'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Source(s) listed in 'build/vignette.rds' but not in package:
  ‘tensorEVD-documentation.Rmd’
'LazyData' is specified without a 'data' directory
checkRd: (-1) NEWS.Rd:427: Lost braces; missing escapes or markup?
   427 |       \item  Changes to \code{simulate.stergm} parameters: addition of \code{duration.dependent} parameter: {Logical: Whether the model terms in formula or model are duration dependent. E.g., if a duration-dependent term  is used in estimation/simulation model, the probability of forming or dissolving a tie may dependent on the age the dyad status. If TRUE, the matrix of tie ages will be allocated.}
       |                                                                                                             ^
checkRd: (-1) discordBDStratTNT-ergmProposal-9267ec8b.Rd:18: Lost braces
    18 | code{\link[ergm:blocks-ergmConstraint]{blocks}} constraints and
       |     ^
checkRd: (-1) discordTNT-ergmProposal-bc75dff0.Rd:9: Lost braces
     9 | code{discordance_fraction} of proposed toggles being made on the set of discordant dyads,
       |     ^
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
Found the following files/directories:
  ‘par-7269706c6579’
Package suggested but not available for checking: ‘gurobi’
File ‘testforDEP/libs/testforDEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
File ‘testthat/libs/testthat.so’:
  Found non-API calls to R: ‘SET_BODY’, ‘SET_CLOENV’, ‘SET_FORMALS’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'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) patch_table_env.Rd:25: Lost braces
    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |               ^
checkRd: (-1) patch_table_env.Rd:25: Lost braces
    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |                                  ^
checkRd: (-1) patch_table_env.Rd:25: Lost braces
    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |                                                ^
checkRd: (-1) patch_table_env.Rd:25: Lost braces
    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |                                                    ^
checkRd: (-1) patch_table_env.Rd:25: Lost braces
    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |                                                       ^
Note: found 37 marked UTF-8 strings
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
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}.}
       |                                              ^
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘forecast’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
Note: found 40 marked UTF-8 strings
'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.
Note: found 3 marked UTF-8 strings
Note: found 4 marked UTF-8 strings
File ‘textrecipes/libs/textrecipes.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
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
File ‘textshaping/libs/textshaping.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'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
Namespace in Imports field not imported from: ‘doRNG’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘ggm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘tgstat/libs/tgstat.so’:
  Found non-API calls to R: ‘R_curErrorBuf’, ‘SET_TYPEOF’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
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
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘MASS’ ‘base’ ‘graphics’ ‘janitor’ ‘rlang’ ‘testthat’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 197527 marked UTF-8 strings
'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.
File ‘tibble/libs/tibble.so’:
  Found non-API call to R: ‘SET_S4_OBJECT’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
File ‘tibblify/libs/tibblify.so’:
  Found non-API calls to R: ‘FRAME’, ‘HASHTAB’, ‘PRENV’, ‘PRVALUE’,
    ‘R_PromiseExpr’, ‘Rf_findVarInFrame3’, ‘SETLENGTH’, ‘SET_BODY’,
    ‘SET_CLOENV’, ‘SET_FORMALS’, ‘SET_GROWABLE_BIT’, ‘SET_TRUELENGTH’,
    ‘STRING_PTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘badger’ ‘ggplot2’ ‘lubridate’ ‘scales’ ‘xgboost’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Ckmeans.1d.dp’ ‘autostats’ ‘badger’ ‘framecleaner’ ‘presenter’
  ‘tidybins’ ‘validata’
  All declared Imports should be used.
Note: found 4546 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'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
File ‘tidygraph/libs/tidygraph.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Note: found 60 marked UTF-8 strings
Note: found 4 marked UTF-8 strings
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:
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
checkRd: (-1) single_imputation.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) single_imputation.Rd:23-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) separate_genes.Rd:14: Lost braces
    14 | microbial genes like AbcD, default [A-Za-z][a-z]{2}[A-Z0-9]+}
       |                                                 ^
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
Note: found 24 marked UTF-8 strings
File ‘tidyr/libs/tidyr.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) get_tidysq_options.Rd:37: Lost braces
    37 | \item tidysq_pillar_max_width [code{integer(1)}]\cr
       |                                    ^
checkRd: (-1) read_fasta.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_fasta.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
Note: found 113 marked UTF-8 strings
Note: found 34206 marked UTF-8 strings
'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>
Note: found 4581 marked UTF-8 strings
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 341 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
File ‘timechange/libs/timechange.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
File ‘timeplyr/libs/timeplyr.so’:
  Found non-API call to R: ‘STRING_PTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'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}
       |                ^
Note: found 2750 marked UTF-8 strings
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
Namespaces in Imports field not imported from:
  ‘cpp11’ ‘dplyr’ ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Note: found 384749 marked UTF-8 strings
'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.}
       |                                           ^
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
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.
Note: found 134043 marked UTF-8 strings
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 ?
Note: found 1 marked UTF-8 string
'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
File ‘tmvnsim/libs/tmvnsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmvtnorm/libs/tmvtnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
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 ?
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
'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
Note: found 91 marked UTF-8 strings
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Package suggested but not available for checking: ‘gurobi’
File ‘torch/libs/torch.so’:
  Found non-API calls to R: ‘PRCODE’, ‘PRENV’, ‘Rf_findVarInFrame3’
File ‘torch/libs/torchpkg.so’:
  Found non-API calls to R: ‘PRCODE’, ‘PRENV’, ‘Rf_findVarInFrame3’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Package suggested but not available for checking: ‘toscaData’
Namespace in Imports field not imported from: ‘hdi’
  All declared Imports should be used.
Note: found 4490 marked UTF-8 strings
Note: found 100 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
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
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Note: found 23 marked UTF-8 strings
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
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
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’
Namespace in Imports field not imported from: ‘class’
  All declared Imports should be used.
Note: found 827 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘transformr/libs/transformr.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) Blavet.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) trans.Rd:46: Lost braces; missing escapes or markup?
    46 | "Found {trans("file", .n = n_files)} in {trans("directory", .n = n_dirs)}".
       |        ^
checkRd: (-1) trans.Rd:46: Lost braces; missing escapes or markup?
    46 | "Found {trans("file", .n = n_files)} in {trans("directory", .n = n_dirs)}".
       |                                         ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘WSGeometry’
Package which this enhances but not available for checking: ‘fwelnet’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'CohortGenerator', 'Capr'
checkRd: (-1) trtsel.Rd:69: Lost braces; missing escapes or markup?
    69 | numeric with two values {0,1} and gaussian(link = "identity") otherwise.
       |                         ^
Namespace in Imports field not imported from: ‘tree’
  All declared Imports should be used.
Package suggested but not available for checking: ‘TreeDistData’
Specified C++11: please drop specification unless essential
Note: found 3 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
File ‘TrialSize/libs/TrialSize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘triangulr/libs/triangulr.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Note: found 2 marked UTF-8 strings
checkRd: (-1) coef.tridim_transformation.Rd:31: Lost braces
    31 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
checkRd: (-1) coef.tridim_transformation.Rd:32: Lost braces
    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
checkRd: (-1) coef.tridim_transformation.Rd:32: Lost braces; missing escapes or markup?
    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
checkRd: (-1) predict.tridim_transformation.Rd:24: Lost braces
    24 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
checkRd: (-1) predict.tridim_transformation.Rd:25: Lost braces
    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
checkRd: (-1) predict.tridim_transformation.Rd:25: Lost braces; missing escapes or markup?
    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
checkRd: (-1) variable_summary.Rd:18: Lost braces; missing escapes or markup?
    18 | data.frame with "{var_name}" column for the mean and
       |                  ^
checkRd: (-1) variable_summary.Rd:19: Lost braces; missing escapes or markup?
    19 | "{var_name}_{prob}" columns for each probability.
       |  ^
checkRd: (-1) variable_summary.Rd:19: Lost braces; missing escapes or markup?
    19 | "{var_name}_{prob}" columns for each probability.
       |             ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘triptych/libs/triptych.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Note: found 192 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ypr_sel.html:113:1 (ypr_sel.Rd:31): Warning: trimming empty <li>
ypr_sel.html:112:1 (ypr_sel.Rd:31): Warning: trimming empty <ul>
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
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’
Namespace in Imports field not imported from: ‘tseries’
  All declared Imports should be used.
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
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'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}.
       |                         ^
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
File ‘tseriesChaos/libs/tseriesChaos.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
File ‘tseriesTARMA/libs/tseriesTARMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crosstalk’
  All declared Imports should be used.
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
File ‘tspmeta/libs/tspmeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘EMD’ ‘vars’
  All declared Imports should be used.
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
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Note: found 1080 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
checkRd: (-1) tweedie-internal.Rd:74: Lost braces
    74 |         doi{10.1093/biomet/74.2.221}
       |            ^
File ‘tweenr/libs/tweenr.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'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
       |                              ^
Note: found 34 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) twosigmag.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |     ^
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |                                  ^
Package which this enhances but not available for checking: ‘sl3’
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |  ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |               ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘typetracer/libs/typetracer.so’:
  Found non-API call to R: ‘SET_BODY’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
File ‘tzdb/libs/tzdb.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
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.
Note: found 2 marked UTF-8 strings
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
Namespaces in Imports field not imported from:
  ‘foreign’ ‘psychTools’ ‘pwr’ ‘rmarkdown’
  All declared Imports should be used.
Note: found 312859 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 468 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
File ‘unigd/libs/unigd.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
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
Note: found 548 marked UTF-8 strings
'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
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
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.
File ‘unnest/libs/unnest.so’:
  Found non-API call to R: ‘STRING_PTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
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.}}
       |                                  ^
Note: found 3347 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 7872 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
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 ?
Note: found 488 marked UTF-8 strings
Package suggested but not available for checking: ‘USA.state.boundaries.data’
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
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: \&
Note: found 17 marked UTF-8 strings
Note: found 50 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
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
Namespace in Imports field not imported from: ‘Cairo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
Namespaces in Imports field not imported from:
  ‘BBmisc’ ‘badger’
  All declared Imports should be used.
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
File ‘valorate/libs/valorate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
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
File ‘varband/libs/varband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) decomposition.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |      ^
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |          ^
checkRd: (-1) moving.estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) datasets.Rd:15: Lost braces
    15 | and dimension information (\code{dim} or code{length}) of each item,
       |                                              ^
GNU make is a SystemRequirements.
File ‘vctrs/libs/vctrs.so’:
  Found non-API calls to R: ‘FRAME’, ‘HASHTAB’, ‘LEVELS’, ‘PRENV’,
    ‘PRVALUE’, ‘R_PromiseExpr’, ‘Rf_findVarInFrame3’, ‘SETLENGTH’,
    ‘SET_BODY’, ‘SET_CLOENV’, ‘SET_ENCLOS’, ‘SET_FORMALS’,
    ‘SET_GROWABLE_BIT’, ‘SET_S4_OBJECT’, ‘SET_TRUELENGTH’,
    ‘STDVEC_DATAPTR’, ‘STRING_PTR’, ‘TRUELENGTH’, ‘UNSET_S4_OBJECT’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
File ‘Vdgraph/libs/Vdgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vdg/libs/vdg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
File ‘vdiffr/libs/vdiffr.so’:
  Found non-API calls to R: ‘Rf_findVarInFrame3’, ‘SETLENGTH’,
    ‘SET_GROWABLE_BIT’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Namespaces in Imports field not imported from:
  ‘DT’ ‘maps’ ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘foreach’ ‘iterators’ ‘maps’ ‘spam’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 128 marked UTF-8 strings
Note: found 49 marked UTF-8 strings
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
File ‘versus/libs/versus.so’:
  Found non-API call to R: ‘STRING_PTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex125.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
File ‘vetr/libs/vetr.so’:
  Found non-API call to R: ‘SET_TYPEOF’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fit.vfp.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LinRegChol.Rd:21: Lost braces; missing escapes or markup?
    21 | Do linear regression of form (X^T O X + P)^{-1} X^T y where O is omega, P is
       |                                            ^
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
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.}
       |                    ^
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘leaflet’ ‘mapview’
  All declared Imports should be used.
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 ?
Note: found 60 marked UTF-8 strings
Note: found 468 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mclust’ ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 2754 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) RVineMatrix.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RVineMatrix.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RVineMatrix.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
Found the following HTML validation problems:
RVineClarkeTest.html:56:32 (RVineClarkeTest.Rd:31): Warning: trimming empty <code>
RVineClarkeTest.html:68:32 (RVineClarkeTest.Rd:41): Warning: trimming empty <code>
File ‘vines/libs/vines.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘viraldomain-Ex.R’ failed
The error most likely occurred in:

> ### Name: normalized_domain_plot
> ### Title: Create a Normalized Domain Plot
> ### Aliases: normalized_domain_plot
> 
> ### ** Examples
> 
> data(viral)
> data(sero)
>  # Adding "jitter_" prefix to original variable
> features <- list(
+   featured_col = "jittered_cd_2022",
+   features_vl = "vl_2022",
+   features_cd = "cd_2022"
+   )
> train_data = viral |>
+ dplyr::select("cd_2022", "vl_2022")
> test_data = sero
> treshold_value = 0.99
> impute_hyperparameters = list(indetect = 40, tasa_exp = 1/13, semi = 123)
> normalized_domain_plot(features, train_data, test_data, treshold_value, impute_hyperparameters)
Error in `recipes::prep()`:
✖ The following variables have the wrong attributes:
  `jittered_log10_imputed_vl_2022` and `jittered_cd_2022`.
Run `lapply(recipes_ptype(rec), attributes)` to see expected attributes. For
`rec` being the name of your recipe.
Backtrace:
     ▆
  1. └─viraldomain::normalized_domain_plot(...)
  2.   ├─applicable::autoplot.apd_pca(...)
  3.   ├─applicable::apd_pca(...)
  4.   └─applicable:::apd_pca.recipe(...)
  5.     ├─hardhat::mold(x, data)
  6.     └─hardhat:::mold.recipe(x, data)
  7.       ├─hardhat::run_mold(blueprint, data = data)
  8.       └─hardhat:::run_mold.default_recipe_blueprint(blueprint, data = data)
  9.         └─hardhat:::mold_recipe_default_process(...)
 10.           ├─recipes::prep(...)
