:
  'conos', 'pagoda2', 'reticulate', 'Seurat', 'SoupX'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pcaMethods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggmcmc', 'Rcpp', 'RcppArmadillo'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinydashboard', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'miniUI', 'shiny', 'shinyFiles'
Package required but not available: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'terra', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘purrrlyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘PowerSDI’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'terra', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flip’

Packages suggested but not available for checking: 'devtools', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'clustree', 'dbscan', 'ggdist'

Package suggested but not available for checking: ‘umap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gamm4', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘estimatr’
Running examples in ‘crossmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cross_fit_robust
> ### Title: Cross fit robust linear models
> ### Aliases: cross_fit_robust
> 
> ### ** Examples
> 
> ## Don't show: 
> if (getRversion() >= "3.5") (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ cross_fit_robust(mtcars, mpg ~ wt, cyl, clusters = list(NULL, am))
+ ## Don't show: 
+ }) # examplesIf
> cross_fit_robust(mtcars, mpg ~ wt, cyl, clusters = list(NULL, am))
Error in cross_fit_robust(mtcars, mpg ~ wt, cyl, clusters = list(NULL,  : 
  The package "estimatr" is required to run `cross_fit_robust()`.
Calls: <Anonymous> ... withVisible -> eval -> eval -> cross_fit_robust -> <Anonymous>
Execution halted
Packages required but not available: 'meta', 'netmeta', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘flextable’

Packages suggested but not available for checking: 'gt', 'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Running examples in ‘crosstalk-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ClientValue
> ### Title: ClientValue object
> ### Aliases: ClientValue
> 
> ### ** Examples
> 
> library(shiny)
Error in library(shiny) : there is no package called ‘shiny’
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(crosstalk)
  > 
  > test_check("crosstalk")
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 1 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • shiny cannot be loaded (2): 'test-crosstalk.R:39:3', 'test-crosstalk.R:47:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-crosstalk.R:81:3'): Shiny modules support SharedData ───────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'shiny'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-crosstalk.R:81:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 1 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'Rcpp', 'STRINGdb'

Package suggested but not available for checking: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'ranger', 'SIS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
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
       |      ^
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘rdist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘tidytext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘np’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'units', 'mapview'

Packages suggested but not available for checking:
  'mapboxapi', 'tigris', 'tidycensus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'tableone'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'lme4', 'sf'

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘urltools’

Package suggested but not available for checking: ‘webmockr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'torch', 'mlr3superlearner'

Package suggested but not available for checking: ‘mma’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'crunchy', 'devtools', 'spelling'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [157s/181s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(
  +     vignettes = TRUE, error = identical(Sys.getenv("GITHUB_ACTION"), "true")
  + )
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available: 'shiny', 'miniUI'

Packages suggested but not available for checking: 'shinytest', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'geosphere', 'marmap', 'shiny', 'shinydashboard', 'shinyjs',
  'swfscDAS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rfast2’

Package suggested but not available for checking: ‘clusterSEs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘spelling’

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: ‘plotly’

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.
checkRd: (-1) calculate_cell_volume.Rd:16: Lost braces; missing escapes or markup?
    16 | V A real number. The volume (in angstroms^3 or angstroms^{-3})
       |                                                          ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘ggrepel’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'reshape2', 'Lmoments', 'ggpubr', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'prodlim', 'riskRegression', 'glmnet', 'caret', 'recipes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'geojsonio', 'gt', 'reshape2', 'rmapshaper', 'sf'
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
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/csdata.Rcheck/vign_test/csdata/vignettes/population_norway_files/figure-html/unnamed-chunk-2-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 20077 bytes
Input file size = 20179 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 15364
  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 = 15364

Output IDAT size = 15364 bytes (4713 bytes decrease)
Output file size = 15442 bytes (4737 bytes = 23.47% decrease)


Quitting from lines 41-66 [unnamed-chunk-3] (population_norway.Rmd)
Error: processing vignette 'population_norway.Rmd' failed with diagnostics:
there is no package called 'gt'
--- 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
Packages required but not available: 'symmoments', 'TruncatedNormal'

Packages suggested but not available for checking:
  'plotly', 'listviewer', 'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘fuzzyjoin’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'rmapshaper'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'ggspatial', 'raster', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'multiApply', 'ClimProjDiags', 'CSTools', 'SPEI', 'lmomco', 's2dv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggrepel', 'leaflet', 'sf'
Packages required but not available: 'glmnet', '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: 'reshape2', 'sf'

Package suggested but not available for checking: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggcorrplot’

Package suggested but not available for checking: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'stars'

Packages suggested but not available for checking:
  'DiagrammeRsvg', 'rnaturalearth'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘benchmarks.Rmd’ using rmarkdown
--- finished re-building ‘benchmarks.Rmd’

--- re-building ‘csfmt_rts_data_v1.Rmd’ using rmarkdown

Quitting from lines 75-181 [unnamed-chunk-2] (csfmt_rts_data_v1.Rmd)
Error: processing vignette 'csfmt_rts_data_v1.Rmd' failed with diagnostics:
there is no package called 'gt'
--- failed re-building ‘csfmt_rts_data_v1.Rmd’

--- re-building ‘cstidy.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/cstidy.Rcheck/vign_test/cstidy/vignettes/cstidy_files/figure-html/unnamed-chunk-5-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 24086 bytes
Input file size = 24188 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 16754
  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 = 16754

Output IDAT size = 16754 bytes (7332 bytes decrease)
Output file size = 16832 bytes (7356 bytes = 30.41% decrease)

--- finished re-building ‘cstidy.Rmd’

SUMMARY: processing the following file failed:
  ‘csfmt_rts_data_v1.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'easyVerification', 's2dv', 'startR', 'multiApply', 'ClimProjDiags',
  'plyr', 'reshape2', 'verification'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survey', 'cgam', 'coneproj'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'shinyMatrix'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘huge’
Package required but not available: ‘mirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'fda', 'gdistance'

Packages suggested but not available for checking: 'dismo', 'crawl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ctsem', 'simStateSpace', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tmle', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Gmedian', 'raster', 'sf', 'terra'

Packages suggested but not available for checking: 'animation', 'move'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'jiebaR', 'plyr'

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: ‘ape’
Packages required but not available: 'PowerTOST', 'OwenQ'

Package suggested but not available for checking: ‘asciicast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'ctmm', 'slouch', 'ClusterR'

Package suggested but not available for checking: ‘phytools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'nodbi', 'V8'

Package suggested but not available for checking: ‘devtools’

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.
Packages required but not available: 'xRing', 'oro.dicom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ctsem', 'OpenMx', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'plyr', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'devtools', 'lme4', 'shiny', 'collapse', 'qgam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tsibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘Hello.csv’
Packages required but not available: 'shiny', 'shinyAce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘urltools’

Packages suggested but not available for checking:
  'countcolors', 'devtools', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘CVXR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘benchr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'tsibble'

Packages suggested but not available for checking:
  'spelling', 'ozmaps', 'GGally', 'ggrepel', 'ggforce', 'stars',
  'units', 'leaflet', 'plotly', 'concaveman', 'sftime'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'stars'

Package suggested but not available for checking: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘seqinr’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping vignette re-building
Packages suggested but not available for checking:
  'shinytest2', 'chromote', 'quarto'

VignetteBuilder package required for checking but not installed: ‘quarto’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(cucumber)
  > 
  > test_check("cucumber")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/cucumber.Rcheck/tests/testthat/setup-disable-crashpad.R"
  Caused by error in `loadNamespace()`:
  ! there is no package called 'chromote'
  Backtrace:
       ▆
    1. ├─testthat::test_check("cucumber")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. ├─base::loadNamespace(x) at tests/testthat/setup-disable-crashpad.R:14:1
   15. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   16. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
   17. │ │   └─base (local) doWithOneRestart(return(expr), restart)
   18. │ └─base::stop(cond)
   19. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   20.   └─rlang::abort(...)
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'glmnet', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'openxlsx', 'DT', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'predtools', 'spelling'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using knitr

Quitting from lines 41-44 [unnamed-chunk-2] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'predtools'
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘TCGAbiolinks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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: 'rstpm2', 'relsurv', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘xhaz’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'spelling', 'later', 'httpuv'
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.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

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’
Packages required but not available: 'Rcpp', 'ddalpha', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'feature', 'geometry', 'hdrcde', 'ks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qgam’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'set', 'do'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘censable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'GGally', 'units'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSpectra', 'ggpubr'

Package suggested but not available for checking: ‘spelling’

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 suggested but not available for checking: ‘gt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_cvdprevent.Rmd’ using rmarkdown

Quitting from lines 28-33 [unnamed-chunk-2] (using_cvdprevent.Rmd)
Error: processing vignette 'using_cvdprevent.Rmd' failed with diagnostics:
there is no package called 'gt'
--- failed re-building ‘using_cvdprevent.Rmd’

SUMMARY: processing the following file failed:
  ‘using_cvdprevent.Rmd’

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

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.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'StMoMo', 'forecast', 'tmap', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'groupdata2', 'lme4', 'plyr', 'pROC', 'rearrr', 'recipes'

Packages suggested but not available for checking:
  'ggimage', 'merDeriv', '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:
  'effects', 'latticeExtra', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘glmnet’
Running examples in ‘cvwrapr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: computeError
> ### Title: Compute CV statistics from a prediction matrix
> ### Aliases: computeError
> 
> ### ** Examples
> 
> set.seed(1)
> x <- matrix(rnorm(500), nrow = 50)
> y <- rnorm(50)
> cv_fit <- kfoldcv(x, y, train_fun = glmnet::glmnet,
+                   predict_fun = predict, keep = TRUE)
Error in loadNamespace(x) : there is no package called ‘glmnet’
Calls: kfoldcv ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cvwrapr)
  > 
  > test_check("cvwrapr")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/cvwrapr.Rcheck/tests/testthat/setup.R"
  Caused by error in `library()`:
  ! there is no package called 'glmnet'
  Backtrace:
       ▆
    1. ├─testthat::test_check("cvwrapr")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library(glmnet) at tests/testthat/setup.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘computeError.Rmd’ using rmarkdown

Quitting from lines 32-42 [unnamed-chunk-3] (computeError.Rmd)
Error: processing vignette 'computeError.Rmd' failed with diagnostics:
there is no package called 'glmnet'
--- failed re-building ‘computeError.Rmd’

--- re-building ‘kfoldcv.Rmd’ using rmarkdown

Quitting from lines 37-40 [unnamed-chunk-3] (kfoldcv.Rmd)
Error: processing vignette 'kfoldcv.Rmd' failed with diagnostics:
there is no package called 'glmnet'
--- failed re-building ‘kfoldcv.Rmd’

SUMMARY: processing the following files failed:
  ‘computeError.Rmd’ ‘kfoldcv.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'Rcpp', 'osqp', 'RcppEigen'

Packages which this enhances but not available for checking:
  'gurobi', 'rcbc', 'cccp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rvcg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘minqa’
Package suggested but not available for checking: ‘Rcpp’
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'raster', 'leaflet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geojsonsf', 'RcppSimdJson', 'sf'

Packages suggested but not available for checking: 'od', 'stplanr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'flexsurv', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'intmap', 'VeryLargeIntegers'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'mixR', 'transport'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) fit.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.Rd:39: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘reshape2’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘cytofan_flow_cytometry.Rmd’ using rmarkdown

Quitting from lines 53-57 [unnamed-chunk-2] (cytofan_flow_cytometry.Rmd)
Error: processing vignette 'cytofan_flow_cytometry.Rmd' failed with diagnostics:
there is no package called 'reshape2'
--- failed re-building ‘cytofan_flow_cytometry.Rmd’

SUMMARY: processing the following file failed:
  ‘cytofan_flow_cytometry.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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: 'reshape2', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'magick', 'Seurat', 'SeuratObject'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'devtools', 'ggrepel', 'ModelMetrics', 'questionr',
  'recipes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

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 suggested but not available for checking: 'shiny', 'golem'
Package suggested but not available for checking: ‘listviewer’

Packages which this enhances but not available for checking:
  'treemap', 'V8'
Packages suggested but not available for checking: 'openxlsx', 'officedown'
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’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(usethis)
  > 
  > test_check("usethis")
  Starting 1 test process
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test01.R:40:5'): typical workflow ───────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'officedown'
  Backtrace:
       ▆
    1. ├─D4TAlink.light::renderTaskRmd(task) at test01.R:40:5
    2. │ └─rmarkdown::render(...)
    3. │   └─rmarkdown:::create_output_format(output_format$name, output_format$options)
    4. │     └─rmarkdown:::create_output_format_function(name)
    5. │       └─base::eval(xfun::parse_only(name))
    6. │         └─base::eval(xfun::parse_only(name))
    7. └─base::loadNamespace(x)
    8.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
    9.     └─base (local) withOneRestart(expr, restarts[[1L]])
   10.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  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: ‘DAAG’
Package required but not available: ‘latticeExtra’

Packages suggested but not available for checking: 'lme4', 'qgam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
       |                 ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘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: 'ggpubr', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fst', 'mixtools', 'sf'

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}"
       |                                         ^
Package required but not available: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dagitty’
Package required but not available: ‘dagitty’

Package suggested but not available for checking: ‘ggdag’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidytext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘codemetar’
Packages required but not available: 'magick', 'pdftools', 'readtext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'phylobase', 'ggtree', 'DAISIE', 'castor'

Packages suggested but not available for checking:
  'diversitree', 'corHMM', 'ggimage'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DDD', 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking:
  'ggtree', 'tidytree', 'ape', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘ranger’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DALEX)
  Welcome to DALEX (version: 2.4.3).
  Find examples and detailed introduction at: http://ema.drwhy.ai/
  Additional features will be available after installation of: ggpubr.
  Use 'install_dependencies()' to get all suggested dependencies
  > 
  > test_check("DALEX")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/DALEX.Rcheck/tests/testthat/helper-objects.R"
  Caused by error in `library()`:
  ! there is no package called 'ranger'
  Backtrace:
       ▆
    1. ├─testthat::test_check("DALEX")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_helpers(".", env)
    7. │           └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("ranger") at tests/testthat/helper-objects.R:10:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'auditor', 'ggrepel', 'lime', 'localModel', 'ranger', 'recipes',
  'reticulate', 'stacks', 'tidymodels'
Running examples in ‘DALEXtra-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.training_test_comparison
> ### Title: Plot and compare performance of model between training and test
> ###   set
> ### Aliases: plot.training_test_comparison
> 
> ### ** Examples
> 
> 
> library("mlr")
Loading required package: ParamHelpers
> library("DALEXtra")
> task <- mlr::makeRegrTask(
+  id = "R",
+   data = apartments,
+    target = "m2.price"
+ )
>  learner_lm <- mlr::makeLearner(
+  "regr.lm"
+ )
> model_lm <- mlr::train(learner_lm, task)
> explainer_lm <- explain_mlr(model_lm, apartmentsTest, apartmentsTest$m2.price, label = "LM")
Preparation of a new explainer is initiated
  -> model label       :  LM 
  -> data              :  9000  rows  6  cols 
  -> target variable   :  9000  values 
  -> predict function  :  yhat.WrappedModel  will be used ( [33m default [39m )
  -> predicted values  :  No value for predict function target column. ( [33m default [39m )
  -> model_info        :  package mlr , ver. 2.19.2 , task regression ( [33m default [39m ) 
  -> predicted values  :  numerical, min =  1792.597 , mean =  3506.836 , max =  6241.447  
  -> residual function :  difference between y and yhat ( [33m default [39m )
  -> residuals         :  numerical, min =  -257.2555 , mean =  4.687686 , max =  472.356  
 [32m A new explainer has been created! [39m 
> 
> learner_rf <- mlr::makeLearner(
+ "regr.ranger"
+ )
Error in requirePackages(package, why = stri_paste("learner", id, sep = " "),  : 
  For learner regr.ranger please install the following packages: ranger
Calls: <Anonymous> ... addClasses -> makeRLearnerInternal -> requirePackages -> stopf
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'daltoolbox', 'glmnet', 'smotefamily'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'dbscan', 'elmNNRcpp', 'forecast', 'reshape', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'sf', 'units', 'smoothr', 'terra', 'shiny', 'leaflet',
  'shinydashboard'

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: 'caper', 'ape', 'picante', 'DDD'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggrepel’

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: ‘zeitgebr’
Package required but not available: ‘crul’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘anytime’
Packages suggested but not available for checking:
  'car', 'DescTools', 'reshape2', 'robslopes'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Epi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘recipes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'xesreadR', 'bupaR', 'edeaR', 'miniUI', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'lfda', 'klaR', 'plotly', 'rARPACK'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'dartR.data', 'ape', 'plyr', 'reshape2', 'StAMPP',
  'SNPassoc'

Packages suggested but not available for checking:
  'devtools', 'dismo', 'gdistance', 'gganimate', 'ggrepel',
  'HardyWeinberg', 'hierfstat', 'leaflet', 'leaflet.minicharts',
  'mmod', 'pegas', 'plotly', 'poppr', 'qvalue', 'Rcpp', 'seqinr', 'sf',
  'shinyBS', 'shinyjs', 'shinythemes', 'shinyWidgets', 'SIBER',
  'terra', 'vcfR', 'fields', 'ggtern'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'adegenet', 'dartR.base', 'dartR.data'

Packages suggested but not available for checking:
  'SIBER', 'fields', 'reshape2', 'spelling'

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'

Packages suggested but not available for checking:
  'SIBER', 'fields', 'leaflet', 'plyr', 'qvalue', 'raster', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'dartR.data', 'ape', 'fields', 'plyr', 'PopGenReport',
  'raster', 'reshape2', 'shiny', 'StAMPP'

Packages suggested but not available for checking:
  'devtools', 'dismo', 'gdistance', 'ggtern', 'gganimate', 'ggrepel',
  'HardyWeinberg', 'hierfstat', 'leaflet', 'leaflet.minicharts',
  'mmod', 'pegas', 'plotly', 'poppr', 'qvalue', 'Rcpp', 'seqinr',
  'shinyBS', 'shinyjs', 'shinythemes', 'shinyWidgets', 'SIBER',
  'terra', 'vcfR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'adegenet', 'dartR.base', 'dartR.data'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'dartR.base', 'dartR.data', 'shiny', 'fields', 'Rcpp',
  'shinyBS', 'shinyjs', 'shinythemes', 'shinyWidgets', 'hierfstat',
  'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'dartR.base', 'dartR.data', 'StAMPP', 'raster'

Packages suggested but not available for checking:
  'mmod', 'dismo', 'gdistance', 'terra', 'sf', '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 required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘urltools’

Packages suggested but not available for checking: 'odbc', 'pool'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'GeneralizedUmatrix', 'RcppArmadillo'

Packages suggested but not available for checking:
  'DataVisualizations', 'geometry', 'spdep',
  'ProjectionBasedClustering', 'parallelDist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'summarytools', 'DT', 'plotly', 'shinyWidgets', 'shinyFiles'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
checkRd: (-1) StartEnd.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) StartEnd.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available:
  'devtools', 'DT', 'golem', 'shiny', 'shinydashboard',
  'shinydashboardPlus', 'shinyjs', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) processFlow.Rd:14: Lost braces
    14 | \item{roundDigits}{Integer. If NA, numerics are not rounded before comparison. If /code{roundDigits} is specified, numerics are 
       |                                                                                        ^
checkRd: (-1) processFlow.Rd:15: Lost braces
    15 | rounded to /code{roundDigits} decimal places using \link[base]{round}.}
       |                 ^
Packages suggested but not available for checking: 'devtools', 'spelling'
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘anytime’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinyBS', 'shinyjs', 'miniUI'

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.
checkRd: (-1) number_of_rows.Rd:30-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) number_of_rows.Rd:33-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_methods.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_methods.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_methods.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_methods.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_source.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_source.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) special_simulation.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) special_simulation.Rd:40-43: Lost braces in \itemize; meant \describe ?
Packages required but not available: 'openxlsx', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'GA', 'Rcpp'

Package suggested but not available for checking: ‘pander’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘datagovsgR-vignette.Rmd’ using rmarkdown

Quitting from lines 32-33 [unnamed-chunk-2] (datagovsgR-vignette.Rmd)
Error: processing vignette 'datagovsgR-vignette.Rmd' failed with diagnostics:
Server Error has occured.
--- failed re-building ‘datagovsgR-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘datagovsgR-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pander’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘my new data set.rds’
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinyWidgets', 'toastui', 'shinybusy'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
checkRd: (-1) build_date_factor.Rd:15: Lost braces; missing escapes or markup?
    15 | Map a vector of dates to a factor at one of these levels {"yearmonth", "yearquarter", "quarter", "month"}
       |                                                          ^
checkRd: (-1) build_date_factor.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{type}{One of {"year", "yearquarter", "yearmonth", "quarter", "month"}}
       |                    ^
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'units'

Packages suggested but not available for checking:
  'GGally', 'anytime', 'DT', 'flexdashboard', 'flexsiteboard',
  'plotly', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pander’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'DT', 'sf'
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package suggested but not available for checking: ‘RSDA’
Error(s) in re-building vignettes:
  ...
--- re-building ‘V1_dataSDA.Rmd’ using rmarkdown

Quitting from lines 21-29 [setup] (V1_dataSDA.Rmd)
Error: processing vignette 'V1_dataSDA.Rmd' failed with diagnostics:
there is no package called 'RSDA'
--- failed re-building ‘V1_dataSDA.Rmd’

SUMMARY: processing the following file failed:
  ‘V1_dataSDA.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘jsonvalidate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'miniUI', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rlabkey’

Package suggested but not available for checking: ‘pryr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'EML', 'shiny'

Packages suggested but not available for checking: 'servr', 'listviewer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ROCnReg’
Packages suggested but not available for checking: 'ape', 'treemap'
Running examples in ‘data.tree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GetPhyloNr
> ### Title: Determine the number a 'Node' has after conversion to a phylo
> ###   object
> ### Aliases: GetPhyloNr
> 
> ### ** Examples
> 
> library(ape)
Error in library(ape) : there is no package called ‘ape’
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
Package required but not available: ‘shiny.semantic’

Packages suggested but not available for checking: 'shiny', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("devtools")
  Error in library("devtools") : there is no package called 'devtools'
  Execution halted
Packages required but not available: 'Rcpp', 'reshape2', 'RcppArmadillo'

Packages suggested but not available for checking:
  'plyr', 'ggmap', 'rworldmap', 'choroplethr', 'parallelDist',
  'ggExtra', 'plotly', 'ggrepel', 'ScatterDensity'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'brms', 'gamm4', 'gt', 'lme4', 'mediation', 'rstanarm'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'Rcpp'

Package suggested but not available for checking: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'DT', 'shiny', 'shinytest2', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'jsonify', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘nanotime’
Package required but not available: ‘shiny’

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: 'Rcpp', 'RcppArmadillo'

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: 'devtools', 'reshape2'
Package required but not available: ‘odbc’

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.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'tidyRSS'

Package suggested but not available for checking: ‘rmapshaper’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'terra'

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.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'caret', 'TSdist', 'parallelDist', 'plyr'

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}.
       |         ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'pander', 'questionr', 'naniar'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'seqHMM', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Package suggested but not available for checking: ‘vcr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
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: 'Rcpp', 'cubature', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bnviewer’

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 required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘odbc’
Package required but not available: ‘GBJ’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dada2', 'plyr', 'ShortRead'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DBTC', 'DT', 'leaflet', 'leaflet.extras', 'shiny', 'shinyFiles',
  'shinyjs', 'shinycssloaders', 'shinydashboard', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'urltools', 'odbc'
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dbx)
  > 
  > test_check("dbx")
  [ FAIL 1 | WARN 0 | SKIP 24 | PASS 84 ]
  
  ══ Skipped tests (24) ══════════════════════════════════════════════════════════
  • !(isPostgres(db) || isMariaDB(db)) || redshift is TRUE (3):
    'test-sqlite.R:7:1', 'test-sqlite.R:7:1', 'test-sqlite.R:7:1'
  • !isPostgres(db) is TRUE (10): 'test-sqlite.R:7:1', 'test-sqlite.R:7:1',
    'test-sqlite.R:7:1', 'test-sqlite.R:7:1', 'test-sqlite.R:7:1',
    'test-sqlite.R:7:1', 'test-sqlite.R:7:1', 'test-sqlite.R:7:1',
    'test-sqlite.R:7:1', 'test-sqlite.R:7:1'
  • On CRAN (4): 'test-mariadb.R:3:1', 'test-mysql.R:3:1', 'test-postgres.R:3:1',
    'test-postgresql.R:3:1'
  • empty test (1): 'test-sqlite.R:7:1'
  • isSQLite(db) is TRUE (1): 'test-sqlite.R:7:1'
  • isSQLite(db) || isSQLServer(db) is TRUE (1): 'test-sqlite.R:7:1'
  • odbc (3): 'test-odbc-mysql.R:3:1', 'test-odbc-postgres.R:3:1',
    'test-odbc-sqlserver.R:3:1'
  • redshift (1): 'test-redshift.R:3:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-sqlite.R:10:3'): connect with url works ────────────────────────
  Error in `dbxConnect(url = "sqlite:///:memory:")`: Install 'urltools' to use url
  Backtrace:
      ▆
   1. └─dbx::dbxConnect(url = "sqlite:///:memory:") at test-sqlite.R:10:3
  
  [ FAIL 1 | WARN 0 | SKIP 24 | PASS 84 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
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
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'rumidas', 'rugarch', 'roll', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) data.Rd:11: Lost braces
    11 | \doi{10.1007/s40258-021-00647-3}{DOI}
       |                                 ^
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shinyBS', 'shinycssloaders', 'shiny', 'shinyWidgets', 'DT', 'idefix'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'tensorflow', 'ape', 'phangorn', 'Rcpp', 'rBayesianOptimization',
  'RcppArmadillo'

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: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DCluster', 'lme4'

Packages suggested but not available for checking: 'INLA', 'latticeExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spdep’

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘phylogram’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'GDINA', 'spelling'

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.
Package required but not available: ‘seqinr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'Rfast', 'RcppArmadillo', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dcov', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dcov', 'Rfast', 'Rfast2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'StanHeaders', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'nnTensor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'gtsummary', 'spelling'
Error(s) in re-building vignettes:
  ...
--- re-building ‘dca.Rmd’ using rmarkdown

Quitting from lines 19-21 [setup] (dca.Rmd)
Error: processing vignette 'dca.Rmd' failed with diagnostics:
there is no package called 'gtsummary'
--- failed re-building ‘dca.Rmd’

SUMMARY: processing the following file failed:
  ‘dca.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'geometry', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dtwclust’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'phytools', 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ranger', 'fastglm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘qpdf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'AER', 'glmnet', 'ranger'

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}}
       |     ^
Package required but not available: ‘dbscan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RSpectra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'mixtools', 'plyr', 'shiny', 'shinydisconnect', 'shinyjs'

Package suggested but not available for checking: ‘ggExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggalt', 'MEGENA', 'plyr'

Package suggested but not available for checking: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'shiny', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'extraDistr', 'ggpubr', 'ggtext', 'ggtree', 'phylobase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'aphid', 'seqinr'

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.
Packages required but not available: 'CVXR', 'caret'

Package suggested but not available for checking: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinyjs', 'shinydashboard', 'shinydashboardPlus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggraph’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'chillR', 'rriskDistributions'

Package suggested but not available for checking: ‘mc2d’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'sf', 'shiny'
Package required but not available: ‘estimatr’

Packages suggested but not available for checking:
  'AER', 'sf', 'reshape2', 'DesignLibrary', 'marginaleffects'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DT’
Packages required but not available:
  'keras', 'tensorflow', 'reticulate', 'tsutils', 'Rlibeemd',
  'TSdeeplearning', 'VMDecomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rlibeemd', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘StratigrapheR’

Packages suggested but not available for checking:
  'EMD', 'Rssa', 'astrochron'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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}),
       |                                                           ^
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'car', 'plyr', 'effects'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘collapse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'ggraph', 'graphlayouts', 'plyr', 'shiny',
  'shinycssloaders', 'spelling', 'vcr'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [4s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(deepdep)
  > 
  > test_check("deepdep")
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 21 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • vcr cannot be loaded (4): 'test-deepdep.R:26:3', 'test-deepdep.R:48:3',
    'test-plot.R:8:1', 'test-plot_downloads.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-deepdep_declutter.R:1:1'): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'vcr'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-deepdep_declutter.R:1:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 21 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'GpGp', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘interp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'glmnet', 'weights'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tokenizers’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'extraDistr', 'Rfast'

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:
  'keras', 'reticulate', 'seqinr', 'tensorflow'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tensorflow', 'tfprobability', 'keras', 'reticulate', 'tfruns'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggforce', 'ggfittext'

Packages suggested but not available for checking:
  'phytools', 'divDyn', 'ape', 'palaeoverse', 'paleotree', 'dispRity',
  'ggtree', 'ggpattern', 'ggrepel', 'rmacrostrat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tensorflow', 'keras', 'tfprobability', 'deepregression', 'mlt',
  'reticulate'

Packages suggested but not available for checking: 'tram', 'cotram'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'xslt', 'reporter', 'libr', 'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'terra', 'plyr', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘units’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'parglm', 'glmmTMB', 'ggpubr', 'ggrepel', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘shiny’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'shinyMatrix', 'shinyBS'

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}.}
       |                                                                                ^
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'lme4', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘GGally’

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
Found the following files/directories:
  ‘smd_table.docx’
Package required but not available: ‘flextable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'ftsa', 'rainbow'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) kin.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:53-61: Lost braces
    53 | {\itemize{
       | ^
checkRd: (-1) kin.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:59-67: Lost braces
    59 | {\itemize{
       | ^
checkRd: (-1) kin2sex.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
Packages required but not available:
  'Rcpp', 'fields', 'spam', 'ClusterR', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ape', 'heatmaply'

Packages which this enhances but not available for checking:
  'WGCNA', 'distory', 'phangorn'
Running examples in ‘dendextend-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: collapse_branch
> ### Title: Collapse branches under a tolerance level
> ### Aliases: collapse_branch
> 
> ### ** Examples
> 
> 
> # # ladderize is like sort(..., type = "node")
> dend <- iris[1:5, -5] %>%
+   dist() %>%
+   hclust() %>%
+   as.dendrogram()
> par(mfrow = c(1, 3))
> dend %>%
+   ladderize() %>%
+   plot(horiz = TRUE)
> abline(v = .2, col = 2, lty = 2)
> dend %>%
+   collapse_branch(tol = 0.2) %>%
+   ladderize() %>%
+   plot(horiz = TRUE)
> dend %>%
+   collapse_branch(tol = 0.2) %>%
+   ladderize() %>%
+   hang.dendrogram(hang = 0) %>%
+   plot(horiz = TRUE)
> 
> par(mfrow = c(1, 2))
> dend %>%
+   collapse_branch(tol = 0.2, lower = FALSE) %>%
+   plot(horiz = TRUE, main = "dendrogram")
> library(ape)
Error in library(ape) : there is no package called ‘ape’
Execution halted
Package required but not available: ‘forecast’

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: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) conifersIP.Rd:9: Lost braces; missing escapes or markup?
     9 | \code{conifersIP} {has following variables:}
       |                   ^
checkRd: (-1) conifersIP.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sync.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reshape2', 'oce', 'plotly', 'Cubist'

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 suggested but not available for checking: ‘tsibble’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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.
Package required but not available: ‘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
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppArmadillo', 'RcppEigen',
  'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'sfheaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggrepel', 'Rtsne'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'OpenMx', 'rvinecopulib'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘telegram.bot’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
       |                            ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'raster', 'sf', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'np', 'geometry', 'RcppArmadillo'

Packages suggested but not available for checking: 'RcppArmadillo', 'fda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping vignette re-building
Package suggested but not available for checking: ‘pander’

VignetteBuilder package required for checking but not installed: ‘pander’
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
Errors in running code in vignettes:
when running code in ‘derivmkts-vignette.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'pander' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘derivmkts-vignette.Rmd’ using ‘UTF-8’... failed to complete the test
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'reshape2', 'plyr', 'GGally'

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: 'ggpattern', 'GGally'
Running examples in ‘descriptio-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggassoc_marimekko
> ### Title: Marimekko plot
> ### Aliases: ggassoc_marimekko
> ### Keywords: multivariate aplot
> 
> ### ** Examples
> 
> data(Movies)
> ggassoc_marimekko(data=Movies, mapping=ggplot2::aes(Genre, Country))
> ggassoc_marimekko(data=Movies, mapping=ggplot2::aes(Genre, Country), type = "patterns")
Error in ggassoc_marimekko(data = Movies, mapping = ggplot2::aes(Genre,  : 
  ggpattern package should be installed to use this type of plot
Execution halted
Package required but not available: ‘reshape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘xplorerr’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'DescTools', 'flextable'

Package suggested but not available for checking: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'pander', 'DT'

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: ‘Rcpp’

Package suggested but not available for checking: ‘RDCOMClient’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'animation', 'shiny', 'RcppArmadillo'

Package suggested but not available for checking: ‘smoots’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reticulate', 'fields', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bs4Dash', 'cicerone', 'golem', 'shinipsum', 'shiny',
  'shinyscreenshot'

Packages suggested but not available for checking: 'chromote', 'shinytest2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'gt', 'devtools', 'ggpattern', 'bestNormalize'
Packages required but not available: 'DeclareDesign', 'estimatr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘highs’

Package which this enhances but not available for checking: ‘gurobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Packages suggested but not available for checking: 'lmerTest', 'afex'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'sitmo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘FME’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
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 suggested but not available for checking: 'dclone', 'dcmle'
Packages required but not available: 'plyr', 'reshape2', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AER’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'liminal'
checkRd: (-1) detour-shiny.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{expr}{an expression that generates a {detourr} widget}
       |                                            ^
checkRd: (-1) show_sage.Rd:80: Lost braces; missing escapes or markup?
    80 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
checkRd: (-1) show_scatter.Rd:67: Lost braces; missing escapes or markup?
    67 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
checkRd: (-1) show_scatter_internal.Rd:65: Lost braces; missing escapes or markup?
    65 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
checkRd: (-1) show_slice.Rd:76: Lost braces; missing escapes or markup?
    76 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
checkRd: (-1) tour_aes.Rd:11: Lost braces; missing escapes or markup?
    11 | Variables are evaluated using {tidyselect} syntax.}
       |                               ^
Packages required but not available: 'autothresholdr', 'plyr', 'Rcpp'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘miniUI’

Packages suggested but not available for checking: 'DT', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘GGally’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dexter', 'shiny', 'shinyBS', 'DT', 'shinyjs', 'shinyFiles',
  'ggExtra'