 11.           └─recipes:::prep.recipe(...)
 12.             └─recipes:::check_training_set(training, x, fresh)
 13.               └─recipes::recipes_ptype_validate(...)
 14.                 └─cli::cli_abort(msg, call = call)
 15.                   └─rlang::abort(...)
Execution halted
'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.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
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
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: found 83 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘vita/libs/vita.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
       |               ^
GNU make is a SystemRequirements.
Note: found 4954 marked UTF-8 strings
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.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
File ‘vroom/libs/vroom.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’, ‘STDVEC_DATAPTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
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 ?
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
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 ?
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'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
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘warp/libs/warp.so’:
  Found non-API calls to R: ‘Rf_findVarInFrame3’, ‘STRING_PTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
File ‘wavelets/libs/wavelets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) anchor_points_grey.Rd:9: Lost braces
     9 | Zeeden et al., (2013) and anchored to the code{\link{astrosignal_example}} \cr
       |                                               ^
checkRd: (-1) retrack_wt_MC.Rd:206: Lost braces
   206 | be off in certain intervals. the link[WaverideR]{retrack_wt_MC} mitigates
       |                                                 ^
checkRd: (-1) retrack_wt_MC.Rd:40: Lost braces
    40 | link[WaverideR]{analyze_wavelet} wavelet function
       |                ^
checkRd: (-1) retrack_wt_MC.Rd:41: Lost braces
    41 | To create a list use the link[base]{list} function}
       |                                    ^
checkRd: (-1) retrack_wt_MC.Rd:44: Lost braces
    44 | To create the matrix use the link[base]{cbind} function and only add the
       |                                        ^
Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
Specified C++11: please drop specification unless essential
checkRd: (-1) accessC.wst.rd:24: Lost braces
    24 | Note that coefficients returned by this function are in emph{packet order}. They can be used \emph{as is} but for many applications it might be more useful to deal with the coefficients in packets: see the function \code{\link{getpacket.wst}} for further details. 
       |                                                             ^
checkRd: (-1) griddata.rd:18: Lost braces
    18 | \code{G}{Codes the value of the linear interpolant matrix for the corresponding entry in \code{gridt}. The value at each point corresponds to the proportion of the original data point pointed to by \code{Gindex} that contributes to the new value at the corresponding \code{gridt} value. See Kovac, (1997), page 81 for further information.}
       |         ^
checkRd: (-1) makegrid.rd:13: Lost braces; missing escapes or markup?
    13 | \item{gridn}{The number of grid points in the dyadic grid that the (x,y) gets interpolated to. By default this is the next power of two larger than the length of {x}.}
       |                                                                                                                                                                   ^
checkRd: (-1) makewpstDO.rd:29: Lost braces
    29 | /bold{12}, 45-56.
       |      ^
checkRd: (-1) wd.object.rd:47: Lost braces
    47 | The wd class of objects has methods for the following generic functions: \code{\link{plot}}, \code{\link{threshold}}, \code{\link{summary}}, \code{\link{print}}, code{\link{draw}}.
       |                                                                                                                                                                       ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 3133 marked UTF-8 strings
Note: found 4413 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Note: found 1668 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘prepr’
checkRd: (-1) wdpa_clean.Rd:23: Lost braces
    23 | \item{crs}{\code{character} or code{integer} object representing a
       |                                    ^
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) get_cid.Rd:58-59: Lost braces
    58 | <structure search> is assembled as "{\code{substructure} |
       |                                     ^
checkRd: (-1) get_cid.Rd:59-60: Lost braces
    59 | \code{superstructure} | \code{similarity} | \code{identity}} / {\code{smiles}
       |                                                                ^
checkRd: (-1) get_cid.Rd:70-71: Lost braces
    70 | "{\code{fastidentity} | \code{fastsimilarity_2d} | \code{fastsimilarity_3d} |
       |  ^
checkRd: (-1) get_cid.Rd:71-72: Lost braces
    71 | \code{fastsubstructure} | \code{fastsuperstructure}}/{\code{smiles} |
       |                                                      ^
checkRd: (-1) Session.Rd:146: Lost braces
   146 | sQuote{page load} timeout specifies a time to wait for the page loading
       |       ^
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
File ‘webreadr/libs/webreadr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘websocket/libs/websocket.so’:
  Found non-API calls to R: ‘Rf_findVarInFrame3’, ‘SETLENGTH’,
    ‘SET_GROWABLE_BIT’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Note: found 14 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘here’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) busTrace.Rd:15: Lost braces
    15 | /href{https://crawdad.org/coppe-ufrj/RioBuses/20180319/}
       |      ^
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
File ‘weightedCL/libs/weightedCL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
       |                         ^
File ‘weightedScores/libs/weightedScores.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
R code(s) listed in 'build/vignette.rds' but not in package:
  ‘wgaim_intro.R’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
Note: found 4102 marked UTF-8 strings
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 ?
Note: found 1 marked UTF-8 string
checkRd: (-1) Hoover.Rd:21: Lost braces; missing escapes or markup?
    21 | Let x_{i} be the income of the i-th person and \eqn{\overline{x}} be the mean income. Then the Hoover index H is:
       |       ^
checkRd: (-1) RicciSchutz.Rd:21: Lost braces; missing escapes or markup?
    21 | In the case of an empirical distribution with n elements where y_{i} denotes the wealth of household i and \eqn{\overline{y}} the sample average, the Ricci and Schutz coefficient can be expressed as:
       |                                                                  ^
Note: found 1 marked UTF-8 string
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 3881 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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 ?
Note: found 933 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Note: found 9378 marked UTF-8 strings
Note: found 154 marked UTF-8 strings
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 ?
Note: found 3 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Note: found 4 marked Latin-1 strings
  Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) item.side.Rd:35: Lost braces
    35 |         code{TRUE}. If any other value, the axis is not drawn.}
       |             ^
Namespaces in Imports field not imported from:
  ‘fdadensity’ ‘locfit’ ‘locpol’ ‘modeest’
  All declared Imports should be used.
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
Namespaces in Imports field not imported from:
  ‘future’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'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.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'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
Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘XNomial/libs/XNomial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rbokeh’
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 268 marked UTF-8 strings
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
File ‘xts/libs/xts.so’:
  Found non-API call to R: ‘SET_TYPEOF’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
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
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
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
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘yuima/libs/yuima.so’:
  Found non-API call to R: ‘SET_TYPEOF’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
File ‘yyjsonr/libs/yyjsonr.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Packages suggested but not available for checking:
  'RNRCS', 'metScanR', 'rnoaa'
'LazyData' is specified without a 'data' directory
Note: found 76 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
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.}
       |                                                                                                            ^
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
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.}
       |                            ^
Note: found 47 marked UTF-8 strings
Found the following HTML validation problems:
kana.html:65:1 (kana.Rd:33): Warning: trimming empty <dt>
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 146804 marked UTF-8 strings
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘Crashpad’
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
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  xtable.A3.Rd: print.xtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) abclass.Rd:133: Lost braces; missing escapes or markup?
   133 |     \code{abclass.control()} returns an object of class {abclass.control}
       |                                                         ^
checkRd: (-1) supclass.Rd:109: Lost braces; missing escapes or markup?
   109 | to solve the equivalent linear programming problem via the package {Rglpk}.
       |                                                                    ^
checkRd: (-1) supclass.Rd:110: Lost braces; missing escapes or markup?
   110 | It is recommended to use a recent version of {GLPK}.
       |                                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  abc.Rd: nnet
  cv4abc.Rd: nnet
  cv4postpr.Rd: nnet
  plot.abc.Rd: nnet
  postpr.Rd: nnet, multinom
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  abcrf.Rd: ranger
  covRegAbcrf.Rd: ranger
  densityPlot.Rd: ranger
  err.regAbcrf.Rd: ranger
  plot.regAbcrf.Rd: ranger
  predict.abcrf.Rd: ranger
  predict.regAbcrf.Rd: predict.ranger, ranger
  predictOOB.Rd: predict.ranger, ranger
  regAbcrf.Rd: ranger
  variableImpPlot.Rd: ranger
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  abctools-package.Rd: abc
  cov.pi.Rd: abc, postpr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  abe.Rd: coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) abess.Rd:260: Lost braces in \itemize; meant \describe ?
checkRd: (-1) abess.Rd:261: Lost braces in \itemize; meant \describe ?
checkRd: (-1) abess.Rd:262: Lost braces in \itemize; meant \describe ?
checkRd: (-1) abess.Rd:263: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coef.abesspca.Rd:16: Lost braces; missing escapes or markup?
    16 | This parameter is omitted if {sparse.type = "kpc"}.}
       |                              ^
checkRd: (-1) coef.abesspca.Rd:22: Lost braces; missing escapes or markup?
    22 | This parameter is omitted if {sparse.type = "fpc"}.}
       |                              ^
checkRd: (-1) generate.data.Rd:51: Lost braces
    51 | code{cortype = 3} denotes the constant structure,
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_ex_data.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_ex_data.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_ex_data.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_ex_data.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_results.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_results.Rd:30: Lost braces in \itemize; meant \describe ?
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   2.9Mb
    libs      1.9Mb
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    include  12.5Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) bind_tweets.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bind_tweets.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) accelimp.Rd:15: Lost braces
    15 | \item[]{...}
       |        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mice.impute.2l.zip.pmm.Rd: mice
  mice.impute.2l.zipln.Rd: mice
  mice.impute.2l.zipln.pmm.Rd: mice
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  acdFit.Rd: solnp
  plotScatterAcd.Rd: stat_smooth
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) overstallwoods.Rd:184-185: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:186-187: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:188-189: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:190-191: Lost braces in \itemize; \value handles \item{}{} directly
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  doACNE.Rd: AffymetrixCelSet, Verbose
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  makeCues.Rd: tuneR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rRegMatch.Rd: daisy, treeClust.dist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
checkRd: (-1) Ehrenfest.Rd:19: Lost braces
    19 | In this experiment there are i balls in Urn I, and remaining 2n-i balls in Urn II. Then at any instance, the probability of selecting a ball from Urn I and placing it in Urn II is i/2n, and the other way of placing a ball from Urn II to Urn I is (2n-i)/2n. At each instant we let the number i of balls in the Urn I to be the state of the system. Thus, the state space is S = { 0, 1, 2, \ldots, 2n }. Then we can pass from state i only to either of the states i-1 or i+1.
       |                                                                                                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) Ehrenfest.Rd:20: Lost braces
    20 | Here, S = {0, 1, \ldots, 2n}. 
       |           ^
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  adjustIntercept.Rd: cpglm, cpglmm, data.table
  findbars.Rd: mkRespMod, mkReTrms, nlformula, subbars
  plotRE.Rd: ggplot2, ggplot
  weights-actuaRE.Rd: cpglm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  autoprune.rd: rpart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) est_S_Plus_Plus_MethodA.Rd:31: Lost braces; missing escapes or markup?
    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
checkRd: (-1) est_S_Plus_Plus_MethodB.Rd:31: Lost braces; missing escapes or markup?
    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method B}
       |                                                          ^
checkRd: (-1) est_S_Star_Plus_MethodA.Rd:29: Lost braces; missing escapes or markup?
    29 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
checkRd: (-1) est_S_Star_Plus_MethodB.Rd:29: Lost braces; missing escapes or markup?
    29 |   \item{trt_diff}{Estimate of treatment difference for S_{*+} using Method B}
       |                                                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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"}
       |     ^
'LazyData' is specified without a 'data' directory
File 'adaptivetau/libs/x64/adaptivetau.dll':
  Found non-API call to R: 'STRING_PTR'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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}.
       |                                                                                                                                                                                                          ^
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
checkRd: (-1) SVMDECON.Rd:23: Lost braces; missing escapes or markup?
    23 | and the best result from three values of v = {0.25, 0.5, 0.75}
       |                                              ^
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AdbiConnection-class.Rd: DBIConnection-class, DBIDriver-class
  AdbiDriver-class.Rd: dbConnect, DBIDriver-class, DBIConnection-class
  AdbiResult-class.Rd: DBIResult-class, DBIObject-class,
    DBIDriver-class, DBIConnection-class
  AdbiResultArrow-class.Rd: DBIResultArrow-class, DBIResult-class,
    DBIObject-class, DBIDriver-class, DBIConnection-class
  dbConnect.Rd: DBIDriver-class, DBIConnection-class, dbConnect,
    dbDisconnect
  dbFetch.Rd: dbFetch, DBIResult-class
  dbSendQuery.Rd: dbSendQuery, dbGetQuery, DBIConnection-class, dbBind,
    DBIResult-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addScales.Rd: panel.text, xyplot, panel.refline
  panel.addScales.Rd: panel.text, panel.refline
  prepanel.trim.Rd: xyplot, prepanel.default.xyplot
  update.scaledTrellis.Rd: update.trellis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   2.9Mb
    libs   1.1Mb
checkRd: (-1) varipart.Rd:19: Lost braces
    19 | \item{type}{a character specifying the algorithm which should be used to adjust R-squared (either \code{"simulated"} or \ code{"parametric"}).}
       |                                                                                                                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  df2genind.Rd: hierarchy
  pairDist.Rd: dist.dna
  strata-methods.Rd: hierarchy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BRB.Rd: infolocs, as.ltraj
  estUD-class.Rd: SpatialPixelsDataFrame-class
  kernelbb.Rd: as.ltraj
  kernelkc.Rd: as.ltraj
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) adeoptions.Rd:21-23: Lost braces
    21 |   \code{epsilon}{  the smallest significant distance between two points
       |                 ^
checkRd: (-1) adeoptions.Rd:25-27: Lost braces
    25 |   \code{shortprint}{  logical.  Defines whether special \code{show}
       |                    ^
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    adelie   1.2Mb
    libs     4.4Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  abouheif.Rd: phylo4d-class
  adephylo-package.Rd: phylo4d-class, phylo4-class
  bullseye.Rd: phylo4-class, phylo4d-class
  distRoot.Rd: phylo4-class, phylo4d-class
  distTips.Rd: phylo4-class, phylo4d-class
  listDD.Rd: phylo4-class, phylo4d-class
  listTips.Rd: phylo4-class, phylo4d-class
  miscUtils.Rd: phylo4-class
  orthobasis.Rd: phylo4-class, phylo4d-class
  orthogram.Rd: phylo4-class, phylo4d-class
  ppca.Rd: phylo4d-class, phylo4-class
  proxTips.Rd: phylo4-class, phylo4d-class
  sp.tips.Rd: phylo4-class, phylo4d-class
  table.phylo4d.Rd: phylo4d-class
  treePart.Rd: phylo4-class, phylo4d-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ScotchWhiskey.Rd: SpatialPointsDataFrame-class, nb2listw,
    SpatialLinesDataFrame-class, dist.binary
  constr.hclust.Rd: tri2nb, nb2listw
  envspace.test.Rd: varpart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
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
       |                                            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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. 
       |                                                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  vars2chr.Rd: exprs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(admiralvaccine)
  > 
  > test_check("admiralvaccine")
  [1] "VAX01DT"
  [1] "VAX02DT"
  [1] "VAX03DT"
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 35 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-derive_vars_merged_vaccine.R:165:3'): derive_vars_merged_vaccine Test 2: Check if supp datasets merged
            properly if they exist ──
  Differences found between the objects!