Package suggested but not available for checking: ‘sirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'dexter'

Package suggested but not available for checking: ‘mirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'dqrng', 'sitmo'

Package suggested but not available for checking: ‘latticeExtra’

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: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'gprofiler2', 'ggpubr', 'signatureSearch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pryr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘quarto’

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘mirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'collapse', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RcppArmadillo', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggpubr’

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: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sgs', 'caret', 'faux'

Package suggested but not available for checking: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'plotly'

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MLInterfaces’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DescTools’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qvalue’
checkRd: (-1) runContrasts.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:82: Lost braces in \itemize; meant \describe ?
Packages required but not available: 'Rcpp', 'collapse', 'sf', 's2'

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.}
       |                                                                         ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘COMPoissonReg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'reshape2', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'GPFDA', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reticulate', 'ggforce', 'reshape2', 'lhs', 'clhs'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gap', 'ape', 'qgam', 'lme4'

Packages suggested but not available for checking:
  'mgcViz', 'spaMM', 'glmmTMB', 'phylolm'

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: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘dhis2r.Rmd’ using rmarkdown

Quitting from lines 36-38 [unnamed-chunk-3] (dhis2r.Rmd)
Error: processing vignette 'dhis2r.Rmd' failed with diagnostics:
HTTP 401 Unauthorized.
--- failed re-building ‘dhis2r.Rmd’

SUMMARY: processing the following file failed:
  ‘dhis2r.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'conquer', 'cubature'

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: ‘DiagrammeRsvg’
Package required but not available: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'politeness', 'doc2concrete', 'vader', 'quanteda'

Package suggested but not available for checking: ‘spacyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'KrigInv', 'GPareto'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'clusterSim', 'klaR', 'NMF', 'Rcpp'

Packages suggested but not available for checking:
  'apcluster', 'blockcluster', 'dbscan', 'kohonen', 'pander', 'Rtsne'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geometry’

Package suggested but not available for checking: ‘rlibkriging’

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>}{}
       |  ^
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) define.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'fixest', 'MatrixExtra', 'did', 'staggered', 'didimputation'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'copBasic', 'factoextra', 'phylogram'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fixest’
Running examples in ‘DiDforBigData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DiD
> ### Title: Combine DiD estimates across cohorts and event times.
> ### Aliases: DiD
> 
> ### ** Examples
> 
> # simulate some data
> simdata = SimDiD(sample_size=200, ATTcohortdiff = 2)$simdata
> 
> # define the variable names as a list()
> varnames = list()
> varnames$time_name = "year"
> varnames$outcome_name = "Y"
> varnames$cohort_name = "cohort"
> varnames$id_name = "id"
> 
> # estimate the ATT for all cohorts at event time 1 only
> DiD(simdata, varnames, min_event=1, max_event=1)
Loading required namespace: fixest
Failed with error:  ‘there is no package called ‘fixest’’
[1] "warning: fixest not found"
Error in str2lang(x) : <text>:2:0: unexpected end of input
1: Y_diff ~ -1 + treated_2007 + treated_2010 + treated_2012 + 
   ^
Calls: DiD ... as.formula -> formula -> formula.character -> str2lang
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Background.Rmd’ using rmarkdown
--- finished re-building ‘Background.Rmd’

--- re-building ‘DiDforBigData.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'fixest''

Quitting from lines 91-92 [unnamed-chunk-7] (DiDforBigData.Rmd)
Error: processing vignette 'DiDforBigData.Rmd' failed with diagnostics:
<text>:2:0: unexpected end of input
1: Y_diff ~ -1 + treated_2007 + treated_2010 + treated_2012 + 
   ^
--- failed re-building ‘DiDforBigData.Rmd’

--- re-building ‘Examples.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'fixest''

Quitting from lines 83-86 [unnamed-chunk-8] (Examples.Rmd)
Error: processing vignette 'Examples.Rmd' failed with diagnostics:
<text>:2:0: unexpected end of input
1: Y_diff ~ -1 + treated_2007 + treated_2010 + treated_2012 + 
   ^
--- failed re-building ‘Examples.Rmd’

--- re-building ‘Theory.Rmd’ using rmarkdown
--- finished re-building ‘Theory.Rmd’

SUMMARY: processing the following files failed:
  ‘DiDforBigData.Rmd’ ‘Examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'YatchewTest', 'nprobust', 'plm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fixest', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'matlib', 'plm', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fixest', 'DIDmultiplegtDYN', 'DIDHAD'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BMisc', 'ggpubr', 'DRDID'

Package suggested but not available for checking: ‘plm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘vcfR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘penalized’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pcaMethods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘JuliaCall’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DOT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'terra', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘shiny’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'reshape2', 'RcppEigen'

Package suggested but not available for checking: ‘parallelDist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘systemfit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gurobi’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘shiny’
Package required but not available: ‘pander’

Packages suggested but not available for checking:
  'Ckmeans.1d.dp', 'FunChisq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘penalized’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'spdep', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'calculus', 'plyr'

Package suggested but not available for checking: ‘ShinyItemAnalysis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'TestDataImputation', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mirt', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinydashboard', 'difR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘penalized’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggrepel’

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’
Skipping checking math rendering: package 'V8' unavailable
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: 'plyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggtext', 'metR', 'PieGlyph'

Packages suggested but not available for checking:
  'DImodelsMulti', 'spelling'

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', 'RSpectra', 'Rtsne', 'energy', 'keras', 'loe', 'reticulate',
  'tensorflow', 'umap'
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
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'simcdm', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘CDM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'shiny'

Packages suggested but not available for checking: 'promises', 'later'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'mvnfast', 'rlemon'

Packages suggested but not available for checking: 'optmatch', 'rrelaxiv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'reshape2', 'glmnet', 'hdm', 'ranger'
Packages required but not available:
  'bigstatsr', 'Rfast', 'Rfast2', 'Rnanoflann', 'rnaturalearth', 'sf'

Package suggested but not available for checking: ‘bigreadr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'alphahull', 'latticeExtra'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'lbfgs', 'RcppArmadillo'

Package suggested but not available for checking: ‘EdSurvey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘mcmcse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rotasym’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘expectreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'TMB', 'rSPDE', 'fmesher', 'tidyterra', 'terra', 'sf', 'RcppEigen'

Package suggested but not available for checking: ‘SpatialEpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'shinytest2'
Packages required but not available:
  'Rcpp', 'rstan', 'SHELF', 'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: ‘rstantools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘TSCAN’

Package suggested but not available for checking: ‘Seurat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘disclapmix’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘fwsim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'pdftools', 'qdap', 'SentimentAnalysis', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sirt', 'cubature'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CVXR', 'extremeStat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GGally', 'ggrepel'

Package suggested but not available for checking: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'golem', 'shiny', 'plotly', 'loadeR', 'shinyjs', 'shinyAce',
  'echarts4r', 'FactoMineR', 'colourpicker', 'shinydashboard',
  'shinycustomloader', 'shinydashboardPlus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

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.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'klaR', 'spelling'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [10s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(discrim)
  Loading required package: parsnip
  > 
  > test_check("discrim")
  [ FAIL 2 | WARN 0 | SKIP 4 | PASS 434 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test-linear-lda.R:112:3', 'test-linear-sparsediscrim.R:199:3',
    'test-naive-Bayes_naivebayes.R:194:3', 'test-quad-qda.R:123:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-naive-Bayes.R:36:1'): (code run outside of `test_that()`) ──────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'klaR'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-naive-Bayes.R:36:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-rda.R:7:1'): (code run outside of `test_that()`) ───────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'klaR'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-rda.R:7:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 4 | PASS 434 ]
  Error: Test failures
  Execution halted
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)
       |                ^
Packages required but not available: 'ranger', 'mvnfast'

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', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'terra', 'sf', 'tmap', 'mapview'
Error(s) in re-building vignettes:
  ...
--- re-building ‘data_vis.Rmd’ using rmarkdown

Quitting from lines 200-216 [unnamed-chunk-13] (data_vis.Rmd)
Error: processing vignette 'data_vis.Rmd' failed with diagnostics:
there is no package called 'mapview'
--- failed re-building ‘data_vis.Rmd’

--- re-building ‘modeling.Rmd’ using rmarkdown
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.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.


Quitting from lines 210-211 [unnamed-chunk-6] (modeling.Rmd)
Error: processing vignette 'modeling.Rmd' failed with diagnostics:
there is no package called 'terra'
--- failed re-building ‘modeling.Rmd’

SUMMARY: processing the following files failed:
  ‘data_vis.Rmd’ ‘modeling.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘terra’

Packages which this enhances but not available for checking:
  'mapmisc', 'INLA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'odbc', 'spelling'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fst', 'collapse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'pryr', 'fst', 'bigreadr'

Packages suggested but not available for checking: 'shiny', 'LaF'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'Rcpp', 'terra'

Package suggested but not available for checking: ‘gstat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mvp’
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
'LazyData' is specified without a 'data' directory
Packages required but not available: 'raster', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ape', 'ade4', 'castor', 'Claddis', 'geometry', 'phangorn',
  'phyclust', 'phylolm'

Package suggested but not available for checking: ‘MCMCglmm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'biomartr', 'seqinr'
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: cut_probes
> ### Title: Cut probes
> ### Aliases: cut_probes
> 
> ### ** Examples
> 
> path <- tempdir()
> dir.create (path)
> # download and save as FASTA "Chlamydia pneumoniae B21 contig00001,
> # whole genome shotgun sequence" (GI = 737435910)
> if (!requireNamespace("rentrez", quietly = TRUE)) {
+ stop("Package \"rentrez\" needed for this function to work. Please install it.", call. = FALSE)}
> reference.string <- rentrez::entrez_fetch(db = "nucleotide", id = 737435910,
+                                          rettype="fasta")
> write( x= reference.string, file = paste0 (path, "/fasta"))
> probes <- cut_probes (ref.seq.from.file = TRUE, fasta.file = paste0(path, "/fasta"),
+                      delete.fasta = TRUE, start = 1000, stop = 1500,
+                      start.correction = FALSE, size = c(400, 500),
+                      delete.incomplete = FALSE,
+                      delete.identical = FALSE, give.probes.id = TRUE, mc.cores = 1)
Error: Package "seqinr" needed for this function to work. Please install it.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'caret', 'raster', 'plyr'

Package suggested but not available for checking: ‘Cubist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'nabor'

Packages suggested but not available for checking:
  'fasterize', 'raster', 'lwgeom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'fields'

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', 'tidytext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘opencpu’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
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: 'glmnet', 'Rforestry'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Package required but not available: ‘Rcpp’

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: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'colourpicker', 'DT', 'extraDistr', 'shiny', 'shinyalert', 'shinyBS',
  'shinyjs', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'learnr', 'spelling'
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'ggdist', 'gk'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'GA', 'AdaptGauss'

Package suggested but not available for checking: ‘parallelDist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'PoissonBinomial', 'revdbayes'
Running examples in ‘distributions3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Frechet
> ### Title: Create a Frechet distribution
> ### Aliases: Frechet
> 
> ### ** Examples
> 
> 
> set.seed(27)
> 
> X <- Frechet(0, 2)
> X
[1] "Frechet(location = 0, scale = 2, shape = 1)"
> 
> random(X, 10)
Error in loadNamespace(x) : there is no package called ‘revdbayes’
Calls: random ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
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))}
       |   ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'odbc', 'spelling'
Package required but not available: ‘ggrepel’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘icosa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geosphere', 'plotly'

Package suggested but not available for checking: ‘pander’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘FME’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘loon.shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Package suggested but not available for checking: ‘entropart’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'Rcpp'

Packages suggested but not available for checking:
  'minqa', 'caper', 'geiger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ggpubr', 'MapGAM', 'RcppEigen'

Package suggested but not available for checking: ‘BOLTSSIRR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RNifti'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BAT', 'SESraster', 'terra'

Package suggested but not available for checking: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'pryr'

Package suggested but not available for checking: ‘flexdashboard’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'units'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'iNEXT', 'sf', 'terra', 'units'

Package suggested but not available for checking: ‘rnaturalearth’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'shiny', 'shinyjs'
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:
  'nardl', 'dynlm', 'AER', 'plyr', 'roll'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘magick’

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: 'glmnet', 'SAM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'MSEtool', 'Rcpp', 'TMB', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'shiny', 'shinythemes', 'RcppArmadillo', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'hrbrthemes', 'mice', 'pagedown', 'shiny'

Packages suggested but not available for checking: 'forecast', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘DT’
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}
       |                                       ^
Packages required but not available:
  'bayesplot', 'ggrepel', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lfda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

Packages suggested but not available for checking: 'reticulate', 'pander'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'colourpicker', 'DiagrammeRsvg', 'odbc', 'pool', 'shiny', 'shinyAce',
  'shinydashboard'
Packages required but not available: 'hclust1d', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'glmnet', 'ks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                 ^
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                             ^
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                                             ^
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                                                         ^
checkRd: (-1) outliers.ranking.Rd:143: Lost braces; missing escapes or markup?
   143 |   where g_{y,i} and g_{x,i} are the two groups involved in the merge at
       |           ^
checkRd: (-1) outliers.ranking.Rd:143: Lost braces; missing escapes or markup?
   143 |   where g_{y,i} and g_{x,i} are the two groups involved in the merge at
       |                       ^
checkRd: (-1) outliers.ranking.Rd:144: Lost braces; missing escapes or markup?
   144 |   step i, and g_{x,i} is the group which X belongs to. Note that if X
       |                 ^
Packages required but not available: 'gRaven', 'gRbase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'multicool', 'Rcpp'

Package suggested but not available for checking: ‘testthis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spdep’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arm', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rdimtools', 'ape', 'phytools', 'ratematrix'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dbscan’

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 suggested but not available for checking: 'lme4', 'pbkrtest'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'tm', 'quanteda', 'glmnet', 'textstem'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'tokenizers.bpe', 'word2vec', 'uwot', 'dbscan', 'udpipe'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'magick', 'pdftools'

Package suggested but not available for checking: ‘webshot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘cubature’
'LazyData' is specified without a 'data' directory
Running examples in ‘docopulae-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nint_integrateNCube
> ### Title: Integrate Hypercube
> ### Aliases: nint_integrateNCube nint_integrateNCube_integrate
> ###   nint_integrateNCube_cubature nint_integrateNCube_SparseGrid
> 
> ### ** Examples
> 
> ## integrate with defaults (stats::integrate)
> nint_integrate(sin, nint_space(nint_intvDim(pi/4, 3*pi/4)))
[1] 1.414214
> 
> 
> dfltNCube = nint_integrateNCube
> 
> ## prepare for integrateA
> ncube = function(f, lowerLimit, upperLimit, ...) {
+     cat('using integrateA\n')
+     integrateA(f, lowerLimit, upperLimit, ..., subdivisions=2)
+ }
> ncube = nint_integrateNCube_integrate(ncube)
> unlockBinding('nint_integrateNCube', environment(nint_integrate))
> assign('nint_integrateNCube', ncube, envir=environment(nint_integrate))
> 
> ## integrate with integrateA
> nint_integrate(sin, nint_space(nint_intvDim(pi/4, 3*pi/4)))
using integrateA
[1] 1.414214
> 
> 
> ## prepare for cubature
> ncube = function(f, lowerLimit, upperLimit, ...) {
+     cat('using cubature\n')
+     r = cubature::adaptIntegrate(f, lowerLimit, upperLimit, ..., maxEval=1e3)
+     return(r$integral)
+ }
> unlockBinding('nint_integrateNCube', environment(nint_integrate))
> assign('nint_integrateNCube', ncube, envir=environment(nint_integrate))
> 
> ## integrate with cubature
> nint_integrate(sin, nint_space(nint_intvDim(pi/4, 3*pi/4)))
using cubature
Error in loadNamespace(x) : there is no package called ‘cubature’
Calls: nint_integrate ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'osmdata', 'Rcpp'

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DoE.wrapper’
Skipping checking math rendering: package 'V8' unavailable
Package which this enhances but not available for checking: ‘gurobi’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lhs’

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
Package required but not available: ‘qpdf’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lme4', 'car', 'dynlm', 'reshape2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘da-logistic-regression.Rmd’ using rmarkdown

Quitting from lines 177-178 [unnamed-chunk-13] (da-logistic-regression.Rmd)
Error: processing vignette 'da-logistic-regression.Rmd' failed with diagnostics:
there is no package called 'reshape2'
--- failed re-building ‘da-logistic-regression.Rmd’

SUMMARY: processing the following file failed:
  ‘da-logistic-regression.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lme4', 'relaimpo', 'systemfit'
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(domir)
  > 
  > test_check("domir")
  Classes and Methods for R originally developed in the
  Political Science Computational Laboratory
  Department of Political Science
  Stanford University (2002-2015),
  by and under the direction of Simon Jackman.
  hurdle and zeroinfl functions by Achim Zeileis.
  Loading required namespace: Formula
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-Dominance_Stats.r:1:1'): (code run outside of `test_that()`) ───
  <packageNotFoundError/error/condition>
  Error in `library(systemfit)`: there is no package called 'systemfit'
  Backtrace:
      ▆
   1. └─base::library(systemfit) at test-Dominance_Stats.r:1:1
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘nabor’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Morpho', 'Rvcg', 'concaveman'

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’.
Package required but not available: ‘tidytext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'reshape2', 'openxlsx'