  
  A summary is given below.
  
  There are columns in BASE that are not in COMPARE !!
  All rows are shown in table below
  
    ==========
     COLUMNS  
    ----------
     IDVARVAL 
    ----------
  
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 35 ]
  Error: Test failures
  Execution halted
File 'admisc/libs/x64/admisc.dll':
  Found non-API calls to R: 'ENVFLAGS', 'SET_ENVFLAGS'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  minimize.Rd: nloptr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kdfun.Rd: divc
  krfun.Rd: divc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) count_cases.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
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.
       |                                                                                                                                                                                                                                                                                              ^
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mixed.Rd: lmerTest, glmer, summary.merMod
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) estimate.affinity.matrix.Rd:31: Lost braces; missing escapes or markup?
    31 | than \code{Y}, then those variables that appear in \code{X} but no in {Y}
       |                                                                       ^
checkRd: (-1) estimate.affinity.matrix.lowrank.Rd:36: Lost braces; missing escapes or markup?
    36 | \code{Y}, then those variables that appear in \code{X} but no in {Y} should
       |                                                                  ^
checkRd: (-1) show.correlations.Rd:47: Lost braces
    47 | code{ndims} dimensions. Defaults to all dimensions unless the latter are
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) getNetworkGridLayout.Rd:6-11: Lost braces
     6 | getCoordinatesFromVertexId2<-function(AFMImage, vId) {
       |                                                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AFM.Rd: gstat, fractaldim, rgl
  AFMFractalDimensionAnalyser-getFractalDimensions.Rd: fractaldim
  AFMImageFractalDimensionMethod-class.Rd: fractaldim
  AFMImageNetworksAnalysis-class.Rd: igraph
  AFMImageVariogramAnalysis-evaluateVariogramModels-method.Rd: gstat
  displayHolesIn3D.Rd: rgl
  displayIn3D.Rd: rgl
  exportToSTL.Rd: rgl
  getCircleSpatialPoints.Rd: SpatialPoints
  putImagesFromAnalysisOnDisk.Rd: rgl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AccurateGLM-class.Rd: cv.glmnet
  coef.AccurateGLM.Rd: coef.glmnet
  predict.AccurateGLM.Rd: predict.glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package which this enhances but not available for checking: 'asreml'
Specified C++11: please drop specification unless essential
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) AEHMLE.Rd:42-45: Lost braces
    42 | \item{basehaz}{: {baseline hazard structure including baseline
       |                  ^
checkRd: (-1) AHMLE.Rd:41-43: Lost braces
    41 | \item{basehaz}{: {baseline hazard structure including baseline
       |                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addNoiseAtEventTimes.Rd: data.table
  makeContWeights.Rd: data.table
  weightPredict.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AICcmodavg-package.Rd: xtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AICc_permanova2.Rd: adonis2
  fit_models.Rd: vegdist, adonis2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) CalOptimalDecision.Rd:45: Lost braces; missing escapes or markup?
    45 | A \code{data.frame} of (1) the probability that the optimal decision for each observation being d in {0,1,...,k}, (2) expected utility of binary version of judge's decision (g_d), (3) expected utility of binary DMF recommendation, and (4) the difference between (2) and (3). If \code{include.utility.diff.mcmc = TRUE}, returns a list of such \code{data.frame} and a \code{data.frame} that includes the result for mean and quantile of \code{Utility.diff.control.mcmc} and \code{Utility.diff.treated.mcmc} across mcmc samples.
       |                                                                                                      ^
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}
       |                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AIPW.Rd: SuperLearner
  AIPW_base.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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:}
       |                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  airGRdatassim.Rd: CreateCalibOptions
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    ShinyGR   4.3Mb
    doc       3.4Mb
'LazyData' is specified without a 'data' directory
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}
       |                                                                   ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  keyword_merge.Rd: stem_strings, lemmatize_strings
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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. 
       |                          ^
checkRd: (-1) interpp.Rd:119: Lost braces
   119 |   If \code{linear} is \\code{TRUE}, linear
       |                             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) buildPhylipLineage.Rd:61: Lost braces; missing escapes or markup?
    61 |                                      names with the format {"Inferred1", "Inferred2", ...}.
       |                                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gridPlot.Rd: ggplot
  plotAbundanceCurve.Rd: ggplot
  plotDiversityCurve.Rd: ggplot
  plotDiversityTest.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.8Mb
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) APEXMS.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) APEXMS.Rd:15: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  amCluster.Rd: dynamicTreeCut, cutreeHybrid
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ASBT.Rd:36-37: Lost braces
    36 | \item{method}{Method for aggregating across categories: {"none", "max",
       |                                                         ^
checkRd: (-1) Aggregator.Rd:26: Lost braces; missing escapes or markup?
    26 | {"none", "max", "sum"}. Default: "none".}
       | ^
checkRd: (-1) DGP.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DGP.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DGP.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DGP.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OLS.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OLS.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OLS.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OLS.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
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 ?
checkRd: (-1) compare_cohorts.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_cohorts.Rd:36: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cleanse.data.frame.Rd: tbl_df
  split_by.data.frame.Rd: tbl_df
  treatment_corr.Rd: tbl_df
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  alphaci.Rd: future.apply
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.ashape3d.Rd: rgl, material3d
  surfaceNormals.Rd: material3d
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
checkRd: (-1) altopt.ic.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'metaboliteIDmapping'
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}}
       |                  ^
Specified C++11: please drop specification unless essential
File 'ambient/libs/x64/ambient.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  write.amelia.Rd: write.dta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  play.Rd: tuneR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ammiBayes.conf.plot.Rd: lattice
  ammiBayes.mean.plot.Rd: lattice
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) aMNLFA.prune.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  amExample1.Rd: allelematch
  amExample2.Rd: allelematch
  amExample3.Rd: allelematch
  amExample4.Rd: allelematch
  amExample5.Rd: allelematch
  amregtest.Rd: allelematch
  artData.Rd: amDataset, allelematch
  artRun.Rd: allelematch
  artVersion.Rd: allelematch-package
  ggSample.Rd: allelematch
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Stratiplot.Rd: xyplot
  caterpillarPlot.Rd: tolerance
  gradientDist.Rd: scores.cca, cca
  logitreg.Rd: brglm
  panel.Stratiplot.Rd: panel.grid
  plot.prcurve.Rd: scores.rda, rda
  prcurve.Rd: rda
  rankDC.Rd: rankindex
  smoothFuns.Rd: gam
  timetrack.Rd: fitted.cca, scores.cca
  varExpl.Rd: cca
  wa.Rd: tolerance, smoothCon, pcls
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
2c2
< This is vegan 2.6-6.1
---
> This is vegan 2.5-7
'LazyData' is specified without a 'data' directory
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Andromeda-class.Rd: RSQLite
  andromeda_constructor.Rd: dplyr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) EKF_1d_interp_joint.Rd:55: Lost braces; missing escapes or markup?
    55 | Prior 1x1 covariance matrix for predicting x_t from x_{t-1}.
       |                                                       ^
checkRd: (-1) EKF_interp_joint.Rd:65: Lost braces; missing escapes or markup?
    65 | Prior 2x2 covariance matrix for predicting x_t from x_{t-1}.
       |                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  make_segments.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) animate.Rd:625-627: Lost braces
   625 | group = function(...) {
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggplot_gtable.Rd: gtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following HTML validation problems:
stat_unique.html:110:1 (stat_unique.Rd:65): Warning: trimming empty <li>
stat_unique.html:109:1 (stat_unique.Rd:65): Warning: trimming empty <ul>
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  anim.save.Rd: saveGIF
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) concat.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                     ^
checkRd: (-1) concat.Rd:35: Lost braces
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                               ^
checkRd: (-1) concat.Rd:35: Lost braces
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  annotate.Rd: htmlwidgets
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    R  34.4Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  HartiganShapes.Rd: procGPA
  LloydShapes.Rd: procGPA
  archetypesBoundary.Rd: stepArchetypes, archetypes
  archetypoids.Rd: archetypes, stepArchetypes
  shapes3dShapes.Rd: shapes3d
  stepArchetypesRawData.Rd: stepArchetypes, archetypes
  stepArchetypoids.Rd: stepArchetypes, archetypes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) PS-methods.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:65-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Sim-Functions.Rd:126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:127-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:138-140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:141-143: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) gof.Rd:32: Lost braces
    32 | Assuming that the data length is \eqn{N} and the number of the parameters in the model is \eqn{p}, eqn{D} and eqn{X^2} are compared to a chi-squared distribution with \eqn{N-p} degrees of freedom.
       |                                                                                                       ^
checkRd: (-1) gof.Rd:32: Lost braces
    32 | Assuming that the data length is \eqn{N} and the number of the parameters in the model is \eqn{p}, eqn{D} and eqn{X^2} are compared to a chi-squared distribution with \eqn{N-p} degrees of freedom.
       |                                                                                                                  ^
checkRd: (-1) iccbin.Rd:23: Lost braces
    23 |   \item{m}{A vector of the numbers of successes (proportions are eqn{y = m / n}).}
       |                                                                     ^
checkRd: (-1) varbin.Rd:22: Lost braces
    22 |   \item{m}{A vector of the numbers of successes (proportions are eqn{y = m / n}).}
       |                                                                     ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  apcluster-methods.Rd: dgTMatrix-class, Matrix-class
  conversions.Rd: dgTMatrix-class, sparseMatrix-class, Matrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) apc.indiv.est.model.Rd:142: Lost braces
   142 | For model testing: \code{\link{apc.indiv.model.table}}, code{\link{apc.indiv.compare.direct}}, \code{\link{waldtest}}, \code{\link{linearHypothesis}}
       |                                                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  apc.indiv.compare.direct.Rd: plm
  apc.indiv.est.model.Rd: plm, svyglm, waldtest, linearHypothesis
  apc.indiv.model.table.Rd: plm, waldtest, linearHypothesis
  apc.plot.data.level.Rd: levelplot, lattice
  apc.plot.fit.residuals.Rd: levelplot, lattice
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  multidna2alignment.Rd: as.alignment
  multidna2genind.Rd: genind-class, DNAbin2genind
  multidna2multiphyDat.Rd: DNAbin2genind
  plot-multidna-method.Rd: image.DNAbin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) aphylo-class.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
checkRd: (-1) raphylo.Rd:33: Lost braces; missing escapes or markup?
    33 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
checkRd: (-1) sim_fun_on_tree.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  aphylo-class.Rd: Ntip, Nnode
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following HTML validation problems:
mislabel.html:25:1 (mislabel.Rd:20): Warning: trimming empty <p>
raphylo.html:25:1 (raphylo.Rd:57): Warning: trimming empty <p>
sim_fun_on_tree.html:25:1 (sim_fun_on_tree.Rd:50): Warning: trimming empty <p>
checkRd: (-1) predict_adjust.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iconplot.Rd:172: Lost braces
   172 |     the height of the area containing the panels and a margin of size code{100 * 0.1} 
       |                                                                           ^
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    documents     2.4Mb
    libs          1.1Mb
    screenshots   1.6Mb
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AQEval.data.Rd: openair, importAURN, importKCL
  find.breaks.Rd: breakpoints
  isolate.signal.Rd: mgcv, gam
  quantify.breaks.Rd: timeAverage, breakpoints, segmented
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   1.6Mb
    doc    1.8Mb
checkRd: (-1) calcEto.Rd:63-64: Lost braces
    63 | \code{ET.Daily:} {daily estimations of reference crop evapotranspiration
       |                  ^
checkRd: (-1) calcEto.Rd:66-67: Lost braces
    66 | \code{Ra.Daily:} {daily estimations of extraterristrial radiation
       |                  ^
checkRd: (-1) calcEto.Rd:69-70: Lost braces
    69 | \code{Slope.Daily:} {daily estimations of slope of vapour pressure curve
       |                     ^
checkRd: (-1) calcEto.Rd:72: Lost braces; missing escapes or markup?
    72 | \code{ET.type:} {type of the estimation obtained}
       |                 ^
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                              ^
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.InfDiag.Rd: ggplot
  plot.Rd: ggplot
  plot.residARpCRM.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'arcgisplaces/libs/x64/arcgisplaces.dll':
  Found non-API calls to R: 'PRCODE', 'PRENV'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Package suggested but not available for checking: 'arcgisbinding'
File 'arcgisutils/libs/x64/arcgisutils.dll':
  Found non-API calls to R: 'PRCODE', 'PRENV'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Package suggested but not available for checking: 'ArchaeoData'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ActivityEvents-class.Rd: TimeSeries-class
  ArchaeoPhases-package.Rd: TimeScale-class
  CumulativeEvents-class.Rd: TimeSeries-class
  activity.Rd: TimeScale-class
  as_events.Rd: TimeScale-class
  as_phases.Rd: TimeScale-class
  bury.Rd: TimeScale-class
  data.frame.Rd: TimeScale-class
  interval_credible.Rd: TimeScale-class
  interval_hdr.Rd: TimeScale-class
  occurrence.Rd: TimeScale-class
  plot_events.Rd: TimeScale-class
  plot_phases.Rd: TimeScale-class
  read_bcal.Rd: TimeScale-class
  read_chronomodel.Rd: TimeScale-class
  read_oxcal.Rd: TimeScale-class
  summary.Rd: TimeScale-class
  tempo.Rd: TimeScale-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.archetypes.Rd: parameters
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addHooksToPrintGitHub.Rd: Repository, archivist-package, alink,
    addHooksToPrint
  archive.Rd: Repository, saveToLocalRepo, md5hash, alink, aoptions
  archivist-github-integration.Rd: Repository
  createGitHubRepo.Rd: createLocalRepo, Repository, oauth2.0_token,
    Tags
  deleteGitHubRepo.Rd: Repository, oauth2.0_token
  pushGitHubRepo.Rd: Repository
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Source(s) listed in 'build/vignette.rds' but not in package:
  'accessibility.Rmd'
  'caching.Rmd'
  'chaining.Rmd'
  'posts.Rmd'
Specified C++11: please drop specification unless essential
checkRd: (-1) estimate_t0.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_t0.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_t0.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:75: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  prune.Rd: rules
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       | ^
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       |                                 ^
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       |                                                ^
checkRd: (-1) uecm.Rd:76: Lost braces; missing escapes or markup?