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', 'lmerTest'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages suggested but not available for checking: 'optmatch', 'DiPs'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'dagitty', 'DOT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'DT', 'latticeExtra', 'shinyjs', 'shinyWidgets', 'shinyBS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RBesT’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘gurobi’
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’.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘optmatch’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘plyr’
Running examples in ‘dostats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dostats
> ### Title: Convenient interface for computing statistics on a vector
> ### Aliases: dostats
> ### Keywords: misc utilities
> 
> ### ** Examples
> 
> data(mtcars)
> library(plyr)
Error in library(plyr) : there is no package called ‘plyr’
Execution halted
Running ‘test_package.R’ [1s/1s]
Running the tests in ‘tests/test_package.R’ failed.
Complete output:
  > library(testthat)
  > library(dostats)
  > test_check("dostats")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 19 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test_compose.R:7:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_dostats.R:1:1'): (code run outside of `test_that()`) ───────────
  <packageNotFoundError/error/condition>
  Error in `library(plyr)`: there is no package called 'plyr'
  Backtrace:
      ▆
   1. └─base::library(plyr) at test_dostats.R:1:1
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 19 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘spam’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rmapshaper', 'sf', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggstance’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘coneproj’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readstata13’

Packages suggested but not available for checking:
  'glmnet', 'ranger', 'AER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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', 'DT', 'plotly', 'shiny', 'shinyWidgets',
  'shinydashboard', 'shinythemes'

Package suggested but not available for checking: ‘shinytest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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 suggested but not available for checking: ‘spelling’
Packages required but not available: 'cubature', 'sf', 'terra'

Package suggested but not available for checking: ‘rgbif’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'alakazam', 'ape', 'ggtree', 'phangorn', 'shazam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'terra', 'tidyterra'
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dbscan', 'ggpubr', 'raster', 'shiny', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘forecast’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'miniUI', 'shinyWidgets', 'shinyAce', 'plyr', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'panelr', 'jtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘interp’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘extraDistr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘RcppDynProg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'BayesianTools', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'daterangepicker', 'DQAstats', 'DT', 'shiny', 'shinyalert',
  'shinydashboard', 'shinyFiles', 'shinyjs', 'shinyWidgets', 'waiter'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘quarto’

Package suggested but not available for checking: ‘DT’

VignetteBuilder package required for checking but not installed: ‘quarto’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'sitmo'

Package suggested but not available for checking: ‘sitmo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'drc', 'devtools'
checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
Running examples in ‘dr4pl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: print.summary.dr4pl
> ### Title: Print the dr4pl object summary to screen.
> ### Aliases: print.summary.dr4pl
> 
> ### ** Examples
> 
> library(drc)  # Needed for the data set 'ryegras'
Error in library(drc) : there is no package called ‘drc’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dr4pl_derivatives.Rmd’ using rmarkdown
--- finished re-building ‘dr4pl_derivatives.Rmd’

--- re-building ‘walk_through_in_R.Rmd’ using rmarkdown

Quitting from lines 21-24 [unnamed-chunk-1] (walk_through_in_R.Rmd)
Error: processing vignette 'walk_through_in_R.Rmd' failed with diagnostics:
there is no package called 'drc'
--- failed re-building ‘walk_through_in_R.Rmd’

SUMMARY: processing the following file failed:
  ‘walk_through_in_R.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'clustermq', 'disk.frame', 'fst', 'ggraph', 'keras', 'qs', 'Rcpp'
Packages required but not available: 'reshape2', 'tokenizers'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'DoubleML', 'glmnet', 'hdi'
Running examples in ‘drape-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: basis_poly
> ### Title: Estimate the score function of the d'th covariate using a
> ###   polynomial basis.
> ### Aliases: basis_poly
> 
> ### ** Examples
> 
> set.seed(0)
> X <- matrix(stats::rnorm(200), ncol=4)
> bs <- basis_poly(X=X, d=1, degree=2)
Error: Package "glmnet" needed for this function to work.
         Please install it.
Execution halted
Running ‘testthat.R’ [17s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(drape)
  > 
  > test_check("drape")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 64 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_regression_functions.R:4:3'): fit_lasso_poly acts correctly ────
  Error: Package "glmnet" needed for this function to work.
           Please install it.
  Backtrace:
      ▆
   1. └─drape:::fit_lasso_poly(X = X, y = y, degree = 2, lambda = 1) at test_regression_functions.R:4:3
  ── Error ('test_score.R:21:3'): basis_poly acts correctly for single df ────────
  Error: Package "glmnet" needed for this function to work.
           Please install it.
  Backtrace:
      ▆
   1. └─drape::basis_poly(X = X, d = 1, degree = 2, lambda = 1) at test_score.R:21:3
   2.   └─drape:::fit_lasso_poly(basis, X[, d], degree = 1, lambda = lambda)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 64 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘shiny’

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:
  'shiny', 'shinycssloaders', 'shinydashboard'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘cubature’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'ade4', 'sde'

Package suggested but not available for checking: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo', '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', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'drc', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'BMisc', 'Rcpp', 'fastglm'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'WGCNA', 'Rfast', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
checkRd: (-1) dreamerplot.Rd:53: Lost braces; missing escapes or markup?
    53 | a dose returns the plot of pr(trt_dose - trt_{reference_dose} | data).}
       |                                              ^
checkRd: (-1) posterior.Rd:70: Lost braces; missing escapes or markup?
    70 | a dose returns the plot of pr(trt_dose - trt_{reference_dose} | data).}
       |                                              ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘stringmagic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'transport', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘learnr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ranger’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DALEX)
  Welcome to DALEX (version: 2.4.3).
  Find examples and detailed introduction at: http://ema.drwhy.ai/
  Additional features will be available after installation of: ggpubr.
  Use 'install_dependencies()' to get all suggested dependencies
  > library(drifter)
  > 
  > test_check("drifter")
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 2 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_calculate_model_drift.R:5:3'): Type of data in the explainer ───
  <packageNotFoundError/error/condition>
  Error in `library("ranger")`: there is no package called 'ranger'
  Backtrace:
      ▆
   1. └─base::library("ranger") at test_calculate_model_drift.R:5:3
  ── Error ('test_calculate_residuals_drift.R:5:3'): Type of data in the explainer ──
  <packageNotFoundError/error/condition>
  Error in `library("ranger")`: there is no package called 'ranger'
  Backtrace:
      ▆
   1. └─base::library("ranger") at test_calculate_residuals_drift.R:5:3
  ── Error ('test_run_drift_checks.R:5:3'): Length of all checks ─────────────────
  <packageNotFoundError/error/condition>
  Error in `library("ranger")`: there is no package called 'ranger'
  Backtrace:
      ▆
   1. └─base::library("ranger") at test_run_drift_checks.R:5:3
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 2 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'seqinr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Ryacas’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DESeq2’

Packages suggested but not available for checking:
  'shiny', 'shinyBS', 'shinycssloaders', 'shinyjs', 'shinyWidgets',
  'sortable', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking: 'DT', 'shinydashboard'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reshape2', 'ranger'

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', 'geometry', 'FCPS', 'ProjectionBasedClustering',
  'DataVisualizations', 'spdep', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'GiRaF', 'Rcpp', 'Seurat', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘np’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'plotly', 'eventPred'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘cubature’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'odbc', 'DT', 'magick', 'DiagrammeRsvg', 'plotly', 'shinytest2'

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.
Packages required but not available: 'ChemmineR', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'odbc', 'gt', 'flextable', 'ggtext'
Error(s) in re-building vignettes:
  ...
--- re-building ‘create_cohorts.Rmd’ using rmarkdown

Quitting from lines 113-152 [unnamed-chunk-9] (create_cohorts.Rmd)
Error: processing vignette 'create_cohorts.Rmd' failed with diagnostics:
there is no package called 'ggtext'
--- failed re-building ‘create_cohorts.Rmd’

--- re-building ‘drug_utilisation.Rmd’ using rmarkdown

Quitting from lines 277-278 [unnamed-chunk-9] (drug_utilisation.Rmd)
Error: processing vignette 'drug_utilisation.Rmd' failed with diagnostics:
there is no package called 'gt'
--- failed re-building ‘drug_utilisation.Rmd’

SUMMARY: processing the following files failed:
  ‘create_cohorts.Rmd’ ‘drug_utilisation.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'GSVA', 'clusterProfiler', 'ChemmineR'

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'shiny', 'lhs', 'plotly'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'lhs', 'plotly'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'kohonen', 'pROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tsoutliers', 'forecast', 'reshape2', 'seastests'

Package suggested but not available for checking: ‘stR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'TMB', 'sem', 'RcppEigen'

Packages suggested but not available for checking:
  'AER', 'phylopath', 'reshape', 'dynlm', 'ggpubr', 'ggraph'

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', 'sf'

Package suggested but not available for checking: ‘lwgeom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fairml', 'regtools', 'qeML', 'ranger', 'plotly', 'freqparcoord',
  'fairness'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'MolgenisAuth', 'urltools'

Package suggested but not available for checking: ‘dsBaseClient’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'terra', 'lidR', 'imager'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mcmcse', 'rust', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'gstat', 'interp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'rtdists', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'dsBase', 'dsBaseClient'
Packages suggested but not available for checking: 'dsBaseClient', 'dsBase'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'mixtools', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'epiR', 'pROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'pROC', 'caret', 'epiR', 'ggpubr', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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 $1e{-06}$.}
       |                                                                                                                                                               ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'oro.nifti', 'oro.dicom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'V8', 'pdftools'

Packages suggested but not available for checking: 'spelling', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'httpuv', 'promises'

Package suggested but not available for checking: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fgsea’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'RcppCCTZ', 'runner', 'units'
Running ‘tinytest.R’ [2s/2s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > if (requireNamespace("tinytest", quietly = TRUE)) {
  +   tinytest::test_package("DTSg")
  + }
  
  test_DTSg.R...................    0 tests    
  test_DTSg.R...................    1 tests [0;32mOK[0m 
  test_DTSg.R...................    2 tests [0;32mOK[0m Missing values are always stripped regardless of the value of a possible "na.rm" argument.
  
  test_DTSg.R...................    3 tests [0;32mOK[0m Missing values are always stripped regardless of the value of a possible "na.rm" argument.
  
  test_DTSg.R...................    4 tests [0;32mOK[0m .n column calculated from .dateTime column.
  
  test_DTSg.R...................    5 tests [0;32mOK[0m .n column calculated from .dateTime column.
  
  test_DTSg.R...................    6 tests [0;32mOK[0m 
  test_DTSg.R...................    7 tests [0;32mOK[0m 
  test_DTSg.R...................    8 tests [0;32mOK[0m 
  test_DTSg.R...................    9 tests [0;32mOK[0m 
  test_DTSg.R...................   10 tests [0;32mOK[0m 
  test_DTSg.R...................   11 tests [0;32mOK[0m 
  test_DTSg.R...................   12 tests [0;32mOK[0m 
  test_DTSg.R...................   13 tests [0;32mOK[0m 
  test_DTSg.R...................   14 tests [0;32mOK[0m Error: Package "RcppCCTZ" must be installed for this approach.
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'nanotime', 'Rcpp', 'RcppCCTZ'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggrepel', 'RSpectra', 'Rcpp', 'reshape2', 'shiny', 'shinyjs',
  'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
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
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
Package required but not available: ‘ggrepel’

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: 'sf', 'spelling'
Package required but not available: ‘crul’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qs’
Package suggested but not available for checking: ‘ggmosaic’
Package required but not available: ‘rstatix’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'qpdf', 'dogesr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘doges-social-network.Rmd’ using rmarkdown

Quitting from lines 27-30 [load] (doges-social-network.Rmd)
Error: processing vignette 'doges-social-network.Rmd' failed with diagnostics:
there is no package called 'dogesr'
--- failed re-building ‘doges-social-network.Rmd’

--- re-building ‘florentine-social-network.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dupNodes.Rcheck/vign_test/dupNodes/vignettes/florentine-social-network_files/figure-html/self.loops-1.png
768x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 55337 bytes
Input file size = 55487 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 43336
  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 = 43336

Output IDAT size = 43336 bytes (12001 bytes decrease)
Output file size = 43414 bytes (12073 bytes = 21.76% decrease)

--- finished re-building ‘florentine-social-network.Rmd’

SUMMARY: processing the following file failed:
  ‘doges-social-network.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'DT', 'reshape2'

Package suggested but not available for checking: ‘bs4Dash’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'cubature', 'Rcpp', 'survey', 'tab'

Package suggested but not available for checking: ‘RcppRoll’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tsDyn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘terra’
Packages required but not available: 'glmnet', 'hglasso'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape', 'Seurat', 'MAST'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GenEst', 'sf'

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.
Packages required but not available: 'RcppZiggurat', 'Rfast'

Package suggested but not available for checking: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘shiny’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'imputeTS', 'greybox', 'matlib', 'narray'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'drc', 'geosphere', 'terra'

Package suggested but not available for checking: ‘gstat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lhs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reticulate', 'rgee', 'terra', 'sf'

Packages suggested but not available for checking:
  'ape', 'CoordinateCleaner', 'magick', 'spThin', 'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggforce', 'rstan'

Packages suggested but not available for checking: 'cmdstanr', 'mice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) dyadic_similarity.Rd:27: Lost braces; missing escapes or markup?
    27 |      For example, the order {a, b, c} implies that a > b, a  > c, and b > c.
       |                             ^
Package required but not available: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gganimate', 'warbleR'

Package suggested but not available for checking: ‘imager’

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.
Package required but not available: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘interp’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'minqa', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dynutils', 'lmds'

Packages suggested but not available for checking:
  'lle', 'Rtsne', 'smacof', 'uwot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DescTools', 'pec', 'prodlim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dynutils', 'ggraph', 'ggrepel', 'GillespieSSA2', 'lmds'

Packages suggested but not available for checking:
  'anndata', 'dynwrap', 'Seurat'

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 suggested but not available for checking:
  'devtools', 'pander', 'DT'
checkRd: (-1) new_log_level.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{log_style}{is a {crayon::style()} that will colorize
       |                       ^
checkRd: (-1) new_log_level.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{msg_style}{is a {crayon::style()} style that will gray scale the
       |                       ^
checkRd: (-1) sys_context.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{"sysname"} : {The operating system name.}
       |                    ^
checkRd: (-1) sys_context.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{"release"} : {The OS release.}
       |                    ^
checkRd: (-1) sys_context.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{"version"} : {The OS version.}
       |                    ^
checkRd: (-1) sys_context.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{"nodename"} : {A name by which the machine is known on the network (if any).}
       |                     ^
checkRd: (-1) sys_context.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{"machine"} : {A concise description of the hardware, often the CPU type.}
       |                    ^
checkRd: (-1) sys_context.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{"login"} : {The user's login name, or "unknown" if it cannot be ascertained.}
       |                  ^
checkRd: (-1) sys_context.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{"user"} : {The name of the real user ID, or "unknown" if it cannot be ascertained.}
       |                 ^
checkRd: (-1) sys_context.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{"r-ver"} : {R Version in (major).(minor) format.}
       |                  ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘Configuration.Rmd’ using rmarkdown

Quitting from lines 57-59 [unnamed-chunk-4] (Configuration.Rmd)
Error: processing vignette 'Configuration.Rmd' failed with diagnostics:
there is no package called 'pander'
--- failed re-building ‘Configuration.Rmd’

--- re-building ‘Formats.Rmd’ using rmarkdown
--- finished re-building ‘Formats.Rmd’

--- re-building ‘Layouts.Rmd’ using rmarkdown
--- finished re-building ‘Layouts.Rmd’

--- re-building ‘Levels.Rmd’ using rmarkdown

Quitting from lines 82-83 [unnamed-chunk-2] (Levels.Rmd)
Error: processing vignette 'Levels.Rmd' failed with diagnostics:
there is no package called 'pander'
--- failed re-building ‘Levels.Rmd’

SUMMARY: processing the following files failed:
  ‘Configuration.Rmd’ ‘Levels.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'plotly'

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 ?
Package required but not available: ‘dynutils’

Package suggested but not available for checking: ‘lhs’

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: \&
'LazyData' is specified without a 'data' directory
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reshape2', 'plyr', 'mice', 'fda', 'car'

Package suggested but not available for checking: ‘RcppGSL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) dynsim.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:57-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘splines2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'proxyC', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'babelwhale', 'dynutils', 'dynparam', 'reshape2'

Packages suggested but not available for checking: 'dyndimred', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gt', 'semPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'anytime', 'accelerometry'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
GNU make is a SystemRequirements.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shinyFiles', 'shinyBS', 'plotly', 'shiny', 'shinythemes', 'shinyjs',
  'RcppEigen', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'hdi', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'leaflet', 'plotly', 'shiny', 'shinydashboard', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘EpiEstim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'spam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'terra', 'sf', 'spelling', 'gdalcubes'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lhs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘recipes’

Packages suggested but not available for checking: 'caret', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BDgraph', 'BGGM', 'bgms', 'qgraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggrepel', 'Seurat', 'fgsea'
Package unavailable to check Rd xrefs: ‘fgsea’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘terra’

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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 required but not available: 'rcompanion', 'FSA', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘PMCMRplus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘diffcoexp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

Package suggested but not available for checking: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'plotly', 'shiny', 'shinycssloaders', 'shinybusy'

Package suggested but not available for checking: ‘qvalue’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘OpenMx’

Package suggested but not available for checking: ‘rpf’