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |   ^
checkRd: (-1) uecm.Rd:76: Lost braces; missing escapes or markup?
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                  ^
checkRd: (-1) uecm.Rd:76-77: Lost braces
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                                             ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  normGeometry.Rd: st_drivers
  normTable.Rd: reorganise
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'area/libs/x64/area.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  arfima.Rd: TrenchMean
  logLik.arfima.Rd: ltsa
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  argonDropNavItem.Rd: argonIcon
  argonInfoCard.Rd: argonIcon
  argonSidebarItem.Rd: argonIcon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.2Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SmoothMultiarrayModel.Rd: ChromosomalModel,
    CopyNumberSegmentationModel
  byPath.AffymetrixFileSet.Rd: GenericDataFile
  calculateBaseline.ChipEffectSet.Rd: getAverageFile
  doCRMAv1.Rd: Verbose
  doCRMAv2.Rd: Verbose
  doFIRMA.Rd: Verbose
  doGCRMA.Rd: Verbose
  doRMA.Rd: Verbose
  justRMA.Rd: Verbose
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  writeDataFrame.AromaUnitSignalBinaryFile.Rd: TabularTextFile
  writeDataFrame.AromaUnitSignalBinarySet.Rd: TabularTextFileSet
  writeDataFrame.AromaUnitTabularBinaryFile.Rd: TabularTextFile
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 43.8Mb
  sub-directories of 1Mb or more:
    R      4.3Mb
    libs  38.9Mb
File 'arrow/libs/x64/arrow.dll':
  Found non-API calls to R: 'LEVELS', 'Rf_findVarInFrame3',
    'SETLENGTH', 'SET_GROWABLE_BIT', 'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  artfima-package.Rd: ltsa
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  anova.art.Rd: Anova
  art.Rd: lmer
  art.con.Rd: contrast, summary.emmGrid, lmer, emmeans
  artlm.Rd: lmer, merMod
  artlm.con.Rd: lmer, merMod
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  is.superset.Rd: ngCMatrix-class
  itemMatrix-class.Rd: ngCMatrix-class
  tidLists-class.Rd: ngCMatrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'arules/libs/x64/arules.dll':
  Found non-API call to R: 'Rf_NonNullStringMatch'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    bin   11.3Mb
    misc   2.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sequencerules-class.Rd: is.redundant
  sequences-class.Rd: tidLists-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'arulesSequences/libs/x64/arulesSequences.dll':
  Found non-API call to R: 'Rf_NonNullStringMatch'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bvn.plot.rd: wireframe
  plot.pairw.rd: multcompLetters
  pseudo.v.Rd: empinf, boot
  qq.Plot.Rd: boot, envelope
  r.pb.rd: corr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  meldCD.Rd: binomMeld.test
  signTest.Rd: mcnemarExactDP, binom.exact
  wmwTest.Rd: wilcox_test
  wsrTest.Rd: wilcoxsign_test
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
checkRd: (-1) convertAlgoPerfToWideFormat.Rd:28: Lost braces
    28 | code{NA} means the performance value is not available, possibly because the algorithm run was aborted.
       |     ^
checkRd: (-1) parseASScenario.Rd:40: Lost braces
    40 |   code{NA} means the cost is not available, possibly because the feature computation was aborted.
       |       ^
checkRd: (-1) parseASScenario.Rd:47: Lost braces
    47 |   code{NA} means the cost is not available, possibly because the feature computation was aborted.
       |       ^
checkRd: (-1) parseASScenario.Rd:55: Lost braces
    55 |   code{NA} means the feature is not available, possibly because the feature computation was aborted.
       |       ^
checkRd: (-1) parseASScenario.Rd:62: Lost braces
    62 |   code{NA} means the feature is not available, possibly because the feature computation was aborted.
       |       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  createCVSplits.Rd: write.arff
  summarizeLlamaExps.Rd: Registry, reduceResultsList
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  alignCross.Rd: subset.cross
  heatMap.Rd: plotRF
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package which this enhances but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                    ^
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                                                                                                                 ^
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                                                                                                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.AssetPricing.Rd:199-200: Lost braces
   199 |   yakka. (Note that \code{flap} stands for dQuote{function list
       |                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nmax3.Rd: pmvnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'asteRiskData'
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.0Mb
checkRd: (-1) readOEM.Rd:34: Lost braces
    34 |   always, the identifier has the format YYYY-NNNP{PP}, where YYYY is the year
       |                                                  ^
checkRd: (-1) readOEM.Rd:36: Lost braces
    36 |   during year YYYY and P{PP} is a part specifier comprising 1 to 3 capital letters
       |                         ^
checkRd: (-1) readOEM.Rd:74-75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readOEM.Rd:76-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readOEM.Rd:80-86: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hpop.Rd: ode
  readGLONASSNavigationRINEX.Rd: nanotime
  readGPSNavigationRINEX.Rd: nanotime
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pickle.Rd: trust
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  confAdjust.Rd: spec.mtm
  lowspec.Rd: rfbaseline, spec.mtm
  mtm.Rd: spec.mtm
  mtmAR.Rd: spec.mtm
  mtmML96.Rd: spec.mtm
  mtmPL.Rd: spec.mtm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AsyK-package.Rd: mse
  Laplace.Rd: mse
  RIG.Rd: mse
  plot.Laplace.Rd: mse
  plot.RIG.Rd: mse
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ATA.BoxCoxAttr.Rd: BoxCox, InvBoxCox, BoxCox.lambda
  ATA.Decomposition.Rd: stlplus
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ataCoKriging.Rd:52: Lost braces; missing escapes or markup?
    52 | only one contrained condition for all points and all variables, \\sum_{i=1}^n\\lambda_i +\\sum_{j=1}^m\\beta_j =1, assuming expected means of variables known and constant with the study area.
       |                                                                       ^
checkRd: (-1) ataCoKriging.Rd:52: Lost braces; missing escapes or markup?
    52 | only one contrained condition for all points and all variables, \\sum_{i=1}^n\\lambda_i +\\sum_{j=1}^m\\beta_j =1, assuming expected means of variables known and constant with the study area.
       |                                                                                                ^
checkRd: (-1) simulation_dgp.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{x_discrete}{TRUE if the distribution of the covariate is uniform on {-3.0, -2.9, ..., 3.0} and
       |                                                                           ^
checkRd: (-1) simulation_dgp.Rd:23: Lost braces
    23 | \item{att_oracle}{the sample analog of E[D{Y(1) - Y(0)}|D=1]}
       |                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) audioSample.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) audioSample.Rd:21: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  auk_country.Rd: countrycode
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_candidate_covariates.Rd:50: Lost braces
    50 | \item \code{covars_data}   {The \code{data.frame} that is filtered out of \code{df} with only the selected \code{covars}}. The values of the
       |                            ^
checkRd: (-1) get_candidate_covariates.Rd:53: Lost braces
    53 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
checkRd: (-1) get_prioritised_covariates.Rd:40: Lost braces
    40 | \item \code{multiplicative_bias}{The absolute log of the multiplicative bias term for each of the auto-selected prioritised covariates}
       |                                 ^
checkRd: (-1) get_recurrence_covariates.Rd:34: Lost braces
    34 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rmd_to_forestharp.Rd: get_source_expressions
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Autoplotprotein-package.Rd:27: Lost braces
    27 | code{\link{help}}
       |     ^
checkRd: (-1) Autoplotprotein.Rd:25: Lost braces
    25 | code{\link{help}}
       |     ^
checkRd: (-1) data.Rd:22: Lost braces
    22 | code{\link{help}}
       |     ^
checkRd: (-1) domain_data.Rd:29: Lost braces
    29 | code{\link{help}}
       |     ^
checkRd: (-1) length_data.Rd:32: Lost braces
    32 | code{\link{help}}
       |     ^
checkRd: (-1) plotdomain.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotmutagensis.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotsite.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) site_data.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
Specified C++11: please drop specification unless essential
'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}.}
       |                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) avar_mo_cpp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_mo_cpp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_mo_cpp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  az_cognitive_service.Rd: az_resource_group
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  aci.Rd: az_resource_group
  acr.Rd: az_resource_group
  aks.Rd: az_resource_group
  create_aci.Rd: az_resource
  create_acr.Rd: az_resource
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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/".}
       |                                                                                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  call_batch_endpoint.Rd: AzureToken
  call_graph.Rd: AzureToken
  graph_login.Rd: get_azure_token
  ms_graph.Rd: get_azure_token
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  az_key_vault.Rd: az_resource_group
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AzureKusto.Rd: dbReadTable, dbWriteTable, dbGetQuery, dbSendStatement
  DBI_query.Rd: dbConnect, dbReadTable, dbWriteTable
  DBI_table.Rd: dbConnect
  az_kusto.Rd: az_resource_group
  copy_to.kusto_database_endpoint.Rd: collect
  kusto-DBI.Rd: dbConnect, dbDisconnect, dbCanConnect, dbExistsTable,
    dbCreateTable, dbRemoveTable, dbReadTable, dbWriteTable,
    dbGetQuery, dbSendQuery, dbFetch, dbSendStatement, dbExecute,
    dbListFields, dbColumnInfo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  queue.Rd: storage_endpoint
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  az_resource_group.Rd: AzureToken
  az_rm.Rd: AzureToken
  az_subscription.Rd: AzureToken
  azure_login.Rd: AzureToken
  call_azure.Rd: AzureToken
  utils.Rd: AzureToken
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  az_storage.Rd: az_resource_group
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  backbone.suggest.Rd: Matrix, igraph
  disparity.Rd: Matrix, igraph
  fdsm.Rd: Matrix, igraph
  fixedcol.Rd: Matrix, igraph
  fixedfill.Rd: Matrix, igraph
  fixedrow.Rd: Matrix, igraph
  global.Rd: Matrix, igraph
  lans.Rd: Matrix, igraph
  mlf.Rd: Matrix, igraph
  osdsm.Rd: Matrix, igraph
  sdsm.Rd: Matrix, igraph
  sparsify.Rd: Matrix, igraph
  sparsify.with.geometric.Rd: Matrix, igraph
  sparsify.with.gspar.Rd: Matrix, igraph
  sparsify.with.hypergeometric.Rd: Matrix, igraph
  sparsify.with.jaccard.Rd: Matrix, igraph
  sparsify.with.localdegree.Rd: Matrix, igraph
  sparsify.with.lspar.Rd: Matrix, igraph
  sparsify.with.meetmin.Rd: Matrix, igraph
  sparsify.with.quadrilateral.Rd: Matrix, igraph
  sparsify.with.simmelian.Rd: Matrix, igraph
  sparsify.with.skeleton.Rd: Matrix, igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BACprior.lm.Rd: regsubsets
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  baf.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  forest_plot.Rd: forestplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   3.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fit_lgmr.Rd: stan_model
  infer_data_and_decision_model.Rd: sampling, tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) contour.angmcmc.Rd:48: Lost braces; missing escapes or markup?
    48 | Ignored if {show.data == FALSE}.}
       |            ^
checkRd: (-1) contour.angmcmc.Rd:51: Lost braces; missing escapes or markup?
    51 | Ignored if {show.data == FALSE}.}
       |            ^
checkRd: (-1) fit_incremental_angmix.Rd:104: Lost braces; missing escapes or markup?
   104 | \item{alpha}{significance level used in the test H_{0K}: expected log predictive density (elpd) for the fitted model with  K components >= elpd for the fitted model
       |                                                    ^
checkRd: (-1) fit_incremental_angmix.Rd:148: Lost braces; missing escapes or markup?
   148 | H_{0K}: expected log predictive density (elpd) for the fitted model with  K components >= elpd for the fitted model
       |   ^
checkRd: (-1) fit_incremental_angmix.Rd:163: Lost braces; missing escapes or markup?
   163 | The incremental fitting stops if  H_{0K} cannot be rejected
       |                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bridge_sampler.angmcmc.Rd: bridge_sampler
  circ_varcor_model.Rd: sobol
  densityplot.angmcmc.Rd: as.mcmc.list
  fit_angmix.Rd: future_lapply
  fit_incremental_angmix.Rd: bridge_sampler
  fix_label.Rd: label.switching
  loo.angmcmc.Rd: waic, loo
  rvmcos.Rd: sobol
  rwnorm2.Rd: rmvnorm
  rwnorm2mix.Rd: rmvnorm
  waic.angmcmc.Rd: waic
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following HTML validation problems:
rwnorm2.html:111:126 (rwnorm2.Rd:60): Warning: trimming empty <code>
rwnorm2.html:115:73 (rwnorm2.Rd:61): Warning: trimming empty <code>
rwnorm2.html:115:146 (rwnorm2.Rd:61): Warning: trimming empty <code>
rwnorm2.html:115:211 (rwnorm2.Rd:61): Warning: trimming empty <code>
rwnorm2.html:119:126 (rwnorm2.Rd:62): Warning: trimming empty <code>
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bamlss-package.Rd: mgcv
  bamlss.Rd: mgcv
  bamlss.frame.Rd: mgcv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'bamlss/libs/x64/bamlss.dll':
  Found non-API call to R: 'SET_TYPEOF'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cohorts.Rd: rich.colors
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'fdpbandsdata'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BANOVA.run.Rd: rstan
  pairs.BANOVA.Rd: rstan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getBanterModel.Rd: randomForest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) barcoding.spe.identify2.Rd:27: Lost braces; missing escapes or markup?
    27 | read.dna() from package {ape} was used to obtain DNAbin object for unaligned non-coding barcodes.
       |                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bartc.Rd: rbart_vi, bart2, dbartsData
  plot.Rd: rpart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.3Mb
File 'base64enc/libs/x64/base64enc.dll':
  Found non-API call to R: 'SETLENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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}
       |                           ^
'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:
    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; }
       |                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BasicTable.Rd: R6Class
  FlexTableRenderer.Rd: R6Class
  FlexTableStyle.Rd: R6Class
  FlexTableStyles.Rd: R6Class
  TableCell.Rd: R6Class
  TableCellRanges.Rd: R6Class
  TableCells.Rd: R6Class
  TableHtmlRenderer.Rd: R6Class
  TableOpenXlsxRenderer.Rd: R6Class
  TableOpenXlsxStyle.Rd: R6Class
  TableOpenXlsxStyles.Rd: R6Class
  TableStyle.Rd: R6Class
  TableStyles.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) nfiMetrics.Rd:23: Lost braces
    23 | code{(4)} the number of
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  readNFI.Rd: read.dbf, RODBC, mdb.get
  urlToTemp.Rd: timeout
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bubbleplot.Rd: scale_colour_gradient2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'BAS/libs/x64/BAS.dll':
  Found non-API call to R: 'SETLENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
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.}
       |                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getExperimentParts.Rd: Job
  reduceResultsExperimentsParallel.Rd: batchMapQuick
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
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
       |                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  JoinTables.Rd: data.table
  Worker.Rd: R6Class
  addExperiments.Rd: data.table
  batchMap.Rd: data.table
  batchMapResults.Rd: data.table
  batchReduce.Rd: data.table
  estimateRuntimes.Rd: data.table
  findJobs.Rd: data.table
  getErrorMessages.Rd: data.table
  getJobTable.Rd: data.table
  grepLogs.Rd: data.table
  killJobs.Rd: data.table
  removeExperiments.Rd: data.table
  resetJobs.Rd: data.table
  runHook.Rd: data.table
  submitJobs.Rd: data.table
  summarizeExperiments.Rd: data.table
  unwrap.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.2Mb
GNU make is a SystemRequirements.
checkRd: (-1) plotDistributions.Rd:32: Lost braces
    32 | plot{...} functions are generated programmatically so the function calls in
       |     ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pwr_curve.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotPost.Rd: hdi
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.bayescomm.Rd: plot.mcmc
  summary.bayescomm.Rd: summary.mcmc
  window.bayescomm.Rd: window.mcmc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  binomialBACT.Rd: bdpnormal
  binomial_analysis.Rd: bdpnormal
  historical_binomial.Rd: bdpnormal
  historical_normal.Rd: bdpnormal
  historical_survival.Rd: bdpnormal
  normalBACT.Rd: bdpnormal
  normal_analysis.Rd: bdpnormal
  survivalBACT.Rd: bdpnormal
  survival_analysis.Rd: bdpnormal
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) bayesDccGarch.Rd:91: Lost braces; missing escapes or markup?
    91 | \item{$H_n1 }{ Bayesian prediction of volatilities and co-volatilities for y_{n+1}.}
       |                                                                              ^
checkRd: (-1) bayesDccGarch.Rd:92: Lost braces; missing escapes or markup?
    92 | \item{$R_n1 }{ Bayesian prediction of coditional correlation for y_{n+1}.}
       |                                                                    ^
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   5.5Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) GroupSingleVoxelFETS.Rd:53: Lost braces
    53 | online trajectories related to the state parameter, the simulated BOLD responses, \mjseqn{\hat{Y}}{ascii}.
       |                                                                                                   ^
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.1Mb
    libs      1.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc   10.8Mb
    libs   1.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  id_activations.posterior.Rd: excursions.inla
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Holt.Rd: auto.arima
  Hw.Rd: auto.arima
  LocalLevel.Rd: auto.arima
  autoplot.ts.Rd: geom_forecast, fortify
  forecast.varstan.Rd: forecast.ts, ets, stlf
  fourier.Rd: seasonaldummy
  garch.Rd: auto.arima
  loo.varstan.Rd: psis, pareto-k-diagnostic, loo_compare
  ssm.Rd: auto.arima
  stan_Holt.Rd: auto.arima
  stan_Hw.Rd: auto.arima
  stan_LocalLevel.Rd: auto.arima
  stan_garch.Rd: auto.arima
  stan_ssm.Rd: auto.arima
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  loo_bgam.Rd: pareto-k-diagnostic, psis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
Found the following HTML validation problems:
getSamples.html:74:1 (getSamples.Rd:35): Warning: trimming empty <h3>
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
GNU make is a SystemRequirements.
checkRd: (-1) gMLE.bb.Rd:18: Lost braces
    18 |   \item{optim.method}{optimization method in \code{optim()}{stats}.}
       |                                                            ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) bma.bx.cy.Rd:69: Lost braces
    69 | the initial values for parameters in models. For example, inits<-function(){list(alpha=0,beta=0,c=0,var1=0.5,r=1,lamda=0.01)}.
       |                                                                            ^
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    help   1.8Mb
    libs   3.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) DE.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DE.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DE.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DE.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.trajectories.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.trajectories.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.trajectories.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.trajectories.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.trajectories.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:34: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.bayeslm.fit.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{X         }{ If call \code{bayeslm} with matrices input \code{x} and {y} but not formula, pass new matrix to predict here. See example for details.}
       |                                                                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hs_gibbs.Rd: summary.mcmc
  summary.bayeslm.fit.Rd: summary.mcmc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LN_hierarchical.Rd: lmer, mcmc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.7Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  convolve.Rd: funnel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) plot-traj.Rd:71: Lost braces; missing escapes or markup?
    71 | the plots are saved into directory {sim.dir}/predictions/migTrajectories.}
       |                                    ^
checkRd: (-1) insert_NAs.Rd:22: Lost braces; missing escapes or markup?
    22 | A data frame where new rows have been inserted to regularize the \code{date} column. This results in values provided for \code{id}, \code{date}, and {dt} while inserting NAs for all other columns. Additionally, observations with duplicate date-times are removed.
       |                                                                                                                                                      ^
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    help   6.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
    doc    1.0Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pull_brmsfit.Rd: brmsfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   3.8Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MCMC-combos.Rd: posterior
  MCMC-diagnostics.Rd: posterior
  MCMC-distributions.Rd: posterior
  MCMC-intervals.Rd: posterior
  MCMC-overview.Rd: posterior
  MCMC-parcoord.Rd: posterior
  MCMC-recover.Rd: posterior
  MCMC-scatterplots.Rd: posterior, ggtitle
  MCMC-traces.Rd: posterior
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  age.specific.migration.Rd: wpp2019
  pop.aggregate.Rd: bayesLife, bayesTFR
  pop.predict.subnat.Rd: bayesTFR, convert.tfr.trajectories
  predict.pop.Rd: bayesLife, convert.e0.trajectories, bayesTFR,
    convert.tfr.trajectories
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.2Mb
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  stan.Rd: stan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AgeC14_Computation.Rd: rjags
  AgeS_Computation.Rd: rjags, runjags
  Age_Computation.Rd: jags.model, rjags
  Age_OSLC14.Rd: rjags, runjags
  Generate_DataFile-deprecated.Rd: read_BIN2R, Luminescence
  Generate_DataFile_MG-deprecated.Rd: read_BIN2R
  Model_Age.Rd: rjags
  Model_AgeC14.Rd: rjags
  Model_AgeS.Rd: rjags
  Model_Palaeodose.Rd: rjags
  Palaeodose_Computation.Rd: jags.model, rjags
  create_DataFile.Rd: RLum.Analysis-class
  plot_MCMC.Rd: rjags
  plot_Scatterplots.Rd: rjags
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) runUI.Rd:11: Lost braces
    11 | Runs a \bold{Shiny} application. This function normally does not return; interrupt bold{R} to stop the application (usually by pressing Ctrl+C or Esc).
       |                                                                                        ^
'LazyData' is specified without a 'data' directory
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 ?
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  c3mtc.Rd: c3
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   1.4Mb
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
       |                                                                                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bcfraildv.Rd: bcfrailph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  shrgamsp.Rd: coxph
  simstdybcf.Rd: coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BchronDensity.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronRSL.Rd:34-41: Lost braces
    34 | itemize{
       |        ^
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BchronDensityFast.Rd: densityMclust
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bcmarg.Rd: gls
  summary.bcmmrm.Rd: glsObject
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) WindowSweep.Rd:32: Lost braces
    32 | `code{\link{GetVT}}`.   Otherwise, any column (e.g. \code{"Depth"}) in the 
       |      ^
checkRd: (-1) WindowSweep.Rd:36: Lost braces
    36 | \code{T.mid}  from the output of the `code{\link{GetVT}}`.}
       |                                           ^
Package suggested but not available for checking: 'BRugs'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) gene_s.Rd:17: Lost braces; missing escapes or markup?
    17 | giving the virus access to the cell and thus facilitating the COVID-19 disease. The gene sequence is mapped to the alphabet {0,1,2,3} via the obvious map A->0, C->1, G->2, T->3.
       |                                                                                                                             ^
checkRd: (-1) sars_cov_2.Rd:16: Lost braces; missing escapes or markup?
    16 | It consists of n = 29903 base pairs. The gene sequence is mapped to the alphabet {0,1,2,3} via the obvious map A->0, C->1, G->2, T->3.
       |                                                                                  ^
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) bde.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:56: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.graph.Rd: plot.igraph
  plot.sim.Rd: plot.igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gettaxo.Rd: taxize
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  default_params_doc.Rd: check_rename_fun
  remove_beastier_folder.Rd: beautier, remove_beautier_folder
  rename_beast2_options_filenames.Rd: check_rename_fun
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bedr.plot.region.Rd: venn.diagram
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CIBER.Rd: ggplot2, biAxisDiamondPlot, diamondPlot, gtable
  determinantStructure.Rd: data.tree
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  behavr.Rd: data.table
  bin_apply.Rd: data.table
  meta.Rd: data.table
  rejoin.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sfa.Rd: ucminf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  press.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 Rd file(s) with Rd \link{} targets missing package
anchors:
  generate_model_data.Rd: tibble
  kit_summary_table.Rd: stanfit
  plot_kit_use.Rd: stanfit, ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
checkRd: (-1) sockeye.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sockeye.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:14: Lost braces in \itemize; meant \describe ?
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  l2array.Rd: abind
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) gen.data.Rd:42: Lost braces
    42 | code{cortype = 2} denotes the constant structure, where the \eqn{(i,j)} entry of covariance
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  functional.betapart.core.Rd: convhulln
  functional.betapart.core.pairwise.Rd: convhulln
  inter_geom.Rd: intersectn
  qhull.opt.Rd: convhulln
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  betategarch-package.Rd: zoo
  tegarchSim.Rd: zoo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Malformed Title field: should not end in a period.
checkRd: (-1) BETSsearch.Rd:56: Lost braces
    56 |        \item{To exclude whole expressions from the search, surround them with code{' '} and insert a \code{~} before each of them.
       |                                                                                   ^
checkRd: (-1) dummy.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{date}{a \code{list}. The periods for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                               ^
checkRd: (-1) dummy.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{from}{An \code{integer vector} The starting period of a sequence of perids for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                                                                         ^
checkRd: (-1) dummy.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{to}{The ending period of a sequence of perids for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                                            ^
'LazyData' is specified without a 'data' directory
788a789
> 
809a811
> 
922a925
> 
943a947
>
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CombinePolygons.Rd: st_union
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) bggCollection.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggCollection.Rd:65-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggCollection.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggCollection.Rd:70-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggCollection.Rd:74-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggCollection.Rd:77-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggGames.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggGames.Rd:70-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggSearch.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggSearch.Rd:68-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggSearch.Rd:72-73: Lost braces in \itemize; meant \describe ?
Running examples in 'bggAnalytics-Ex.R' failed
The error most likely occurred in:

> ### Name: bgg_merge
> ### Title: Merge data from two bggAPI objects
> ### Aliases: bgg_merge
> 
> ### ** Examples
> 
> 
> sr <- bggSearch$new("Terraforming Mars")
> gm <- bggGames$new(sr$ids)
Warning in open.connection(x, "rb") :
  cannot open URL 'https://boardgamegeek.com/xmlapi2/thing?id=420095,167791,380299,401513,328871,371070,358738,358739,358741,358740,381143,376868,344634,376937,322281,265081,395612,339849,241497,311247,312319,332774,419696,255681,370074,400568,375783,296298,346129,377179,218127,408591,265083,265084,364339,401114,406019,358525,352525,406001,230241,247030,387809,381423,230123,202825,226297,416029,390472,422435,365385,296108,380939,273473,279345,359145,365384,231965,254538,379201,326379&stats=1': HTTP status was '400 Bad Request'
Error in open.connection(x, "rb") : 
  cannot open the connection to 'https://boardgamegeek.com/xmlapi2/thing?id=420095,167791,380299,401513,328871,371070,358738,358739,358741,358740,381143,376868,344634,376937,322281,265081,395612,339849,241497,311247,312319,332774,419696,255681,370074,400568,375783,296298,346129,377179,218127,408591,265083,265084,364339,401114,406019,358525,352525,406001,230241,247030,387809,381423,230123,202825,226297,416029,390472,422435,365385,296108,380939,273473,279345,359145,365384,231965,254538,379201,326379&stats=1'
Calls: <Anonymous> ... read_xml.character -> read_xml.connection -> open -> open.connection
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   1.1Mb
    libs   1.5Mb
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) sp_bgsmtr.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{c.star}{The threshold for computing posterior tail probabilities p_{ij} for Bayesian FDR as defined in Section 3.2 of  Song, Ge et al.(2019). If not specified the default is to set this threshold as the minimum posterior standard deviation, where the minimum is taken over all regression coefficients in the model.}
       |                                                                          ^
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bhm-package.Rd: coxph, survival
  bhm.Rd: coxph
  brm.Rd: coxph
  mpl.Rd: coxph
  resboot.Rd: coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 149.2Mb
  sub-directories of 1Mb or more:
    include  148.1Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) module_calibrationfile_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_correctedplots_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_correctedstats_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_fileupload_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_info_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_log_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_modelselection_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_plotting_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_results_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_settings_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_statistics_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  detect_keys.Rd: read_rmd
  doi2bib.Rd: cr_cn
  reflist.Rd: write_rmd, render_rmd
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  diagnosticTest.Rd: additivityTests
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}.
       |                                                                                                                                                                                                                                                                                  ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'ffbase'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  setupX.Rd: cv.ncvreg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++14: please drop specification unless essential
checkRd: (-1) bdm.ptsne.Rd:47: Lost braces; missing escapes or markup?