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: ‘LaF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'pdftools', 'qs', 'readxlsb'
Packages required but not available: 'sdcTable', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'DHARMa', 'DT', 'flexdashboard', 'glmmTMB'
Packages required but not available:
  'bshazard', 'censored', 'flexsurv', 'flexsurvcure', 'openxlsx',
  'plotly'

Package suggested but not available for checking: ‘spelling’

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: ‘randomcoloR’
Packages required but not available: 'SpecsVerification', 'Rcpp'

Package suggested but not available for checking: ‘verification’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘gurobi’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qcr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggrepel', 'reshape2'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'survey', 'BIFIEsurvey', 'mice', 'car', 'reshape2', 'plyr',
  'miceadds', 'EffectLiteR', 'estimatr', 'eatGADS', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'univariateML', 'extraDistr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘glmnet’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'terra'

Packages suggested but not available for checking:
  'fields', 'rnaturalearth'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'C50', 'pROC', 'smotefamily'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ashr', 'mixsqp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'terra', 'tidyterra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘drc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘labdsv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
Package required but not available: ‘rsdmx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Ecfun’

Packages suggested but not available for checking: 'plm', 'systemfit'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'DT', 'golem', 'magick', 'openxlsx', 'plyr', 'shiny', 'shinyjs',
  'shinyWidgets', 'tidyxl'

Packages suggested but not available for checking: 'shinytest2', 'webshot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fda’

Packages suggested but not available for checking:
  'car', 'DescTools', 'Ecdat', 'pryr', 'ipumsr', 'bayesplot', 'bssm',
  'openxlsx', 'drc', 'prodlim', 'plyr', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'sf', 'leaflet'
Package suggested but not available for checking: ‘sf’
Package required but not available: ‘animation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geosphere’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘bayesm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'plyr', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geouy', 'srvyr', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'caret', 'WGCNA', 'pander'

Packages suggested but not available for checking:
  'factoextra', 'pROC', 'glmnet'

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 suggested but not available for checking: ‘terra’
Error(s) in re-building vignettes:
  ...
--- re-building ‘advanced_vignette.Rmd’ using rmarkdown

Quitting from lines 13-25 [setup] (advanced_vignette.Rmd)
Error: processing vignette 'advanced_vignette.Rmd' failed with diagnostics:
there is no package called 'terra'
--- failed re-building ‘advanced_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘advanced_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'sf', 'rasterVis', 'landscapemetrics', 'rasterDT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'EML', 'emld', 'geosphere'

Packages suggested but not available for checking:
  'ritis', 'taxize', 'worrms', 'ggrepel', 'usmap', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mvabund', 'plyr'

Packages suggested but not available for checking: 'ggraph', 'labdsv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggmcmc’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'reshape2', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'picante', 'FD'

Packages suggested but not available for checking:
  'raster', 'alphahull', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘seacarb’
Packages suggested but not available for checking: 'ape', 'picante'
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
checkRd: (-1) ecolRxC.Rd:161-166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:167-175: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:176-178: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:179-185: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:186-192: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:193-201: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:202-208: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:209-216: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:217-221: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'spelling', 'ggraph'
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rdiversity', 'blockmodels', 'bipartite', 'Rcpp', 'RcppEigen',
  'RcppGSL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggraph’
Packages required but not available: 'reshape2', 'bipartite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mvabund', 'ecoCopula'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'ecotraj', 'smacof'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
GNU make is a SystemRequirements.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘FD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ade4', 'adehabitatHR', 'biomod2', 'dismo', 'terra', 'ks', 'nabor'

Packages suggested but not available for checking: 'alphahull', 'ape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mvabund', 'ecoCopula'

Packages suggested but not available for checking:
  'ade4', 'caper', 'car', 'DAAG', 'DHARMa', 'GGally', 'glmnet',
  'gllvm', 'glmmTMB', 'lme4', 'MCMCglmm', 'pgirmess', 'phylobase',
  'phylosignal', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'qgraph', 'philentropy', 'plyr', 'reshape', 'Rmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘openxlsx’
Package suggested but not available for checking: ‘standartox’
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'ape', 'smacof', 'hrbrthemes', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'glmnet', 'CVXR', 'multiridge', 'pROC', 'JOPS'

Packages suggested but not available for checking: 'ggraph', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'smoof', 'Rcpp', 'reshape2', 'plotly'

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: 'caret', 'transport'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'dae', 'lmerTest', 'predictmeans'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'crosstable', 'openxlsx', 'plotly', 'quarto'
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bupaR', 'shiny', 'miniUI', 'shinyTime'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) read.edf.Rd:30: Lost braces
    30 | Kemp B., V\"{a}rri, A., Rosa, A.C., Nielsen, K.D. and Gade, J. (1992).
       |             ^
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'tokenizers', 'devtools'
Packages required but not available: 'Rcpp', 'reticulate', 'interp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘huge’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘dae’

Packages suggested but not available for checking:
  'openxlsx2', 'blocksdesign'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'reshape2', 'RcppArmadillo'

Package suggested but not available for checking: ‘simcdm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinyjs', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'miniUI', 'DT', 'shinyWidgets', 'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'OCNet', 'rivnet', 'BayesianTools', 'DHARMa', 'terra',
  'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘vcr’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(EDIutils)
  > 
  > test_check("EDIutils")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/EDIutils.Rcheck/tests/testthat/setup-EDIutils.R"
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("EDIutils")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at tests/testthat/setup-EDIutils.R:7:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lbfgs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'energy', 'dHSIC', 'rBayesianOptimization'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘opGMMassessment’

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 required but not available:
  'car', 'Dire', 'LaF', 'lme4', 'wCorr', 'WeMix'

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.
Packages required but not available: 'lme4', 'MCMCvis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'forecast', 'Rlibeemd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'nnfor', 'Rlibeemd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'keras', 'tensorflow', 'reticulate', 'tsutils', 'Rlibeemd',
  'TSdeeplearning'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rlibeemd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'Rlibeemd'

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 suggested but not available for checking: 'shiny', 'DT'
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) eesim.Rd:148-151: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) eesim.Rd:152-155: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) eesim.Rd:156-158: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'EFAtools', 'mirt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ddpcr', 'ranger', 'reticulate', 'Rcpp', 'RcppArmadillo'

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: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sf’
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown

Quitting from lines 47-50 [setup] (example.Rmd)
Error: processing vignette 'example.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building ‘example.Rmd’

SUMMARY: processing the following file failed:
  ‘example.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘gstat’

Packages suggested but not available for checking: 'fields', 'animation'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pcalg’

Package suggested but not available for checking: ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fixest’

Package suggested but not available for checking: ‘plm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'DT', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'seqinr', 'shiny', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'afex', 'BayesFactor', 'brms', 'car', 'gt', 'lme4', 'lmerTest',
  'rstanarm', 'rstantools'
Error(s) in re-building vignettes:
  ...
--- re-building ‘anovaES.Rmd’ using rmarkdown
--- finished re-building ‘anovaES.Rmd’

--- re-building ‘convert_p_OR_RR.Rmd’ using rmarkdown
--- finished re-building ‘convert_p_OR_RR.Rmd’

--- re-building ‘convert_r_d_OR.Rmd’ using rmarkdown
--- finished re-building ‘convert_r_d_OR.Rmd’

--- re-building ‘effectsize.Rmd’ using rmarkdown
--- finished re-building ‘effectsize.Rmd’

--- re-building ‘effectsize_API.Rmd’ using rmarkdown
--- finished re-building ‘effectsize_API.Rmd’

--- re-building ‘from_test_statistics.Rmd’ using rmarkdown

Quitting from lines 235-244 [unnamed-chunk-13] (from_test_statistics.Rmd)
Error: processing vignette 'from_test_statistics.Rmd' failed with diagnostics:
could not find function "emmeans"
--- failed re-building ‘from_test_statistics.Rmd’

--- re-building ‘interpret.Rmd’ using rmarkdown
--- finished re-building ‘interpret.Rmd’

--- re-building ‘standardized_differences.Rmd’ using rmarkdown
--- finished re-building ‘standardized_differences.Rmd’

--- re-building ‘statistical_power.Rmd’ using rmarkdown
--- finished re-building ‘statistical_power.Rmd’

--- re-building ‘xtabs.Rmd’ using rmarkdown
--- finished re-building ‘xtabs.Rmd’

SUMMARY: processing the following file failed:
  ‘from_test_statistics.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'survey'

Packages suggested but not available for checking:
  'pbkrtest', 'heplots', 'car', 'alr4', 'robustlmm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'DIFlasso', 'DIFboost'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'TMB', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fungible', 'GGally', 'ggpubr', 'qgraph', 'semPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'StanHeaders', 'RcppEigen'

Package suggested but not available for checking: ‘eggCountsExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'gstat', 'shiny', 'SpatialTools'

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘srvyr’

Packages suggested but not available for checking: 'survey', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EGRET’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fields’

Package suggested but not available for checking: ‘EGRETci’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'quanteda', 'tm'

Package suggested but not available for checking: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘vegdata’
Error(s) in re-building vignettes:
  ...
--- re-building ‘eHOF.Rnw’ using knitr

Quitting from lines 34-43 [prep] (eHOF.Rnw)
Error: processing vignette 'eHOF.Rnw' failed with diagnostics:
there is no package called 'vegdata'
--- failed re-building ‘eHOF.Rnw’

SUMMARY: processing the following file failed:
  ‘eHOF.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'glmnet', 'logistf'
Running examples in ‘EHR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Logistf
> ### Title: Firth's penalized-likelihood logistic regression with more
> ###   decimal places of p-value than 'logistf' function in the R package
> ###   'logistf'
> ### Aliases: Logistf
> 
> ### ** Examples
> 
> data(dataPheWAS)
> fit <- Logistf(X264.3 ~ exposure + age + race + gender, data=dd)
Error: Logistf requires the logistf package, please install it.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plotly’

Packages suggested but not available for checking: 'devtools', 'dbscan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘plotly’
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘GA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘EIVignette.Rmd’ using rmarkdown

Quitting from lines 16-20 [setup] (EIVignette.Rmd)
Error: processing vignette 'EIVignette.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘EIVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘EIVignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggmap', 'sf'

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: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘cubature’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'blme', 'reshape2', 'shiny', 'shinydashboard',
  'shinycssloaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'raster'

Packages suggested but not available for checking: 'lwgeom', 'units'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggrepel', 'ggiraphExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ks', 'mapsf', 'sf'

Package suggested but not available for checking: ‘ggspatial’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'DT', 'reshape2', 'shinyWidgets', 'shinydashboard'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sparseFLMM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘crul’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) AuditErrors.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) compute.audit.errors.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) compute.stark.t.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) find.q.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) find.q.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) stark.test.Rd:50: Escaped LaTeX specials: \$
checkRd: (-1) stark.test.Rd:101: Escaped LaTeX specials: \$ \$
checkRd: (-1) tri.audit.sim.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) tri.calc.sample.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) tri.sample.Rd:34: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) weight.function.Rd:16: Escaped LaTeX specials: \_
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) electData.Rd:16: Lost braces; missing escapes or markup?
    16 | Variables: \code{id}  = {identification number},
       |                         ^
checkRd: (-1) electData.Rd:17: Lost braces; missing escapes or markup?
    17 | \code{state} = {state}, \code{age} = age in years on a shifted scale (current age minus 70),
       |                ^
checkRd: (-1) summary.elect.Rd:25: Lost braces; missing escapes or markup?
    25 |  TRUE for output on start-state totals e_{r.} (for \code{S}>0)
       |                                          ^
Packages required but not available:
  'sf', 'terra', 'units', 'slippymath', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggmap', 'terra'

Package suggested but not available for checking: ‘rgbif’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking: 'melt', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) prepareInitsLM.Rd:21-23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘wdm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ICSNP’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘calibrator’
checkRd: (-1) elliptic-package.Rd:92: Lost braces
    92 |     J. Kotus and M. Urb\'{a}nski 2003.  \emph{Hausdorff dimension and Hausdorff
       |                          ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘ellipticpaper.Rnw’ using Sweave

Attaching package: ‘elliptic’

The following objects are masked from ‘package:stats’:

    sd, sigma

The following object is masked from ‘package:base’:

    is.primitive

Loading required package: emulator
Loading required package: mvtnorm
Loading required package: calibrator
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘calibrator’

Error: processing vignette 'ellipticpaper.Rnw' failed with diagnostics:
 chunk 50 (label = bacco_flow) 
Error in p.eqn8.supp(theta = c(0, 1/2), D1 = D1.elliptic, D2 = D2.elliptic,  : 
  could not find function "p.eqn8.supp"

--- failed re-building ‘ellipticpaper.Rnw’

--- re-building ‘residuetheorem.Rnw’ using Sweave

Attaching package: ‘elliptic’

The following objects are masked from ‘package:stats’:

    sd, sigma

The following object is masked from ‘package:base’:

    is.primitive

--- finished re-building ‘residuetheorem.Rnw’

SUMMARY: processing the following file failed:
  ‘ellipticpaper.Rnw’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'KernelKnn', 'Rcpp', 'RcppArmadillo'

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
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'BAMMtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘aniDom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'pROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'EloRating', 'Rcpp', 'rstan', 'rstantools', 'aniDom', 'RcppEigen',
  'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shiny.i18n', 'shinybrowser'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mediation', 'minfi',
  'IlluminaHumanMethylationEPICanno.ilm10b4.hg19',
  'IlluminaHumanMethylation450kanno.ilmn12.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘urltools’

Packages suggested but not available for checking: 'cld2', 'cld3'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'glmnet', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'suntools', 'RcppArmadillo'

Packages suggested but not available for checking: 'move', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'recipes', 'uwot'

Packages suggested but not available for checking:
  'keras', 'lme4', 'rstanarm', 'tensorflow'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rtsne', 'umap', 'uwot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'car'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'EMD', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'openxlsx', 'reshape2', 'HLMdiag', 'saeRobust', 'spdep'

Packages suggested but not available for checking: 'simFrame', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
License stub is invalid DCF.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EMD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'caret', 'RcppArmadillo'

Packages suggested but not available for checking: 'bootnet', 'qgraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘V8’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'gganimate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'units', 'raster', 'sf'

Package suggested but not available for checking: ‘lwgeom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) EmiStatR-methods.Rd:86: Lost braces; missing escapes or markup?
    86 | execute {EmiStatR} function
       |         ^
checkRd: (-1) input-class.Rd:136: Lost braces; missing escapes or markup?
   136 |     \item{EmiStatR}{\code{signature(x = "input")}: execute {EmiStatR} function }
       |                                                            ^
Packages required but not available: 'bigmemory', 'glmnet'

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘jsonld’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘emld’

Packages suggested but not available for checking:
  'EML', 'units', 'shiny', 'shinyjs', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'bayesplot', 'brms', 'car', 'compositions', 'mediation', 'pbkrtest',
  'lme4', 'lmerTest'

Packages which this enhances but not available for checking:
  'CARBayes', 'MCMCglmm', 'mice', 'rstanarm', 'sommer'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'reshape', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘GGally’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) macacaModels.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) macacaModels.Rd:10-11: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘openxlsx’
Running examples in ‘emphatic-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: write_xlsx
> ### Title: Write an emphatic data.frame to an Excel workbook
> ### Aliases: write_xlsx
> 
> ### ** Examples
> 
> mtcars |>
+    hl('blue') |>
+    write_xlsx(tempfile())
Error in write_xlsx(hl(mtcars, "blue"), tempfile()) : 
  write_xlsx(): Need to have `openxlsx` installed
Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘Cyclops’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) WRegTest.Rd:43: Lost braces
    43 | For ordinary least squares estimator, \code{psifun} should be the identity function psifun <- function(t){t}.
       |                                                                                                          ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plm', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sampleSelection’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mlpack', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'httpuv', 'V8'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) droso.Rd:8: Lost braces; missing escapes or markup?
     8 | The dataset contains 400 true donor sites, 400 false donor sites and 50 false sites as test set. Each sequence is of 40 nucleotides long. The conserved di-nucleotides GT are present at $21^{st}$ and $22^{nd}$ positions respectively.
       |                                                                                                                                                                                              ^
checkRd: (-1) droso.Rd:8: Lost braces; missing escapes or markup?
     8 | The dataset contains 400 true donor sites, 400 false donor sites and 50 false sites as test set. Each sequence is of 40 nucleotides long. The conserved di-nucleotides GT are present at $21^{st}$ and $22^{nd}$ positions respectively.
       |                                                                                                                                                                                                            ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'hawkes', 'ACDm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘file.path(temp_dir, gp2.csv)’
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘energy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'reshape', 'robustHD'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘torch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'raster', 'dismo', 'maxnet', 'glmnet', 'rangeModelMetadata'

Packages suggested but not available for checking:
  'spocc', 'rasterVis', 'sf', 'blockCV', 'devtools', 'latticeExtra',
  'ecospat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'AICcmodavg', 'DT', 'ks', 'maxnet', 'predicts', 'ranger', 'sf',
  'shiny', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dismo', 'lhs', 'ENMeval', 'ggpubr', 'terra', 'raster'

Packages suggested but not available for checking:
  'hypervolume', 'leaflet', 'ecospat', 'ranger', 'caret', 'CalibratR',
  'ape', 'reshape2', 'fastshap', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘webshot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘seqinr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fields’
Package required but not available: ‘EnsembleBase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fields’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘EnsembleBase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'EnsembleBase', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'crch', 'SpecsVerification', 'scoringRules', 'pROC'
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