    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                         ^
checkRd: (-1) bdm.ptsne.Rd:47: Lost braces; missing escapes or markup?
    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                                                                                   ^
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
File 'bignum/libs/x64/bignum.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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. }
       |                                                                                                                                                                                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DBI.Rd: DBIObject-class, DBIDriver-class, DBIConnection-class,
    DBIResult-class
  bigquery.Rd: DBIDriver-class, DBIConnection-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'bigrquery/libs/x64/bigrquery.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DBI.Rd: DBIResult-class, DBIConnection-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LDpred2.Rd: SFBM-class, nb_cores
  SCT.Rd: FBM.code256-class, nb_cores, big_spLogReg, big_spLinReg
  bed_MAF.Rd: nb_cores
  bed_counts.Rd: nb_cores
  bed_cprodVec.Rd: nb_cores
  bed_prodVec.Rd: nb_cores
  bed_projectPCA.Rd: as_scaling_fun, nb_cores
  bed_projectSelfPCA.Rd: nb_cores
  bed_randomSVD.Rd: nb_cores
  bed_scaleBinom.Rd: nb_cores
  bed_tcrossprodSelf.Rd: as_scaling_fun
  bigSNP-class.Rd: FBM.code256-class
  bigsnpr-package.Rd: FBM.code256-class, nb_cores
  snp_MAF.Rd: FBM.code256-class, nb_cores
  snp_MAX3.Rd: FBM.code256-class
  snp_PRS.Rd: FBM.code256-class, big_univLinReg, big_univLogReg
  snp_asGeneticPos.Rd: nb_cores
  snp_autoSVD.Rd: FBM.code256-class, as_scaling_fun, nb_cores
  snp_beagleImpute.Rd: nb_cores
  snp_clumping.Rd: nb_cores, FBM.code256-class
  snp_cor.Rd: FBM.code256-class, nb_cores
  snp_fastImpute.Rd: FBM.code256-class, nb_cores, FBM
  snp_fastImputeSimple.Rd: FBM.code256-class, nb_cores
  snp_gc.Rd: big_univLinReg, big_univLogReg
  snp_lassosum2.Rd: SFBM-class, nb_cores
  snp_ld_scores.Rd: FBM.code256-class, nb_cores
  snp_ldsc.Rd: nb_cores, SFBM-class
  snp_manhattan.Rd: big_univLinReg, big_univLogReg
  snp_pcadapt.Rd: FBM.code256-class, nb_cores
  snp_plinkIBDQC.Rd: nb_cores
  snp_plinkKINGQC.Rd: nb_cores
  snp_prodBGEN.Rd: nb_cores
  snp_qq.Rd: big_univLinReg, big_univLogReg
  snp_readBGEN.Rd: nb_cores
  snp_readBed.Rd: nb_cores
  snp_simuPheno.Rd: FBM.code256-class, nb_cores
  snp_split.Rd: FBM.code256-class, foreach, nb_cores
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following HTML validation problems:
snp_ldsc.html:134:1 (snp_ldsc.Rd:74): Warning: trimming empty <dt>
Specified C++11: please drop specification unless essential
checkRd: (-1) FBM-class.Rd:97: Lost braces; missing escapes or markup?
    97 | to be used by package {bigmemory}.
       |                       ^
checkRd: (-1) FBM-class.Rd:99: Lost braces; missing escapes or markup?
    99 | to be used by package {bigmemory}.
       |                       ^
checkRd: (-1) big_read.Rd:57: Lost braces; missing escapes or markup?
    57 | Read a file as a Filebacked Big Matrix by using package {bigreadr}.
       |                                                         ^
Specified C++11: please drop specification unless essential
checkRd: (-1) VARXFit.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXLagCons.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXLagCons.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
File 'Binarize/libs/x64/Binarize.dll':
  Found non-API call to R: 'SET_TYPEOF'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  compute.sigma.star.Rd: nearPD, phi2tetra, is.positive.definite
  jointly.generate.binary.normal.Rd: nearPD, rmvnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) aa.index.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:15: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:16: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:17: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:18: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:20-23: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) example.data.Rd:33-37: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) example.data.Rd:38-39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) example.data.Rd:40-41: Lost braces in \enumerate; meant \describe ?
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  read_audio.Rd: Wave
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) ringApply.Rd:9: Lost braces; missing escapes or markup?
     9 |   \item{lv}{{numeric} position, or {character} name, of an
       |                                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  anova.modelFrame.Rd: anova.lme
  frametoLme.Rd: lme, nlme, groupedData
  lmeForm.Rd: groupedData
  modelFrame.Rd: lme, nlme, groupedData
  muleMan.Rd: groupedData, mgram, ecodist
  shiftFrame.Rd: groupedData
  summary.modelFrame.Rd: summary.lme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bilat.Rd: intersect.owin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DynamicGrowth.Rd: geom_line
  FitDynamicGrowth.Rd: geom_line, geom_point
  FitDynamicGrowthMCMC.Rd: geom_line, geom_point
  FitIsoGrowth.Rd: modFit, geom_line, geom_point
  FitMultipleDynamicGrowth.Rd: geom_line
  FitMultipleGrowthMCMC.Rd: geom_line
  FitSecondaryGrowth.Rd: modFit
  GlobalGrowthFit.Rd: geom_line
  GrowthFit.Rd: geom_line, geom_point
  GrowthPrediction.Rd: geom_line
  GrowthUncertainty.Rd: geom_line, geom_ribbon
  IsothermalGrowth.Rd: geom_line
  StochasticGrowth.Rd: geom_line, geom_ribbon
  TimeDistribution.Rd: geom_histogram
  check_growth_guess.Rd: ggplot
  dBaranyi.Rd: ode
  fit_growth.Rd: modFit, modMCMC
  fit_isothermal_growth.Rd: modFit
  fit_multiple_growth.Rd: modFit
  fit_multiple_growth_MCMC.Rd: modMCMC
  fit_secondary_growth.Rd: modFit
  get_dyna_residuals.Rd: modFit, modCost
  get_multi_dyna_residuals.Rd: modFit
  predict_dynamic_growth.Rd: ode
  predict_growth.Rd: ode
  show_guess_dynamic.Rd: ggplot
  show_guess_primary.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fit_dynamic_inactivation.Rd: modFit, FME
  fit_inactivation_MCMC.Rd: modMCMC, FME
  get_prediction_cost.Rd: modCost
  predict_inactivation.Rd: ode, deSolve
  sample_IsoFit.Rd: mvrnorm
  sample_dynaFit.Rd: modFit, mvrnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ROC.Rd:55: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:56: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:57: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:58: Lost braces in \enumerate; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  auxBiom.Rd: glmnet
  biom.options.Rd: glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package which this enhances but not available for checking: 'asreml'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  heat_map.Rd: facet_wrap
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) simulation.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:60-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:65: Lost braces in \itemize; meant \describe ?
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    help   2.6Mb
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}.
       |                                                                                                                                                                              ^
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      1.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coxphHaz.Rd: coxph, survfit
  muhaz2.Rd: muhaz
  survrate.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  covsum_nested.Rd: mixed
  rm_covsum_nested.Rd: covsum, mixed, outTable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  D2.disc.Rd: lda
  aer.Rd: lda
  confusionmatrix.Rd: lda
  sHe.Rd: levelplot
  samplesize.Rd: boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  betalinkr.Rd: vegdist, betadiver
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Depends: includes the non-default packages:
  'colorspace', 'deldir', 'rgl', 'tcltk', 'tcltk2', 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
checkRd: (-1) FighterAircraft.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bi_scale_color.Rd: geom_sf, scale_color_manual
  bi_scale_fill.Rd: geom_sf, scale_fill_manual
  bi_theme.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  connectivity.map.Rd: poly2nb, knn2nb, graph2nb
  gearybi.test.Rd: listw2U
  localmoran.bi.Rd: localG
  moranbi.test.Rd: moran, moran.mc, listw2U
  moranbir.test.Rd: listw2U
  spcorrelogram.bi.Rd: nblag
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  waic.cumhist.Rd: loo-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
checkRd: (-1) keypos.rd:27: Lost braces
    27 |   an integer vector of the same length as code{x} containing positions relativ to code{sort(unique(x), na.last=FALSE)}
       |                                               ^
checkRd: (-1) keypos.rd:27: Lost braces
    27 |   an integer vector of the same length as code{x} containing positions relativ to code{sort(unique(x), na.last=FALSE)}
       |                                                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bit64-package.rd: bit, bitwhich, &.bit, &.bitwhich
  cache.rd: still.identical, na.count, nvalid, is.sorted, nunique,
    nties
  hashcache.rd: ramsort, ramsortorder, ramorder, nunique
  ramsort.integer64.rd: ramsort, ramsortorder, ramorder
  sort.integer64.rd: ramsort, ramsortorder
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  make_jive.Rd: make.simmap, as.phylo
  plot_jive.Rd: vioplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'bit/libs/x64/bit.dll':
  Found non-API calls to R: 'SETLENGTH', 'STRING_PTR', 'VECTOR_PTR'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
File 'BiTrinA/libs/x64/BiTrinA.dll':
  Found non-API call to R: 'SET_TYPEOF'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.biwavelet.Rd: image.plot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bizicount.Rd: DHARMa
  zic.reg.Rd: DHARMa
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coxlps.Rd: Surv, coxph
  curelps.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
Package suggested but not available for checking: 'cmdstanr'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R          1.2Mb
    libs       5.3Mb
    testdata   1.4Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bcfa.Rd: lavaan, lavaan-class
  bgrowth.Rd: lavaan
  blavFitIndices.Rd: lavaan-class
  blavInspect.Rd: lavaan, lavInspect
  blavaan-class.Rd: standardizedSolution, fitMeasures
  blavaan.Rd: lavaan, lavaan-class
  bsem.Rd: lavaan, lavaan-class
  ppmc.Rd: lavaan-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) RLdata500.Rd:8: Lost braces
     8 | A data frame with five variables: \code{fname_c1},\code{lname_c1},  \code{by}, code{bm}, \code{bd}.
       |                                                                                    ^
checkRd: (-1) identity.RLdata500.Rd:15: Lost braces
    15 | format A vector that contains the code{id}
       |                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  blmer.Rd: merMod-class
  bmerMod-class.Rd: merMod-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) durban.Rd:16: Lost braces; missing escapes or markup?
    16 | This data set was obtained from the durban.rowcol {agridat} example in package 'agridat' 
       |                                                   ^
checkRd: (-1) fraction.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fraction.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fraction.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_density.Rd:25: Lost braces; missing escapes or markup?
    25 | evenly spaced points between \code{min} and {max}.
       |                                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  build_dir.Rd: render
  html_page.Rd: html_document2, output_format
  hugo_cmd.Rd: server_config
  read_toml.Rd: raw_string
  serve_site.Rd: server_config
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bluebike.Rd:17: Lost braces
    17 | \item{\code{import_month_data}}\cr {Takes in numeric year/month values and imports data from \href{https://www.bluebikes.com/system-data}{Blue Bikes System Data} for the specified time}
       |                                    ^
checkRd: (-1) bluebike.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{\code{station_distance}}\cr {Returns stations with distance in ascending order given the user's current location}
       |                                   ^
checkRd: (-1) bluebike.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{\code{station_radius}}\cr {Plots the position of the stations within walking distance (500 m), and present the basic information about the stations via leaflet}
       |                                 ^
checkRd: (-1) bluebike.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{\code{trip_distance}}\cr {Computes the geographical distance between the start and end stations}
       |                                ^
checkRd: (-1) bluebike.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{\code{trip_history_sample}} \cr {A sample of 1000 trip data entries from February 2022}
       |                                       ^
checkRd: (-1) bluebike.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{\code{station_data}} \cr {A dataset that includes identification, position, and other basic information about bluebike stations}
       |                                ^
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bmem.Rd: sem
  power.bmem.Rd: model.syntax
  power.curve.Rd: model.syntax
  summary.power.Rd: lavaan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bmem.Rd: sem
  bmem.bs.Rd: sem
  bmem.em.Rd: sem
  bmem.em.boot.Rd: sem
  bmem.em.jack.Rd: sem
  bmem.list.Rd: sem
  bmem.list.boot.Rd: sem
  bmem.list.jack.Rd: sem
  bmem.mi.Rd: sem
  bmem.mi.boot.Rd: sem
  bmem.mi.jack.Rd: sem
  bmem.pair.Rd: sem
  bmem.pair.boot.Rd: sem
  bmem.pair.jack.Rd: sem
  bmem.sobel.Rd: sem
  popPar.Rd: lavaan
  power.basic.Rd: model.syntax
  power.boot.Rd: model.syntax
  power.curve.Rd: model.syntax
  summary.power.Rd: lavaan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
checkRd: (-1) dot-pred_array_to_df.Rd:20: Lost braces; missing escapes or markup?
    20 | Helper function for as.data.frame.{fitted, forecast}. Converts predictive array to data.frame.
       |                                   ^
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  summary.bmmfit.Rd: summary.brmsfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BMSC_pareto_k_table.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:57-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:60-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:64-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:67-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Bspatial.Rd: spLM
  Bsptime.Rd: spDynLM, spT.time, spLM
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
checkRd: (-1) autoplot.tsregime.Rd:20: Lost braces
    20 | Graph for the stochastic processes of the object \ dQuote {\ code {tsregime}} for: Output process and if they exist for: Threshold process and Covariates process. In the case that there are missing data, a red line is drawn at the indicated time.
       |                                                           ^
checkRd: (-1) autoplot.tsregime.Rd:20: Lost braces; missing escapes or markup?
    20 | Graph for the stochastic processes of the object \ dQuote {\ code {tsregime}} for: Output process and if they exist for: Threshold process and Covariates process. In the case that there are missing data, a red line is drawn at the indicated time.
       |                                                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  autoplot.Rd: autolayer, ggplot, fortify
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BMTfit.Rd: mledist, fitdist, fitdistrplus, gofstat, plotdist,
    cdfcomp, bootdist, mmedist, qmedist, mgedist
  BMTfit.mge.Rd: mledist, mgedist, fitdistrplus, fitdist
  BMTfit.mle.Rd: mledist, fitdistrplus, fitdist
  BMTfit.mme.Rd: mledist, mmedist, fitdistrplus, fitdist
  BMTfit.mpse.Rd: mledist, fitdistrplus, fitdist
  BMTfit.mqde.Rd: mledist, fitdistrplus, fitdist
  BMTfit.qme.Rd: mledist, qmedist, fitdistrplus, fitdist
  mpsedist.Rd: mledist, fitdistrplus, mmedist, qmedist, mgedist
  mqdedist.Rd: mledist, fitdistrplus, mmedist, qmedist, mgedist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  network.run.Rd: jags.model
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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) {
       |                           ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) strength.viewer.Rd:148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:152: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |               ^
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |                                             ^
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
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 ?
Packages suggested but not available for checking:
  'adiposerefdata', 'musclerefdata'
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  selected_vars.Rd: cv.glmnet, cv.gamlr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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>
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/BonEV.Rcheck/00install.out' for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   7.7Mb
    libs   1.1Mb
installed size is 40.5Mb
  sub-directories of 1Mb or more:
    include  10.5Mb
    lib      29.5Mb
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nnet.Rd: MvnPrior
  suggest.burn.Rd: SuggestBurnLogLikelihood
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coefs.plsRglm.CSim.Rd: plsRglm
  coefs.sgpls.CSim.Rd: plsRglm
  permcoefs.plsRglm.CSim.Rd: plsRglm
  permcoefs.sgpls.CSim.Rd: plsRglm
  signpred2.Rd: visweb
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  catsM.Rd: cats
  censboot.Rd: coxph, survfit
  motor.Rd: mcycle
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'doMC'
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
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  As2Vs.Rd: ff
  bootSVD.Rd: ff
  fastSVD.Rd: ff
  ffmatrixmult.Rd: ff
  getMomentsAndMomentCI.Rd: ff
  reindexMatricesByK.Rd: ff
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  graphoptBbd.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getImpExtra.Rd: ranger
  getImpLegacyRf.Rd: ranger
  getImpRf.Rd: ranger
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
Error(s) in re-building vignettes:
--- re-building 'BOSO.Rmd' using rmarkdown

Quitting from lines 56-79 [unnamed-chunk-3] (BOSO.Rmd)
Error: processing vignette 'BOSO.Rmd' failed with diagnostics:
[ENOENT] Failed to remove 'D:/temp/RtmpEfs69L/file3187c63a5ef1': no such file or directory
--- failed re-building 'BOSO.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  legend.grob.Rd: draw.key
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  boxcoxtype.Rd: alldist, allvc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'box/libs/x64/box.dll':
  Found non-API calls to R: 'ENVFLAGS', 'SET_ENVFLAGS'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  box_dir_diff.Rd: digest
  box_upload_new.Rd: httr
  boxr_S3_classes.Rd: as_tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  print.xtable.Rd: xtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
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 | $$SD = sqrt(sum(x_{i+1} - xbar)^2/n-1)$$
       |                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bp_report.Rd: grid.arrange
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  predict.BTm.Rd: predict.glmmPQL
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  braidReports-package.Rd: braidrm-package
  es8analysis.Rd: es8olatmz, runBRAIDanalysis
  makeBRAIDreport.Rd: runBRAIDanalysis, scale_fill_gradientn,
    geom_point, geom_line
  potentiationPlot.Rd: geom_ribbon, geom_point, geom_line, geom_hline
  voronoi.Rd: geom_polygon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_global.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  brainR-package.Rd: contour3d, rgl
  makeScene.Rd: contour3d, nifti-class
  write4D.Rd: writeOBJ, writeSTL, contour3d
  write4D.file.Rd: writeOBJ, writeSTL, contour3d
  writeTrianglesSTL.Rd: writeSTL
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  brnb.Rd: negbin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Found the following HTML validation problems:
Bridge.html:80:32 (Bridge.Rd:63): Warning: trimming empty <code>
Bridge.html:85:32 (Bridge.Rd:65): Warning: trimming empty <code>
checkRd: (-1) printHands.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) printHands.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) printHands.Rd:42: Lost braces in \itemize; meant \describe ?
'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) assertall.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) assertall.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) assertall.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) assertall.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brmsmargins.Rd:129: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brmsmargins.Rd:130: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brmsmargins.Rd:131: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brmsmargins.Rd:132: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) builders.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:55: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  builders.Rd: make_standata, as_draws_df
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'cmdstanr'
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R     3.7Mb
    doc   3.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  conditional_effects.brmsfit.Rd: geom_jitter, geom_rug, geom_smooth,
    geom_point, geom_errorbar, geom_contour, geom_raster, facet_wrap,
    scale_colour_grey, scale_colour_gradient, ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  createBarPrior.Rd: fitCyclopsModel
  createFastBarPrior.Rd: fitCyclopsModel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'glmmADMB'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  glance.survfit.Rd: summary.survfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/BRugs.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  insertTab.Rd: tabPanel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bsitar.Rd: opencl, save_pars, brmsfit_needs_refit
  update_model.bgmfit.Rd: brms
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    components   1.0Mb
    fonts        2.9Mb
    lib          4.9Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) bscontrol.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{opt.solver}{a character string in the set {'enum', 'enum_c', 'gurobi', 'cplex', 'lpSolve', 'greedy'} indicating the optimization solver to be used in the program. The choice of 'cplex' requires the package \code{cplexAPI}, 'gurobi' requires the package \code{gurobi}, and 'lpSolve' requires the package \code{lpSolve}. These solver options are only available in the full version at \url{https://github.com/profyliu/bsnsing/}. The default (and the best) is 'enum_c'.}
       |                                                 ^
checkRd: (-1) bscontrol.Rd:45: Lost braces; missing escapes or markup?
    45 | \item{opt.model}{a character string in the set {'gini','error'} indicating the optimization model to solve in the program. The default is 'gini'. The 'error' option is not available in the current version.}
       |                                                ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  add.dynamic.regression.Rd: SdPrior
  add.monthly.annual.cycle.Rd: zoo
  bsts.Rd: zoo
  descriptive-plots.Rd: zoo, yearmon
  mbsts.Rd: SpikeSlabPrior
  plot.bsts.mixed.Rd: TimeSeriesBoxplot
  to.posixt.Rd: yearmon
  wide.to.long.Rd: zoo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) terms.BTM.Rd:23-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) terms.BTM.Rd:26-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) terms.data.frame.Rd:25-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) terms.data.frame.Rd:32-38: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BT.Rd: rpart, rpart.control
  BT_Call.Rd: rpart.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
checkRd: (-1) pnbd.mcmc.DrawParameters.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pnbd.mcmc.DrawParameters.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  abe.mcmc.DrawParameters.Rd: mcmc.list
  pggg.mcmc.DrawParameters.Rd: mcmc.list
  pnbd.mcmc.DrawParameters.Rd: mcmc.list
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) bubbleHMLegends.Rd:42: Lost braces; missing escapes or markup?
    42 | function. If {sizeBreaks} vector is supplied then this will be ignored and
       |              ^
checkRd: (-1) bubbleHeatmap.Rd:96: Lost braces; missing escapes or markup?
    96 | function. If {sizeBreaks} vector is supplied then this will be ignored and
       |              ^
checkRd: (-1) multiPlotInput.Rd:117: Lost braces; missing escapes or markup?
   117 | \code{unitBase}. This will be supplied to pretty function. If {sizeBreaks} is
       |                                                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  read_excel_workbook.Rd: read_excel
  read_gsheets.Rd: read_sheet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  brkpt.Rd: glm.nb
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lifecycles.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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 ?
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.8Mb
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  balancedFolds.Rd: EPSGO
  coef.intsearch.Rd: EPSGO
  plot.summary.int.Rd: EPSGO
  stabpath.Rd: glmnet
  summary.intsearch.Rd: EPSGO
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  deleteZeroComponents.Rd: merMod
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
File 'Cairo/libs/x64/Cairo.dll':
  Found non-API call to R: 'Rf_gsetVar'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
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 suggested but not available for checking: 'ReGenesees'
checkRd: (-1) calibration_bands.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{y}{response variable (in {0,1}).}
       |                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) heage.Rd:18: Lost braces
    18 | B{\"o}hning, D.  and Schlattmann, P. and Lindsay, B. (1992). \dQuote{Computer-Assisted Analysis of Mixtures (C.A.MAN): Statistical Algorithms}. \emph{Biometrics}. \bold{48}, 283--303.
       |  ^
checkRd: (-1) hepab.Rd:5: Lost braces
     5 | Hepatitis B data from Schlattmann and B{\"o}hning (1993).
       |                                        ^
checkRd: (-1) hepab.Rd:19: Lost braces
    19 | Schlattmann, P. and B{\"o}hning, D. (1993). \dQuote{Mixture models and disease mapping}. \emph{Statistics in Medicine}. \bold{12}, 1943--1950.
       |                      ^
checkRd: (-1) mixalg.Rd:117: Lost braces
   117 | D. B{\"o}hning, P. Schlattmann, B.G. Lindsay: C.A.MAN - Computer Assisted
       |     ^
checkRd: (-1) thai_cohort.Rd:19: Lost braces
    19 | Schelp, F., P. Vivatanasept, P. Sitaputra, S. Sornmani, P. Pongpaew, N. Vudhivai, S. Egormaiphol, and D. B{\"o}hning.  \dQuote{Relationship of the morbidity of under-fives to anthropometric measurements and community health intervention.} \emph{Trop Med Parasitol}, 1990, 41(2), 121--126.
       |                                                                                                           ^
checkRd: (-1) Recording.Rd:112: Lost braces; missing escapes or markup?
   112 | Stop recording images with {camcorder}.
       |                            ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BuildGeneSets.Rd: edgeR, org.Hs.eg.db, org.Mm.eg.db
  CAMML.Rd: vamForSeurat
  ChIMP.Rd: vamForSeurat
  GetGeneSets.Rd: org.Hs.eg.db, org.Mm.eg.db
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc        2.2Mb
    pictures   4.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_coef-commOccu-method.Rd: fit
  plot_effects-commOccu-method.Rd: fit
  predict-commOccu-method.Rd: fit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) macrocaic.Rd:31: Lost braces; missing escapes or markup?
    31 |      {RRD = ln(N_1/N_2)}
       |      ^
checkRd: (-1) macrocaic.Rd:34: Lost braces; missing escapes or markup?
    34 |      {PDI = (N_1/(N_1 + N_2))-0.5}
       |      ^
checkRd: (-1) pd.calc.Rd:33: Lost braces
    33 |   \item{Length of tip branch lengths (TIPS)}{Length of tip branch lengths (TIPS)}{Unlike UEH, this measure does not use the unique paths to each tips on the \strong{subtree} and instead gives the sum of the unique branches leading to the tips on the \strong{complete tree}.}
       |                                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  comparative.data.Rd: reorder.phylo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CalculateGlobalSens.Rd: sensRange
  CalculateLocalSens.Rd: sensFun, sensRange
  DesignSurvey.Rd: svydesign
  PlotLocalSens.Rd: element_text
  SetRanges.Rd: sensRange
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  myCarousel.Rd: carouselItem
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
File 'carbondate/libs/x64/carbondate.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  persistence.prob.Rd: coxph, survreg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) fitweibull.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitweibull.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitweibull.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) zipcode.Rd:14: Lost braces; missing escapes or markup?
    14 | This is a dataset from the archived/orphaned {zipcode} package.
       |                                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  setup_statevars.Rd: deSolve
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  caretList.Rd: train, trainControl
  metrics.Rd: train
  predict.caretStack.Rd: predict.train
  varImp.caretEnsemble.Rd: varImp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) NEWS.Rd:96: Lost braces
    96 |     \item code{train} now removes duplicate models in the tuning grid. Duplicates could occur for models with discrete parameters.
       |               ^
checkRd: (-1) calibration.Rd:46: Lost braces; missing escapes or markup?
    46 | formula. This argument is not used for \code{xyplot.calibration}. For {ggplot.calibration}, \code{data}
       |                                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  train.Rd: recipe
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) build_for_cran.Rd:13: Lost braces
    13 | The exit status code{R CMD build}, invisibly.
       |                     ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) compareCoefs.Rd:30: Lost braces
    30 | \item{pvals}{If code{TRUE} (the default is \code{FALSE}), print two-sided p-values
       |                     ^
checkRd: (-1) mcPlots.Rd:38: Lost braces; missing escapes or markup?