Packages suggested but not available for checking: 'ggforce', 'qwraps2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'ggpubr', 'reshape2'

Package suggested but not available for checking: ‘ade4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggrepel', 'hrbrthemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mixtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) entropy.Dirichlet.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:42: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘drc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'ape', 'picante'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rdisop', 'animation', 'mixtools'

Packages suggested but not available for checking:
  'xcms', 'MSnbase', 'plotly', 'shiny', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'concaveman', 'fields', 'sf', 'terra'

Packages suggested but not available for checking: 'RStoolbox', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'bio3d', 'phangorn', 'philentropy', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'ecp'

Package suggested but not available for checking: ‘openair’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'ipaddress', 'spelling'
Running examples in ‘envvar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: envvar_get_url
> ### Title: Environment variables for internet and network-related values
> ### Aliases: envvar_get_url envvar_get_ipaddress
> 
> ### ** Examples
> 
> 
> # Get a URL value and ensure that it is https
> envvar_set("TEST_URL" = "https://google.com:80/?a=1&b=2")
> envvar_get_url("TEST_URL", validate = \(x) x$scheme == "https")
<httr2_url> https://google.com:80/?a=1&b=2
• scheme: https
• hostname: google.com
• port: 80
• path: /
• query:
  • a: 1
  • b: 2
> 
> # Get an IP address value and ensure that it is IPv4
> envvar_set("TEST_HOST" = "192.168.1.15")
> envvar_get_ipaddress("TEST_HOST", validate = ipaddress::is_ipv4)
Error in envvar_get_ipaddress("TEST_HOST", validate = ipaddress::is_ipv4) : 
  The package "ipaddress" is required.
Calls: envvar_get_ipaddress -> <Anonymous>
Execution halted
Package required but not available: ‘GenEst’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rvg', 'flextable', 'magick', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
Packages suggested but not available for checking:
  'ggcorrplot', 'reshape2', 'RSpectra'
checkRd: (-1) misClustRate.Rd:18: Lost braces; missing escapes or markup?
    18 | Compute the empirical MCR, assuming that #{cluster} = #{block},
       |                                           ^
checkRd: (-1) misClustRate.Rd:18: Lost braces; missing escapes or markup?
    18 | Compute the empirical MCR, assuming that #{cluster} = #{block},
       |                                                        ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'glmnet', 'timeROC'

Package suggested but not available for checking: ‘c060’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tsibble', 'fabletools', 'feasts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'openxlsx', 'fst', 'feather', 'ggtext', 'ggdist'
Running examples in ‘epiCleanr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: consistency_check
> ### Title: Consistency Check Function
> ### Aliases: consistency_check
> 
> ### ** Examples
> 
> # check the consistency between malaria tests and cases
> 
> # get path
> path <- system.file(
+         "extdata",
+         "fake_epi_df_togo.rds",
+          package = "epiCleanr")
> 
> fake_epi_df_togo <- import(path)
Warning: Missing `trust` will be set to FALSE by default for RDS in 2.0.0.
> 
> consistency_check(fake_epi_df_togo,
+                   tests = c("malaria_tests","cholera_tests"),
+                   cases = c("malaria_cases", "cholera_cases"))
Consistency test passed for malaria_tests vs malaria_cases: There are more tests than there are cases!
Consistency test failed for cholera_tests vs cholera_cases: There are 1 (0.11%) rows where cases are greater than tests.
Error in loadNamespace(x) : there is no package called ‘ggtext’
Calls: consistency_check ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package suggested but not available for checking: ‘shiny’
Packages required but not available:
  'ggraph', 'leaflet', 'spdep', 'treemapify'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'odbc', 'phonics'

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.
Package required but not available: ‘reshape2’

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.
Packages required but not available: 'leaflet', 'ggmap', 'geosphere'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'grf', 'MatchIt', 'policytree', 'survey', 'svyVGAM'

Package suggested but not available for checking: ‘CVXR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'spelling', 'devtools'
Packages required but not available: 'TMB', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘adaptMCMC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

Package suggested but not available for checking: ‘epidict’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'EpiEstim', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'plotly'

Packages suggested but not available for checking:
  'ade4', 'fields', 'forecast', 'imputeTS', 'lme4', 'rworldmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'ade4', 'fields', 'forecast', 'imputeTS', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'Rcpp'

Packages suggested but not available for checking:
  'ergm.ego', 'egor', 'ndtv', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'GA', 'Rcpp', 'reshape2', 'vcfR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'runner', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking: 'cmdstanr', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggrepel', 'qgcomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'transport', 'Rcpp'

Packages suggested but not available for checking: 'spdep', 'emdbook'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'etm', 'plyr'

Packages suggested but not available for checking:
  'lme4', 'demography', 'popEpi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flextable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pander', 'sf', 'flextable'

Package suggested but not available for checking: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘episcan_1geno_cc.txt’ ‘episcan_1geno_quant.txt’
  ‘episcan_2geno_cc.txt’ ‘episcan_2geno_quant.txt’
Packages required but not available: 'devtools', 'seqinr', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dagitty', 'ggdag'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking: 'DT', 'pander'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘epiR’

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: 'ggrepel', 'MM4LMM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'crul', 'DT', 'emayili', 'httpuv', 'plotly', 'openxlsx', 'plyr',
  'shiny', 'tidytext'

Package suggested but not available for checking: ‘taskscheduleR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'shinyjs', 'shinydashboard', 'DT', 'shinycssloaders',
  'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'qs', 'poems', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘geosphere’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ciTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘units’

Package suggested but not available for checking: ‘decido’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'terra', 'sf', 'ape', 'Rcpp'

Packages suggested but not available for checking:
  'tmap', 'spdep', 'exactextractr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘units’

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: 'shiny', 'shinytest2'
Running examples in ‘epoxy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: run_epoxy_example_app
> ### Title: Example epoxy Shiny apps
> ### Aliases: run_epoxy_example_app
> 
> ### ** Examples
> 
> # List examples by passing `name = NULL`
> run_epoxy_example_app(name = NULL)
Error in run_epoxy_example_app(name = NULL) : 
  The package "shiny" is required.
Calls: run_epoxy_example_app -> <Anonymous>
Execution halted
Running ‘testthat.R’ [9s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(epoxy)
  > 
  > test_check("epoxy")
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 322 ]
  
  ══ Skipped tests (10) ══════════════════════════════════════════════════════════
  • On CRAN (9): 'test-epoxy_transform_inline.R:99:3',
    'test-epoxy_transform_inline.R:108:3', 'test-epoxy_transform_inline.R:121:3',
    'test-shiny_ui_epoxy_html-list.R:1:1',
    'test-shiny_ui_epoxy_html-no-shiny.R:1:1',
    'test-shiny_ui_epoxy_markdown.R:1:1', 'test-shiny_ui_epoxy_mustache.R:1:1',
    'test-shiny_word-list.R:1:1', 'test-transformers.R:379:3'
  • RSQLite cannot be loaded (1): 'test-epoxy.R:336:2'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-deprecated.R:108:3'): deprecated shiny functions: renderEpoxy() ──
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `render_epoxy(..., env = env)`: The package "shiny" is required.
  Backtrace:
       ▆
    1. ├─lifecycle::expect_deprecated(renderEpoxyHTML()) at test-deprecated.R:108:17
    2. │ └─testthat::expect_warning(...)
    3. │   └─testthat:::expect_condition_matching(...)
    4. │     └─testthat:::quasi_capture(...)
    5. │       ├─testthat (local) .capture(...)
    6. │       │ └─base::withCallingHandlers(...)
    7. │       └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    8. └─epoxy::renderEpoxyHTML()
    9.   └─epoxy::render_epoxy(..., env = env)
   10.     └─rlang::check_installed("shiny")
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 322 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epoxy-report.Rmd’ using rmarkdown
--- finished re-building ‘epoxy-report.Rmd’

--- re-building ‘epoxy-script.Rmd’ using rmarkdown
--- finished re-building ‘epoxy-script.Rmd’

--- re-building ‘epoxy-shiny.Rmd’ using rmarkdown

Quitting from lines 18-24 [unnamed-chunk-1] (epoxy-shiny.Rmd)
Error: processing vignette 'epoxy-shiny.Rmd' failed with diagnostics:
there is no package called 'shiny'
--- failed re-building ‘epoxy-shiny.Rmd’

--- re-building ‘inline-reporting.Rmd’ using rmarkdown
Warning: The `data` chunk option was deprecated in epoxy 0.2.0.
ℹ Please use the `.data` option (note the leading dot) instead.
ℹ The deprecated feature was likely used in the epoxy package.
  Please report the issue at <https://github.com/gadenbuie/epoxy/issues>.
--- finished re-building ‘inline-reporting.Rmd’

SUMMARY: processing the following file failed:
  ‘epoxy-shiny.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'car', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘xslt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'eplusr', 'fst', 'psychrolib', 'units'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'shiny', 'DT', 'ggiraph', 'ggiraphExtra', 'shinycssloaders',
  'shinyWidgets', 'FSA', 'PMCMRplus'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'DescTools', 'rstatix', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'DescTools', 'ggcorrplot', 'pROC', 'ThresholdROC', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xslt', 'katex'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'equateIRT', 'Rcpp', 'RcppArmadillo', 'RcppDist'

Package suggested but not available for checking: ‘mirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'shinyWidgets', 'forecast', 'lme4', 'texPreview', 'gtsummary',
  'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘units’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plm', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘cubature’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘mzR’
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Tm.Rd:46-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:49-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:52-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:55-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:58-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:36-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:40-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:43-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:47-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:57-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:60-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:63-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:66-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:69-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:75-77: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘gt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘order_of_entities.Rmd’ using rmarkdown
--- finished re-building ‘order_of_entities.Rmd’

--- re-building ‘step_by_step.Rmd’ using rmarkdown

Quitting from lines 34-93 [setup] (step_by_step.Rmd)
Error: processing vignette 'step_by_step.Rmd' failed with diagnostics:
there is no package called 'gt'
--- failed re-building ‘step_by_step.Rmd’

SUMMARY: processing the following file failed:
  ‘step_by_step.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘systemfit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘Rcpp’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'egor', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggrepel’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Goeyvaerts_reproduction.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'ggrepel''

Quitting from lines 157-158 [unnamed-chunk-16] (Goeyvaerts_reproduction.Rmd)
Error: processing vignette 'Goeyvaerts_reproduction.Rmd' failed with diagnostics:
'autoplot()' method for 'gofN' objects requires packages 'ggplot2' and 'ggrepel'.
--- failed re-building ‘Goeyvaerts_reproduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Goeyvaerts_reproduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘latticeExtra’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘EpiEstim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ifa.Rd:16: Lost braces; missing escapes or markup?
    16 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then Sigma^{-1} 
       |                                                                         ^
checkRd: (-1) ifa.Rd:17: Lost braces; missing escapes or markup?
    17 | has the corresponding q-factor decomposition Sigma^{-1}=diag(phi)(I-theta theta')diag(phi), where theta is a mxq matrix and phi the vector of 
       |                                                    ^
checkRd: (-1) ifa.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{iSB}{m x q matrix (diag(Psi)+BB')^{-1}B.}
       |                                         ^
checkRd: (-1) isqrtfa.Rd:15: Lost braces; missing escapes or markup?
    15 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then the function returns a matrix Omega such that Sigma^{-1} = Omega Omega'. Equivalently,
       |                                                                                                                       ^
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘simcdm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'miniUI', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'raster', 'rasterVis'

Packages suggested but not available for checking: 'pander', 'plyr', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'mvnfast', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘esreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘trialr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggdist', 'ggtext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'sf', 'shiny', 'units'

Packages suggested but not available for checking:
  'colourpicker', 'DT', 'leafem', 'leaflet', 'raster', 'shinybusy',
  'shinydashboard', 'shinyjs', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'terra', 'IRISSeismic', 'shiny', 'reticulate', 'extraDistr', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘CompAREdesign’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'smoots', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

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.
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DT', 'ggpubr'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'js', 'openxlsx', 'qs', 'Rcpp', 'Rvcg', 'shiny', 'shinyWidgets'

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'datamods', 'shiny', 'shinybusy', 'shinyWidgets'

Packages suggested but not available for checking:
  'rvg', 'hrbrthemes', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'shiny', 'shinydashboard', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'brms', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'GA', 'autoimage'

Packages suggested but not available for checking: 'spelling', 'V8'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘extraDistr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking:
  'AER', 'RcppEigen', 'car'

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.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ETAS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ETC-package.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ETC-package.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ETC-package.Rd:32: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geometry', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘urltools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'energy', 'fda.usc', 'NetworkDistance', 'TDA'

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fixest', 'marginaleffects'

Packages suggested but not available for checking: 'did', 'gt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘xslt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinydashboard', 'shinyWidgets', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'polylabelr', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘CommonDataModel’

Package suggested but not available for checking: ‘DatabaseConnector’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pdftools’

Packages suggested but not available for checking:
  'tidytext', 'wordcloud', 'ggiraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'urltools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RefManageR’

Packages suggested but not available for checking: 'giscoR', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'inaparc', 'ppclust', 'FRESA.CAD', 'NMF', 'Rtsne', 'uwot'
checkRd: (-1) FuzzyCluster.Rd:15: Lost braces; missing escapes or markup?
    15 | A list of cluster labels and a R object of class "fcm {ppclust}"
       |                                                       ^
checkRd: (-1) pamCluster.Rd:15: Lost braces; missing escapes or markup?
    15 | A list of cluster labels and a R object of class "pam {cluster}"
       |                                                       ^
Running examples in ‘Evacluster-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FuzzyCluster
> ### Title: Fuzzy C-means Clustering Algorithm
> ### Aliases: FuzzyCluster
> 
> ### ** Examples
> 
> library(datasets)
> data(iris)
> 
> rndSamples <- sample(nrow(iris),100)
> trainData <- iris[rndSamples,]
> testData <- iris[-rndSamples,]
> 
> cls <- FuzzyCluster(trainData[,1:4],3)
Error in loadNamespace(x) : there is no package called ‘inaparc’
Calls: FuzzyCluster ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'caret', 'ggdist', 'glmnet', 'grf', 'rqPen'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'ggcorrplot', 'reshape2'

Package suggested but not available for checking: ‘pander’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'pRecipe', 'raster'

Packages suggested but not available for checking: 'ggpubr', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘SpatialExtremes’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘interp’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'EventDetectR', 'shinyBS', 'shiny', 'shinydashboard', 'shinyjs',
  'plotly', 'DT'

Packages suggested but not available for checking: 'shinytest', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'imputeTS', 'forecast'

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘prodlim’
Running ‘testthat.R’ [7s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(eventglm)
  > 
  > test_check("eventglm")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 28 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-jackknife-agree.R:2:5'): Jackknife agrees with prodlim ─────────
  <packageNotFoundError/error/condition>
  Error in `library(prodlim)`: there is no package called 'prodlim'
  Backtrace:
      ▆
   1. └─base::library(prodlim) at test-jackknife-agree.R:2:5
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 28 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'plotly', 'rstpm2', 'tmvtnsim', 'flexsurv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'rstpm2', 'flexsurv', 'shiny'

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
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'glmnet', 'dbscan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'estimatr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rpact', 'gestate'
Error(s) in re-building vignettes:
  ...
--- re-building ‘eventTrack.Rmd’ using rmarkdown

Quitting from lines 42-43 [unnamed-chunk-1] (eventTrack.Rmd)
Error: processing vignette 'eventTrack.Rmd' failed with diagnostics:
there is no package called 'rpact'
--- failed re-building ‘eventTrack.Rmd’

SUMMARY: processing the following file failed:
  ‘eventTrack.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) glr.Rd:5: Lost braces
     5 |   Conducts a generalized likelihood ratio test testing whether {\eqn{\beta \in}  (-\code{c},\code{c})}. Covariates can be accommodated.
       |                                                                ^
checkRd: (-1) glr.Rd:34: Lost braces
    34 |   This is a similar function to the main function \code{evian}. Instead of testing H0: \eqn{\beta}=0, it tests for whether H0:{\eqn{\beta \in} (-\code{c},\code{c})}.
       |                                                                                                                               ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'rstan', 'rstanarm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggdist', 'meta', 'EmpiricalCalibration', 'Cyclops'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) fmgammagpd.Rd:183: Lost braces; missing escapes or markup?
   183 |  \item {nlumgammagpd} and {proflumgammagpd} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], sigmau, xi)}
       |                           ^
checkRd: (-1) fmgammagpdcon.Rd:181: Lost braces; missing escapes or markup?
   181 |  \item {nlumgammagpdcon} and {proflumgammagpdcon} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], xi)}
       |                              ^
checkRd: (-1) kernels.Rd:87: Lost braces
    87 | code{\link[evmix:kernels]{kd*}}  and \code{\link[evmix:kernels]{kp*}} give the
       |     ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'seqinr', 'ape', 'geiger', 'shiny', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘AlphaSimR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'reshape2', 'ape', 'Morpho', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geometry', 'interp', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'geomorph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rrepast', 'reshape', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'deeptime', 'ggrepel', 'ggtree', 'treeio', 'Rtsne', 'devtools'

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.
Packages required but not available: 'dbscan', 'plotly'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘evclust’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'shiny', 'shinydashboard', 'shinyWidgets', 'spelling'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) stop_rule.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stop_rule.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stop_rule.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stop_rule.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘DHARMa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'rEDM', 'reticulate'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'shinythemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'raster', 'sf'

Package suggested but not available for checking: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘ExactData’
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘learnr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'extraDistr', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'magick', 'openxlsx', 'qpdf'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘SpatialTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘tidycensus’
Package required but not available: ‘ipaddress’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘js’
Package required but not available: ‘fmesher’

Packages suggested but not available for checking: 'INLA', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppRoll', 'RcppArmadillo'

Package suggested but not available for checking: ‘revdbayes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'crch', 'brms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plm', 'shiny', 'DT', 'shinycssloaders'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'glmnet'

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: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'weaana', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'smoof', 'cec2013'
checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:42: Lost braces
    42 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
checkRd: (-1) ccF.Rd:41: Lost braces
    41 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
Packages required but not available:
  'BayesX', 'Rcpp', 'fields', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'DESeq2', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'schemr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'cvms', 'ggpmisc', 'ggpubr', 'plotly'

Packages suggested but not available for checking:
  'plotROC', 'reshape2', 'ranger', 'precrec'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘semiArtificial’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'lemon', 'mediation', 'shiny', 'shinydashboard', 'weights'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DT', 'plotly', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'shiny', 'DT'

Packages suggested but not available for checking:
  'FactoMineR', 'ade4', 'GDAtools', 'quanteda', 'quanteda.textmodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'rvg', 'flextable', 'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

Package suggested but not available for checking: ‘qpdf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rnaturalearth', 'sf', 'plyr', 'PupillometryR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'blockmodels', 'RcppArmadillo'

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 suggested but not available for checking: 'DT', 'openxlsx', 'fst'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘recipes’

Package suggested but not available for checking: ‘almanac’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) MatIn.Rd:6: Lost braces
     6 | Computation of aggregation matrices for generalized interactions that are used in code{\link{extRC}} to estimate extended RC models.
       |                                                                                       ^
checkRd: (-1) plot.Rd:5: Lost braces
     5 | \description{It plots the output of code{\link{extRC}} function for a vector of lambda values.}
       |                                         ^
checkRd: (-1) print.Rd:5: Lost braces
     5 | \description{Given the output of code{\link{extRC}} function, it is written in a readable form.}
       |                                      ^
checkRd: (-1) summary.Rd:5: Lost braces
     5 | \description{Summary method for the output of code{\link{extRC}} function.}
       |                                                   ^
Package required but not available: ‘fda’

Packages suggested but not available for checking: 'fields', 'extraDistr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'mixtools', 'Rcpp', 'threshr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Lmoments’

Package suggested but not available for checking: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lmomco', 'extRemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'exuberdata', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'openxlsx', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) va.Rd:80: Lost braces
    80 | \doi{10.1016/s0002-9394(02)01825-1}{Beck et al.}, and
       |                                    ^
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Packages required but not available: 'ggforce', 'magick', 'rdist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'lme4', 'glmmTMB'
Error(s) in re-building vignettes:
  ...
--- re-building ‘divergence_vignette.Rmd’ using rmarkdown

Quitting from lines 26-60 [unnamed-chunk-1] (divergence_vignette.Rmd)
Error: processing vignette 'divergence_vignette.Rmd' failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘divergence_vignette.Rmd’

--- re-building ‘growth_curve_analysis_vignette.Rmd’ using rmarkdown

Quitting from lines 26-57 [unnamed-chunk-1] (growth_curve_analysis_vignette.Rmd)
Error: processing vignette 'growth_curve_analysis_vignette.Rmd' failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘growth_curve_analysis_vignette.Rmd’

--- re-building ‘onset_contingent_analysis_vignette.Rmd’ using rmarkdown

Quitting from lines 30-61 [unnamed-chunk-1] (onset_contingent_analysis_vignette.Rmd)
Error: processing vignette 'onset_contingent_analysis_vignette.Rmd' failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘onset_contingent_analysis_vignette.Rmd’

--- re-building ‘preparing_your_data_vignette.Rmd’ using rmarkdown

Quitting from lines 59-75 [unnamed-chunk-1] (preparing_your_data_vignette.Rmd)
Error: processing vignette 'preparing_your_data_vignette.Rmd' failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘preparing_your_data_vignette.Rmd’

--- re-building ‘window_analysis_vignette.Rmd’ using rmarkdown

Quitting from lines 26-56 [unnamed-chunk-1] (window_analysis_vignette.Rmd)
Error: processing vignette 'window_analysis_vignette.Rmd' failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘window_analysis_vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘divergence_vignette.Rmd’ ‘growth_curve_analysis_vignette.Rmd’
  ‘onset_contingent_analysis_vignette.Rmd’
  ‘preparing_your_data_vignette.Rmd’ ‘window_analysis_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'klaR', 'lhs', 'mvnfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘drc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) EEzGP_fit.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EEzGP_fit.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EEzGP_predict.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EEzGP_predict.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_fit.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_fit.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_predict.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_predict.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LEzGP_fit.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LEzGP_fit.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LLF_gradients.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LLF_gradients.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'DT', 'ggrepel', 'miniUI', 'shiny', 'tsibble', 'tsibbledata'
Running examples in ‘ezplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: agg_data
> ### Title: Aggregates data
> ### Aliases: agg_data
> 
> ### ** Examples
> 
> suppressPackageStartupMessages(library(tsibble))
Error in library(tsibble) : there is no package called ‘tsibble’
Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ezplot)
  > suppressPackageStartupMessages(library(tsibble))
  Error in library(tsibble) : there is no package called 'tsibble'
  Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bar_plot.Rmd’ using rmarkdown

Quitting from lines 20-25 [setup] (bar_plot.Rmd)
Error: processing vignette 'bar_plot.Rmd' failed with diagnostics:
there is no package called 'tsibble'
--- failed re-building ‘bar_plot.Rmd’

--- re-building ‘basics.Rmd’ using rmarkdown

Quitting from lines 29-34 [unnamed-chunk-1] (basics.Rmd)
Error: processing vignette 'basics.Rmd' failed with diagnostics:
there is no package called 'tsibble'
--- failed re-building ‘basics.Rmd’

--- re-building ‘line_plot.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (line_plot.Rmd)
Error: processing vignette 'line_plot.Rmd' failed with diagnostics:
there is no package called 'tsibble'
--- failed re-building ‘line_plot.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown

Quitting from lines 24-30 [setup] (overview.Rmd)
Error: processing vignette 'overview.Rmd' failed with diagnostics:
there is no package called 'tsibble'
--- failed re-building ‘overview.Rmd’

--- re-building ‘variable_plot.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (variable_plot.Rmd)
Error: processing vignette 'variable_plot.Rmd' failed with diagnostics:
there is no package called 'tsibble'
--- failed re-building ‘variable_plot.Rmd’

SUMMARY: processing the following files failed:
  ‘bar_plot.Rmd’ ‘basics.Rmd’ ‘line_plot.Rmd’ ‘overview.Rmd’
  ‘variable_plot.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'car', 'lme4', 'plyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'shiny', 'shinydashboard', 'weights'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GA', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'paws.application.integration', 'paws.compute', 'paws.storage',
  'paws.security.identity', 'jsonvalidate'

Packages suggested but not available for checking:
  'paws.common', 'devtools'

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
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'NMF', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fabletools', 'ATAforecasting', 'tsibble', 'tsbox'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fabletools', 'fable', 'tsibble', 'tsibbledata'

Packages suggested but not available for checking:
  'Rcpp', 'feasts', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'fabletools', 'tsibble', 'prophet'

Package suggested but not available for checking: ‘tsibbledata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fabletools', 'Rcpp', 'tsibble'

Packages suggested but not available for checking:
  'feasts', 'forecast', 'MTS', 'spelling', 'tsibbledata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tsibble', 'ggdist'

Packages suggested but not available for checking:
  'fable', 'feasts', 'spelling', 'tsibbledata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sae’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'mvnfast', 'extraDistr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘magick’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rugarch', 'HH'
checkRd: (-1) fmCov.Rd:37: Lost braces; missing escapes or markup?
    37 | where, \code{alpha(i)} is the intercept, \code{f(t)} is a {K x 1} vector of 
       |                                                           ^
checkRd: (-1) plot.ffm.Rd:82: Lost braces; missing escapes or markup?
    82 | \item{las}{one of {0, 1, 2, 3} to set the direction of axis labels, same as
       |                   ^
checkRd: (-1) summary.ffm.Rd:39: Lost braces; missing escapes or markup?
    39 | Returned object is of class {summary.ffm}.
       |                             ^
Packages suggested but not available for checking: 'HH', 'rugarch'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rARPACK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ade4', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'FactoMineR', 'ggpubr', 'reshape2', 'ggrepel'

Package suggested but not available for checking: ‘ade4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘FactoMineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'DT', 'ggrepel'

Packages suggested but not available for checking: 'missMDA', 'Factoshiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    minor changes
Packages required but not available: 'Rcpp', 'stochvol', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'FactoMineR', 'shiny', 'FactoInvestigate', 'DT', 'colourpicker',
  'ggrepel', 'shinydashboard', 'shinyjqui', 'missMDA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'caret', 'FuzzyDBScan', 'factoextra', 'spelling'
Running examples in ‘FACT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ClustPredictor
> ### Title: Clustering Predictor Object
> ### Aliases: ClustPredictor
> 
> ### ** Examples
> 
> require(factoextra)
Loading required package: factoextra
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘factoextra’
> require(FuzzyDBScan)
Loading required package: FuzzyDBScan
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘FuzzyDBScan’
> multishapes <- as.data.frame(multishapes[, 1:2])
Error: object 'multishapes' not found
Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FACT)
  > 
  > test_check("FACT")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/FACT.Rcheck/tests/testthat/setup.R"
  Caused by error in `library()`:
  ! there is no package called 'FuzzyDBScan'
  Backtrace:
       ▆
    1. ├─testthat::test_check("FACT")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library(FuzzyDBScan) at tests/testthat/setup.R:2:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘RProtoBuf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'MFPCA', 'fda', 'fda.usc', 'funData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSpectra', 'Rcpp', 'RcppEigen'

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.
Packages required but not available:
  'shiny', 'shinydashboard', 'shinycssloaders', 'golem'

Packages suggested but not available for checking:
  'spelling', 'EFA.MRFA', 'EFA.dimensions', 'EFAtools', 'EGAnet',
  'MBESS', 'energy', 'ggcorrplot', 'semPlot', 'sirt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) happy.Rd:14: Lost braces
    14 |                  code{Pretty happy} <  \code{Very happy}}
       |                      ^
Package required but not available: ‘ranger’

Packages suggested but not available for checking:
  'magick', 'ggraph', 'pdftools', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'jsonld', 'DiagrammeRsvg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

Packages suggested but not available for checking: 'cccp', 'CVXR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ranger', 'spelling', 'ggrepel'
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fairmodels)
  > 
  > 
  > test_check("fairmodels")
  Welcome to DALEX (version: 2.4.3).
  Find examples and detailed introduction at: http://ema.drwhy.ai/
  Additional features will be available after installation of: ggpubr.
  Use 'install_dependencies()' to get all suggested dependencies
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/fairmodels.Rcheck/tests/testthat/helper_objects.R"
  Caused by error in `library()`:
  ! there is no package called 'ranger'
  Backtrace:
       ▆
    1. ├─testthat::test_check("fairmodels")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_helpers(".", env)
    7. │           └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("ranger") at tests/testthat/helper_objects.R:2:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Packages required but not available: 'caret', 'devtools', 'pROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'devtools', 'hunspell', 'rasciidoc', 'spelling'

VignetteBuilder package required for checking but not installed: ‘rasciidoc’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘huge’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sf’
checkRd: (-1) fra_sf.Rd:22: Lost braces; missing escapes or markup?
    22 | A map of France as {sf} object. Can be used as dataset or for maps
       |                    ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘fakir-example.Rmd’ using rmarkdown

Quitting from lines 19-23 [unnamed-chunk-2] (fakir-example.Rmd)
Error: processing vignette 'fakir-example.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building ‘fakir-example.Rmd’

SUMMARY: processing the following file failed:
  ‘fakir-example.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'LipidMS', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘DepthProc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BART', 'Ecdat', 'fastglm', 'glmnet', 'isotree', 'qvalue', 'ranger'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape’

Package suggested but not available for checking: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'plyr', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) pi0FAMT.Rd:18: Lost braces
    18 | \code{pi0}{The estimated proportion \code{pi0} of null hypotheses.}}
       |           ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sensitivity’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sem', 'mirt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'miniUI', 'shinyWidgets', 'Benchmarking', 'shinycssloaders',
  'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSpectra', 'splines2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'fMultivar', 'energy'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'openxlsx', 'plyr', 'RcppRoll'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RSpectra', 'RcppArmadillo'

Package suggested but not available for checking: ‘invertiforms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reticulate', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'fastglm', 'forecast', 'glmnet', 'Rcpp', 'RcppArmadillo', 'RcppClock'

Packages suggested but not available for checking:
  'breakfast', 'CptNonPar', 'RcppClock', 'reshape2', 'stepR',
  'VARDetect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'BMisc', 'collapse', 'dreamerr', 'parglm'

Package suggested but not available for checking: ‘did’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'raster', 'RcppArmadillo'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'cAIC4', 'refund', 'Rfast', 'lmeresampler'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'OpenImageR', 'RcppArmadillo'

Package suggested but not available for checking: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MatrixExtra', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bigmemory', 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘caret’
Packages required but not available:
  'Rcpp', 'caret', 'timeROC', 'RcppEigen'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rARPACK’

Packages suggested but not available for checking: 'coxKM', 'SKAT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RcppNumerical', 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cheapr', 'collapse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'plyr', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'mosaicCalc', 'faraway', 'DAAG', 'car', 'alr4', 'BradleyTerry2',
  'cubature'
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RSpectra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'ggrepel', 'qs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'DT', 'shiny', 'shinyFeedback', 'shinyjs', 'waiter'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'ranger', 'shapviz'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rtsne', 'uwot', 'ashr', 'Rcpp', 'ggrepel', 'plotly', 'RcppArmadillo'

Package suggested but not available for checking: ‘Ternary’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RcppRoll’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'Rcpp'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘collapse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘multgee’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'princurve', 'Rtsne', 'umap'

Package suggested but not available for checking: ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘crul’
checkRd: (-1) Error-Classes.Rd:107-119: Lost braces
   107 |   \item \code{do_verbose(response, template)} {
       |                                               ^
checkRd: (-1) Error.Rd:33-45: Lost braces
    33 |   \item \code{do(response, mssg)} {
       |                                   ^
Running ‘test-all.R’ [1s/2s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("fauxpas")
  Loading required package: fauxpas
  [ FAIL 1 | WARN 0 | SKIP 8 | PASS 0 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test-Error.R:4:3', 'test-Error.R:50:3', 'test-children.R:4:3',
    'test-children.R:28:3', 'test-fail-well.R:2:3', 'test-http.R:4:3',
    'test-http.R:18:3', 'test-http.R:38:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-http_star.R:4:1'): (code run outside of `test_that()`) ─────────
  <packageNotFoundError/error/condition>
  Error in `library("crul")`: there is no package called 'crul'
  Backtrace:
      ▆
   1. └─base::library("crul") at test-http_star.R:4:1
  
  [ FAIL 1 | WARN 0 | SKIP 8 | PASS 0 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘lme4’

Packages suggested but not available for checking: 'ggExtra', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bvartools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package suggested but not available for checking: ‘interp’
Running examples in ‘fBasics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NormalityTests
> ### Title: Tests for normality
> ### Aliases: NormalityTests normalTest ksnormTest shapiroTest
> ###   jarqueberaTest dagoTest jbTest adTest cvmTest lillieTest pchiTest
> ###   sfTest
> ### Keywords: htest
> 
> ### ** Examples
> 
> ## Don't show: 
> set.seed(1234)
> ## End(Don't show)
> x <- rnorm(100)
> 
> ## Kolmogorov-Smirnov one-sampe test
> ksnormTest(x)

Title:
 Asymptotic one-sample Kolmogorov-Smirnov test

Test Results:
  STATISTIC:
    D: 0.161
  P VALUE:
    Alternative Two-Sided: 0.01124 
    Alternative      Less: 0.796 
    Alternative   Greater: 0.00562 

> 
> ## Shapiro-Wilk test
> shapiroTest(x)

Title:
 Shapiro - Wilk Normality Test

Test Results:
  STATISTIC:
    W: 0.9659
  P VALUE:
    0.01078 

> 
> ## Jarque-Bera Test
> jarqueberaTest(x)

Title:
 Jarque-Bera Normality Test

Test Results:
  STATISTIC:
    X-squared: 5.9288
  P VALUE:
    Asymptotic p Value: 0.05159 

> jbTest(x)
Error in linearInterpp(x, y, z, xo = xo, yo = yo) : 
  Needs Package 'interp' which is not installed
Calls: jbTest -> .jb.test -> .pjb -> linearInterpp
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'fastglm', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) FBN.histogramMaxima.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:40: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cubature', 'ks', 'rstanarm'

Package suggested but not available for checking: ‘BayesFactor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fractional', 'POSetR', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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.
Package required but not available: ‘fMultivar’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DataVisualizations’

Packages suggested but not available for checking:
  'mlpack', 'dbscan', 'kohonen', 'ADPclust', 'DatabionicSwarm',
  'subspace', 'apcluster', 'pdfCluster', 'parallelDist', 'plotly',
  'ProjectionBasedClustering', 'GeneralizedUmatrix', 'densityClust',
  'energy', 'tclust', 'Spectrum', 'genie', 'reshape2', 'PPCI',
  'clustrd', 'smacof', 'prclust', 'VarSelLCM', 'mixtools', 'HDclassif',
  'leiden', 'clusterSim', 'NetworkToolbox', 'ClusterR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.Rprofile’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fda’

Package suggested but not available for checking: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dbscan', 'fdasrvf', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'fda', 'funData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'fdapace', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'fdapace'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
checkRd: (-1) simulation_model9.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                              ^
checkRd: (-1) simulation_model9.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                                           ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking: 'ks', 'minqa'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'fdapace', 'golem', 'shiny', 'plotly', 'reshape2', 'bs4Dash',
  'shinyWidgets', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RcppEigen', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'fdapace', 'FastGP'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fds’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'fdapace', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'ks', 'RcppArmadillo'

Package suggested but not available for checking: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fields', 'Rcpp', 'tolerance', 'RcppArmadillo'

Package suggested but not available for checking: ‘interp’

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: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'fda', 'fields', 'refund'
Note: skipping ‘FLAM_canada.Rnw’ due to unavailable dependencies:
  'fda', 'fields'
Note: skipping ‘FLAM_fuel.Rnw’ due to unavailable dependencies:
  'fda', 'fields'
Note: skipping ‘FLAM_viscosity.Rnw’ due to unavailable dependencies:
  'fda', 'fields'
Note: skipping ‘density-on-scalar_birth.Rnw’ due to unavailable dependencies:
  'fda', 'fields'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking:
  'rtdists', 'reshape2', 'ggforce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arulesViz', 'FactoMineR'

Packages suggested but not available for checking:
  'car', 'caret', 'fds', 'glmnet', 'kohonen', 'questionr', 'Rtsne',
  'text2vec', 'wordcloud'

Package which this enhances but not available for checking: ‘NMF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Fgmutils', 'randomcoloR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ade4', 'ape', 'geometry'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘qvalue’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) p.fdr.Rd:30: Lost braces
    30 | \item{adjust.method}{A string used to identify the p-value and false discovery rate adjustment method. Defaults to \code{BH}. Options are \code{BH}, \code{BY}, code{Bon},\code{Holm}, \code{Hoch}, and \code{Sidak}.}
       |                                                                                                                                                                     ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rainbow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'PoissonBinomial', 'DiscreteFDR', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geometry', 'geosphere'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fabletools', 'tsibble'

Packages suggested but not available for checking:
  'tsibbledata', 'fable', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DatabaseConnector’

Package suggested but not available for checking: ‘Eunomia’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'glmnet', 'pROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ClustImpute’
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FeatureImpCluster)
  Loading required package: data.table
  > 
  > test_check("FeatureImpCluster")
  # NAs in variables:
    V1   V2    x    y cat1 cat2 
     0    0    0    0    0    0 
  0 observation(s) with NAs.
  
  Estimated lambda: 2.193463 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 12 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-permmisclassrate.R:31:1'): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'ClustImpute'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-permmisclassrate.R:31:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 12 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘ks’

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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'GGally', 'fixest', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'DT', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidytext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readsdmx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gstat', 'automap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'miniUI', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geojsonsf', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'sae', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'gganimate', 'ggrepel', 'ggforce', 'GpGp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plyr', 'timetk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggdist’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'jpmesh', 'raster', 'sf', 'stars', 'terra', 'units'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'fgeo.plot', 'spelling'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggrepel’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fgeo.plot’

Packages suggested but not available for checking: 'DT', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'splines2', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fdapace’

Package suggested but not available for checking: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'oeli', 'padr', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘BSSasymp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'flexsurv', 'GGally'
Note: skipping ‘linear.Rnw’ due to unavailable dependencies: 'GGally'
Note: skipping ‘survival.Rnw’ due to unavailable dependencies: 'flexsurv'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'tidybayes', 'RcppEigen', 'RcppNumerical', 'RcppZiggurat'

Packages suggested but not available for checking: 'ape', 'phyloseq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'golem', 'shiny', 'DT', 'shinythemes', 'blocksdesign',
  'shinycssloaders', 'plotly', 'shinyalert', 'desplot', 'shinyjs'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘interp’

Package suggested but not available for checking: ‘AlphaSimR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spam’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'httpuv', 'later', 'reqres'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FIESTAutils', 'gdalraster', 'sf'

Package suggested but not available for checking: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gdalraster', 'mase', 'Rcpp', 'sae', 'sf', 'terra', 'units'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘magick’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'microeco', 'ape'

Packages suggested but not available for checking:
  'seqinr', 'phyloseq', 'TreeSummarizedExperiment'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'reticulate', 'spelling'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'KRIS', 'rARPACK'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CVXR', 'Rcpp', 'ROptSpace', 'RSpectra', 'nabor', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'shiny', 'shinyWidgets', 'shinyjs', 'shinyBS', 'rclipboard'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GGally', 'lme4', 'mice', 'pROC'

Packages suggested but not available for checking:
  'rstan', 'survey', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking:
  'ggtext', 'socialmixr', 'spelling'

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
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lutz’

Package suggested but not available for checking: ‘vcr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spectralGraphTopology', 'CVXR'

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.
Package required but not available: ‘EML’

Package suggested but not available for checking: ‘crul’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'shinyAce', 'shinyFiles', 'shinyjqui', 'shinyvalidate',
  'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Packages required but not available: 'arm', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reticulate’
Package required but not available: ‘pdftools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidycensus’

Packages suggested but not available for checking: 'leaflet', 'sf', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ape’
Package required but not available: ‘tune’

Packages suggested but not available for checking:
  'BradleyTerry2', 'klaR', 'lme4', 'ranger', 'recipes', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
Packages required but not available:
  'Rcpp', 'klaR', 'GGally', 'Rcmdr', 'plyr', 'reshape', 'car',
  'RcppGSL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spectralGraphTopology’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sdprisk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggpubr', 'ggraph', 'udpipe', 'wordcloud'

Packages suggested but not available for checking:
  'DT', 'shiny', 'shinyBS', 'shinydashboard', 'shinyjs', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'modeltime', 'Cubist', 'feasts', 'glmnet', 'hts', 'plyr', 'recipes',
  'timetk', 'tune'

Packages suggested but not available for checking: 'Boruta', 'corrr', 'qs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘XBRL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'miniUI', 'shiny'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reshape2’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘twinning’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DiagrammeRsvg’
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘aricode’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'TMB'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'fishtree', 'geiger', 'phytools'

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.
Package required but not available: ‘respirometry’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'golem', 'sf', 'shiny', 'shinyBS', 'shinyjs', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ape’

Packages suggested but not available for checking:
  'diversitree', 'geiger', 'hisse', 'phytools', 'picante', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rnaturalearth’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'spelling'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'varian', 'leaflet', 'sf', 'leafgl', 'raster', 'terra', 'rayshader',
  'reshape2'

Packages suggested but not available for checking:
  'CopernicusDEM', 'DT', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) fitConic.Rd:66-73: Lost braces
    66 | \code{parA }{vector of the six "ABCDEF" coefficients
       |             ^
checkRd: (-1) fitConic.Rd:67: Lost braces
    67 | \code{RSS }{'root sum square' figure of merit describing the relative fit quality}
       |            ^
checkRd: (-1) fitConic.Rd:68: Lost braces
    68 | \code{iters }{number of iterations at convergence}
       |              ^
checkRd: (-1) fitConic.Rd:69-71: Lost braces
    69 | \code{exitCode }{1 means ellipse, 2 means hyperbola, 3 means parabola.
       |                 ^
checkRd: (-1) rotateA.Rd:59: Lost braces; missing escapes or markup?
    59 | For \code{xyrot} {a Nx2 array of the x,y coordinates of the rotated data set. }
       |                  ^
Package suggested but not available for checking: ‘mc2d’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ICSNP’

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'Rfast', 'simlandr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'flextable', 'reshape2', 'spelling'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'flextable', 'golem', 'shiny', 'shinydashboard', 'shinyscreenshot'

Package suggested but not available for checking: ‘gridlayout’

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: ‘ks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'DT', 'shiny'

Packages suggested but not available for checking:
  'emdbook', 'flexsurv', 'GLDEX', 'mc2d', 'nCDunnett', 'QRM', 'ReIns',
  'reliaR', 'revdbayes', 'SMR', 'STAR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'shiny', 'miniUI', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'elo', 'spelling'
Package suggested but not available for checking: ‘fivethirtyeightdata’
checkRd: (-1) food_world_cup.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:75: Lost braces in \itemize; meant \describe ?
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
Package required but not available: ‘BayesFactor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'cubature', 'qpdf'
Error(s) in re-building vignettes:
  ...
--- re-building ‘FixedPoint.Rmd’ using rmarkdown

Quitting from lines 546-580 [unnamed-chunk-12] (FixedPoint.Rmd)
Error: processing vignette 'FixedPoint.Rmd' failed with diagnostics:
there is no package called 'cubature'
--- failed re-building ‘FixedPoint.Rmd’

SUMMARY: processing the following file failed:
  ‘FixedPoint.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'dreamerr', 'stringmagic'

Packages suggested but not available for checking:
  'plm', 'pander', 'pdftools', 'AER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) distribution_vector.Rd:14: Lost braces; missing escapes or markup?
    14 | All standard distributions from {stats} package are covered. For a list
       |                                 ^
'LazyData' is specified without a 'data' directory
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'rARPACK', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'lhs', 'plotly', 'plyr', 'shiny', 'smoof'
checkRd: (-1) convertInitDesignToGrid.Rd:11: Lost braces; missing escapes or markup?
    11 | The initial design, consisting of \code{d + 1} columns ({d} dimensions and
       |                                                         ^
Running ‘test-features.R’ [0s/1s]
  Running ‘test-general.R’ [9s/12s]
Running the tests in ‘tests/test-general.R’ failed.
Complete output:
  > library(testthat)
  > 
  > # test general stuff:
  > test_check("flacco", filter = "^base")
  Loading required package: flacco
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 149 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-base-createInitialSample.R:11:3'): Basic Initial Samples ───────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lhs'
  Backtrace:
      ▆
   1. ├─flacco::createInitialSample(200, 4, control = list(init_sample.type = "lhs")) at test-base-createInitialSample.R:11:3
   2. └─base::loadNamespace(x)
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-base-printFeatureObject.R:68:3'): Usage of regular and smoof functions ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'smoof'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-base-printFeatureObject.R:68:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 149 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘eurostat’
Package required but not available: ‘glmnet’

Package suggested but not available for checking: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggforce’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppGSL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘forecast’
Running examples in ‘flap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flap
> ### Title: Forecast Linear Augmented Projection
> ### Aliases: flap
> 
> ### ** Examples
> 
> # Generate example data
> # T = 70, m = 20
> train <- matrix(rnorm(70 * 20),ncol = 20)
> 
> # Obtain the forecast and the residual of the original series
> mdl <- apply(train, 2, forecast::ets)
Error in loadNamespace(x) : there is no package called ‘forecast’
Calls: apply ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ebnm’

Packages suggested but not available for checking: 'ashr', 'RcppML'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) flashlight.Rd:53: Lost braces; missing escapes or markup?
    53 | like those in package {MetricsWeighted}.}
       |                       ^
checkRd: (-1) grouped_stats.Rd:49: Lost braces; missing escapes or markup?
    49 | {MetricsWeighted}.}
       | ^
checkRd: (-1) plot_counts.Rd:45: Lost braces; missing escapes or markup?
    45 | Experimental. Uses package {ggpubr} to rearrange the figure.
       |                            ^
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘pander’
Error(s) in re-building vignettes:
  ...
--- re-building ‘flattabler.Rmd’ using rmarkdown

Quitting from lines 38-42 [unnamed-chunk-2] (flattabler.Rmd)
Error: processing vignette 'flattabler.Rmd' failed with diagnostics:
there is no package called 'pander'
--- failed re-building ‘flattabler.Rmd’

SUMMARY: processing the following file failed:
  ‘flattabler.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'caret', 'ranger'

Packages suggested but not available for checking: 'mice', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ContaminatedMixt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘openxlsx2’

Packages suggested but not available for checking: 'gtsummary', 'flextable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mirt’
checkRd: (-1) fmp.Rd:45: Lost braces; missing escapes or markup?
    45 | If k = 0: (xi_1, ..., x_{C_i - 1}, omega)
       |                         ^
checkRd: (-1) fmp.Rd:47: Lost braces; missing escapes or markup?
    47 | If k = 1: (xi_1, ..., x_{C_i - 1}, omega, alpha1, tau1)
       |                         ^
checkRd: (-1) fmp.Rd:49: Lost braces; missing escapes or markup?
    49 | If k = 2: (xi_1, ..., x_{C_i - 1}, omega, alpha1, tau1, alpha2, tau2)
       |                         ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'Ecdat', 'glmnet', 'lme4'
Running examples in ‘flexmix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FLXMRglmnet
> ### Title: FlexMix Interface for Adaptive Lasso / Elastic Net with GLMs
> ### Aliases: FLXMRglmnet FLXMRglmnet-class
> ### Keywords: regression cluster
> 
> ### ** Examples
> 
>     set.seed(12)
>     p <- 10
>     beta <- matrix(0, nrow = p + 1, ncol = 2)
>     beta[1,] <- c(-1, 1)
>     beta[cbind(c(5, 10), c(1, 2))] <- 1
> 
>     nobs <- 100
>     X <- matrix(rnorm(nobs * p), nobs, p)
>     mu <- cbind(1, X) %*% beta
>     z <- sample(1:ncol(beta), nobs, replace = TRUE)
>     y <- mu[cbind(1:nobs, z)] + rnorm(nobs)
>     data <- data.frame(y, X)
>     ## The maximum number of iterations is reduced to
>     ## avoid a long running time.
>     fo <- sample(rep(seq(10), length = nrow(data)))
>     ex1 <- flexmix(y ~ ., data = data, k = 2, cluster = z,
+                    model = FLXMRglmnet(foldid = fo),
+                    control = list(iter.max = 2))
Error in loadNamespace(x) : there is no package called ‘glmnet’
Calls: flexmix ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘GJRM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
Error(s) in re-building vignettes:
  ...
--- re-building ‘main_vignette.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/flexOR.Rcheck/vign_test/flexOR/vignettes/main_vignette_files/figure-html/apply_flexOR-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7832 bytes
Input file size = 8690 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 7220
  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 = 7220

Output IDAT size = 7220 bytes (612 bytes decrease)
Output file size = 7298 bytes (1392 bytes = 16.02% decrease)


Quitting from lines 115-191 [plotly] (main_vignette.Rmd)
Error: processing vignette 'main_vignette.Rmd' failed with diagnostics:
there is no package called 'plotly'
--- failed re-building ‘main_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘main_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'bayesplot', 'RcppEigen',
  'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Epi’

Packages suggested but not available for checking: 'relsurv', 'mexhaz'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'smerc', 'spdep', 'spatialreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flexdashboard’

Package suggested but not available for checking: ‘spelling’

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.
Packages required but not available: 'Rcpp', 'rstpm2'

Packages suggested but not available for checking:
  'splines2', 'flexsurvcure', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gdtools’

Packages suggested but not available for checking:
  'chromote', 'doconv', 'equatags', 'lme4', 'magick', 'officedown',
  'pdftools', 'webshot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'survminer', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sf’
Packages required but not available: 'bazar', 'pryr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geosphere', 'ggrepel', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'geosphere', 'ggmap', 'fields', 'RcppArmadillo', 'sf', 'suntools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘parzer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plyr’

Packages suggested but not available for checking:
  'devtools', 'multipanelfigure', 'pander'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cherry', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'interp', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘brms’

Packages suggested but not available for checking:
  'RcppEigen', 'rstan', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘TLMoments’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'survcomp', 'reshape', 'glmnet', 'caret', 'RcppArmadillo',
  'ast2ast'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Package suggested but not available for checking: ‘reticulate’
Package required but not available: ‘Gmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘quarto’

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'caret', 'fastshap'

Packages suggested but not available for checking:
  'adabag', 'arm', 'C50', 'Cubist', 'glmnet', 'ipred', 'keras', 'klaR',
  'kohonen', 'penalized', 'plyr', 'ranger', 'rrcovHD', 'RSNNS',
  'shapviz'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nomnoml’

Package suggested but not available for checking: ‘esquisse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) flowdata.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{Flow}{Water flow, in m^{3}/s}
       |                              ^
Package required but not available: ‘params’

Package suggested but not available for checking: ‘reshape2’

Package which this enhances but not available for checking: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'Rcpp', 'mirt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘fluxfinder-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ffi_qaqc
> ### Title: Generate a QA/QC document
> ### Aliases: ffi_qaqc
> 
> ### ** Examples
> 
> # Toy data
> cars$Plot <- c("A", "B")
> fd <- ffi_compute_fluxes(cars, "Plot", "speed", "dist")
> x <- ffi_qaqc(fd, group_column = "Plot")


processing file: qaqc.Rmd
Warning in file(con, "w") :
  cannot open file 'qaqc.knit.md': Read-only file system
Error in file(con, "w") : cannot open the connection
Calls: ffi_qaqc ... <Anonymous> -> <Anonymous> -> write_utf8 -> writeLines -> file
Execution halted
Found the following files/directories:
  ‘qaqc_files’
Package required but not available: ‘ggforce’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘flux.CH4.txt’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.