    38 |   axis.  To plot against a factor, you need to specify the full name of one of the indicator variables that define the factor.  For example, for a factor called \code{type} with levels \code{A}, \code{B} and {C}, using the usual drop-first level parameterization of the factor, the regressors for \code{type} would be \code{typeB} or \code{typeC}.  Similarly, to plot against the regressor \code{log(X4)}, you must specify \code{"log((X4)"}, not \code{"X4"}.
       |                                                                                                                                                                                                                 ^
checkRd: (-1) scatterplot.Rd:137: Lost braces
   137 | For  \code{style="filled"} several subarguments modify the appearance of the region:  code{alpha} is a number between 0 and 1 that specifies opacity with defualt 0.15, \code{border}, \code{TRUE} or \code{FALSE} specifies a border for the envelope, and \code{vertical} either \code{TRUE} or \code{FALSE}, modifies the behavior of the envelope at the edges of the graph.
       |                                                                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Anova.Rd: anova.coxph
  Boot.Rd: boot, boot.array, boot.ci, plot.boot, empinf
  Ellipses.Rd: cov.trob
  S.Rd: multinom, polr, summary.multinom
  ScatterplotSmoothers.Rd: gam, rqss, qss
  avPlots.Rd: cov.trob
  boxCox.Rd: boxcox
  boxCoxVariable.Rd: boxcox
  hist.boot.Rd: boot, boot.ci
  influence-mixed-models.Rd: lme
  marginalModelPlot.Rd: gam
  poTest.Rd: polr
  scatter3d.Rd: gam
  scatterplot.Rd: cov.trob
  scatterplotMatrix.Rd: cov.trob, gam, rqss
  symbox.Rd: boxcox
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'rnaturalearthhires'
File 'cartographer/libs/x64/cartographer.dll':
  Found non-API call to R: 'PRVALUE'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dotDensityLayer.Rd: st_sample
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    www  12.1Mb
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Source(s) listed in 'build/vignette.rds' but not in package:
  'competingRisk.Rmd'
  'customizingpopTime.Rmd'
  'plotabsRisk.Rmd'
  'plotsmoothHazard.Rmd'
  'popTime.Rmd'
  'smoothHazard.Rmd'
  'time-varying-covariates.Rmd'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  popTime.Rd: theme_minimal, geom_ribbon, geom_point,
    scale_color_manual, scale_fill_manual, theme, facet_wrap,
    scale_colour_manual
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CreateSpacetimeFolds.Rd: trainControl
  bss.Rd: train, trainControl
  errorProfiles.Rd: rollapply
  ffs.Rd: train, trainControl
  global_validation.Rd: train, postResample, confusionMatrix
  nndm.Rd: trainControl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) slpDGCM.Rd:130-133: Lost braces
   130 | \code{x1, x2, x3, \dots}- {input to the model, there must be one column
       |                           ^
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    doc  19.9Mb
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 ?
checkRd: (-1) colAUC.Rd:79: Lost braces
    79 |      Meteorol. Soc. textbf{30} 291-303. 
       |                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  catpredi.Rd: mgcv
  catpredi.survival.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++14: please drop specification unless essential
'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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cauphylm.Rd: nloptr
  fitCauchy.Rd: nloptr
  fitCauchy.internal.Rd: nloptr
  fit_function.Rd: nloptr
  hdi.ancestralCauchy.Rd: HDInterval
  printRTreeTest.Rd: ape
  rTraitCauchy.Rd: ape
  simulateTipsCauchy.Rd: ape
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'cauphy/libs/x64/cauphy.dll':
  Found non-API call to R: 'SET_TYPEOF'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) as.mbsts.Rd:71: Lost braces; missing escapes or markup?
    71 |   \item{states.samples}{(\code{niter}- \code{burn}) draws from p(alpha_t | Y_{1:T}).}
       |                                                                              ^
checkRd: (-1) mcmc.Rd:61: Lost braces; missing escapes or markup?
    61 |   \item{states.samples}{(\code{niter}- \code{burn}) draws from p(alpha_t | Y_{1:T}).}
       |                                                                              ^
Package suggested but not available for checking: 'rkeops'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  make_model.Rd: dagitty
  print.causal_model.Rd: dagitty
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  causalSLSE.Rd: vcovHC.default
  extract-causalslse-method.Rd: extract, texreg
  extract-slseFit-method.Rd: extract, texreg
  predict.Rd: vcovHC.default
  summary.Rd: vcovHC.default
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File 'cba/libs/x64/cba.dll':
  Found non-API call to R: 'Rf_NonNullStringMatch'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) cbc_design.Rd:160: Lost braces; missing escapes or markup?
   160 | see \code{?DoE.base::fac.design} as well as the JSS article on the {DoE.base}
       |                                                                    ^
checkRd: (-1) cbc_design.Rd:174: Lost braces; missing escapes or markup?
   174 | well as the JSS article on the {DoE.base} package (Grömping, 2018).
       |                                ^
checkRd: (-1) cbc_design.Rd:197: Lost braces; missing escapes or markup?
   197 | {idefix} package (Traets et al, 2020).
       | ^
checkRd: (-1) cbc_power.Rd:70: Lost braces; missing escapes or markup?
    70 | estimation. See the {logitr} documentation for details about other
       |                     ^
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Rcpp_CONEC-class.Rd: C++Object-class
  Rcpp_CPS-class.Rd: C++Object-class
  Rcpp_CTRL-class.Rd: C++Object-class
  Rcpp_DCP-class.Rd: C++Object-class
  Rcpp_DLP-class.Rd: C++Object-class
  Rcpp_DNL-class.Rd: C++Object-class
  Rcpp_DQP-class.Rd: C++Object-class
  Rcpp_PDV-class.Rd: C++Object-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cchs.Rd: Surv, coxph, coxph.object, coxph.control, cch
  cchsData.Rd: nwtco, cch
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) CUR.Rd:25: Lost braces; missing escapes or markup?
    25 | The number of low-dimension of C (J1 < {N,M}).
       |                                        ^
checkRd: (-1) CUR.Rd:29: Lost braces; missing escapes or markup?
    29 | The number of low-dimension of R (J2 < {N,M}).
       |                                        ^
checkRd: (-1) CX.Rd:23: Lost braces; missing escapes or markup?
    23 | The number of low-dimension (J < {N,M}).
       |                                  ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cct-class.Rd: rjags-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) data.dtmr.Rd:57: Lost braces; missing escapes or markup?
    57 | \code{RU}: {Referent units}
       |            ^
checkRd: (-1) data.dtmr.Rd:59: Lost braces; missing escapes or markup?
    59 | \code{PI}: {Partitioning and iterating attribute}
       |            ^
checkRd: (-1) data.dtmr.Rd:61: Lost braces; missing escapes or markup?
    61 | \code{APP}: {Appropriateness attribute}
       |             ^
checkRd: (-1) data.dtmr.Rd:63: Lost braces; missing escapes or markup?
    63 | \code{MC}: {Multiplicative Comparison attribute}
       |            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  G.start.Rd: lsei
  cds.Rd: lsei
  cdstoclue.Rd: cl_agreement
  gen.cop.Rd: copClayton
  group.ALS.Rd: lsei
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
    libs   1.7Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tobit1.Rd: gam, ziplss
  tobit2.Rd: gam, ziplss
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Unexported objects imported by ':::' calls:
  'copula:::dCdu' 'copula:::fitCopStart'
  See the note in ?`:::` about the use of this operator.
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
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
       |                    ^
'LazyData' is specified without a 'data' directory
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,
       |          ^
Specified C++11: please drop specification unless essential
checkRd: (-1) performParallelNLMERun.Rd:22: Lost braces
    22 | \item{partialJob}{is /code{TRUE} if it is not required to stop the job
       |                           ^
checkRd: (-1) performParallelNLMERun.Rd:25: Lost braces
    25 | \item{allowIntermediateResults}{is /code{TRUE} if intermediate results
       |                                         ^
Problems with news in 'NEWS.md':
No news entries found.
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
checkRd: (-1) cfc.tbasis.Rd:23: Lost braces
    23 | Assuming one-dimensional \code{p1} and \code{p2} for clarity, the algorithm calculates cumulative incidence function for cuase 1 using a recursive formula: \code{ci1[n+1] = ci1[n] + dci1[n]}, where \code{dci1[n] = 0.5*(p2[n] + p2[n+1])*(p1[n] - p1[n+1])}. The increment in cumulative incidence function for cause 2 is similarly calculated, \code{dci2[n] = 0.5*(p1[n] + p1[n+1])*(p2[n] - p2[n+1])}. These equations guarantee that \code{dci1[n] + dci2[n] = p1[n]*p2[n] - p1[n+1]*p2[n+1]}. Event-free probability is simply calculated as code{efp[n] = p1[n]*p2[n]}. Taken together, this numerical integration ensures that \code{efp[n+1] - efp[n] + dci1[n] + dci2[n] = 0}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cfda-package.Rd: create.basis
  compute_optimal_encoding.Rd: create.basis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cforward.Rd: Surv, concordancefit, coxph
  estimate_concordance.Rd: Surv, concordancefit, coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  boot.cgaim.Rd: doParallel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    include  38.4Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) comparisonsTable.cgOneFactorFit.Rd:47: Lost braces
    47 |         call (see {\dots } section below.)
       |                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  anorexiaFT.Rd: anorexia
  boxplot.cgOneFactorData.Rd: survfit
  comparisonsGraph.cgOneFactorComparisonsTable.Rd: panel.text
  comparisonsTable.cgOneFactorFit.Rd: rlm
  comparisonsTable.cgPairedDifferenceFit.Rd: rlm
  comparisonsgraph.Rd: panel.text
  descriptiveTable.cgOneFactorData.Rd: survfit
  downweightedTable.Rd: rlm
  downweightedTable.cgOneFactorFit.Rd: rlm
  downweightedTable.cgPairedDifferenceFit.Rd: rlm
  fit.cgOneFactorData.Rd: rlm, survreg, gls
  fit.cgPairedDifferenceData.Rd: rlm
  kmGraph.Rd: label
  kmGraph.cgOneFactorData.Rd: label
  prepareCGOneFactorData.Rd: Surv, survreg, logtrans
  print.cgOneFactorComparisonsTable.Rd: rlm
  print.cgOneFactorFit.Rd: rlm
  print.cgOneFactorGlobalTest.Rd: rlm
  print.cgOneFactorGrpSummaryTable.Rd: rlm
  print.cgOneFactorSampleSizeTable.Rd: rlm
  print.cgPairedDifferenceComparisonsTable.Rd: rlm
  print.cgPairedDifferenceFit.Rd: rlm
  summary.cgOneFactorFit.Rd: rlm
  summary.cgPairedDifferenceFit.Rd: rlm
  varianceGraph.cgOneFactorFit.Rd: vgam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cpt.geo-class.Rd: ggplot2
  data.set.Rd: data.set-methods
  data.set_-.Rd: data.set<--methods
  pen.value.Rd: pen.value-methods
  pen.value_-.Rd: pen.value<--methods
  test.stat.Rd: test.stat-methods
  test.stat_-.Rd: test.stat<--methods
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.
       |                                          ^
checkRd: (-1) Hausdorff.dist.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{vec1}{A \code{integer} vector forms a subset of {1, 2, ..., n}.}
       |                                                       ^
checkRd: (-1) Hausdorff.dist.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{vec2}{A \code{integer} vector forms a subset of {1, 2, ..., n}.}
       |                                                       ^
checkRd: (-1) online.univar.multi.Rd:47-57: Lost braces
    47 | online.univar.one2 = function(y_vec, gamma, tau_gamma, ...){
       |                                                            ^
checkRd: (-1) online.univar.multi.Rd:50-55: Lost braces
    50 |   while(FLAG == 0 & t <= length(y_vec)){
       |                                        ^
checkRd: (-1) online.univar.multi.Rd:71-89: Lost braces
    71 | online.univar.one3 = function(y_vec, tau_vec, ...){
       |                                                   ^
checkRd: (-1) online.univar.multi.Rd:72-74: Lost braces
    72 |   if(length(y_vec) != length(tau_vec)){
       |                                       ^
checkRd: (-1) online.univar.multi.Rd:77-87: Lost braces
    77 |   while(FLAG == 0 & t <= length(y_vec)){
       |                                        ^
checkRd: (-1) online.univar.multi.Rd:81-86: Lost braces
    81 |     while(j < J & FLAG == 0){
       |                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  changepointsVar-package.Rd: lars
  jumpointsVar.Rd: lars
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
checkRd: (-1) create_unit_tests.Rd:17: Lost braces; missing escapes or markup?
    17 | Create `{testthat}` test cases for the code.
       |         ^
'LazyData' is specified without a 'data' directory
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"}.
       |                                                                               ^
File 'checkglobals/libs/x64/checkglobals.dll':
  Found non-API call to R: 'Rf_isValidString'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Package suggested but not available for checking: 'darts'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  checkpoint.Rd: pkgdepends
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pipe.Rd: magrittr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hats_alignSpectra2D.Rd: rowDist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  aovPCAloadings.Rd: GraphicsOptions
  plot2Loadings.Rd: GraphicsOptions
  plotLoadings.Rd: GraphicsOptions
  plotSpectra.Rd: GraphicsOptions
  reviewAllSpectra.Rd: GraphicsOptions
  sPlotSpectra.Rd: GraphicsOptions
  surveySpectra.Rd: GraphicsOptions
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hommelFast.Rd: hommel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'countreg'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  chillR-package.Rd: ggplot2
  plot_phenology_trends.Rd: fields, ggplot2
  plot_scenarios.Rd: ggplot2, patchwork
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) C316.amp.Rd:28-32: Lost braces
    28 |     40 x {
       |          ^
checkRd: (-1) C317.amp.Rd:28-32: Lost braces
    28 |     40 x {
       |          ^
checkRd: (-1) C60.amp.Rd:63-67: Lost braces
    63 |     40 x {
       |          ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  chkpt_brms.Rd: brms
  make_brmsfit.Rd: brms
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    help   2.2Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggpng.Rd: ggsave
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'entab'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  insert_chunkwise_into.Rd: tbl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) chunker-methods.Rd:63: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:64: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:70: Lost braces in \enumerate; meant \describe ?
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
       |                                             ^
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
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.
       |                       ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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.
       |            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  circ.plot.Rd: eqscplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.circular.Rd: eqscplot
  rose.diag.Rd: eqscplot
  windrose.Rd: eqscplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) doseFind.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) doseFind.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) doseFind.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dbExecQuery.Rd: dbSendQuery, dbClearResult, dbGetQuery
  lbsClear.Rd: dbCommit, dbRollback
  lbsDeleteAllAuthorsDocuments.Rd: dbCommit, dbRollback
  lbsTidy.Rd: dbCommit, dbRollback
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) data_generator.Rd:93: Lost braces; missing escapes or markup?
    93 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                     ^
checkRd: (-1) data_generator.Rd:93: Lost braces; missing escapes or markup?
    93 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                             ^
checkRd: (-1) data_generator.Rd:95: Lost braces; missing escapes or markup?
    95 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++}, S_{*+}
       |                                                                 ^
checkRd: (-1) data_generator.Rd:95: Lost braces; missing escapes or markup?
    95 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++}, S_{*+}
       |                                                                         ^
checkRd: (-1) data_generator_loop.Rd:96: Lost braces; missing escapes or markup?
    96 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                     ^
checkRd: (-1) data_generator_loop.Rd:96: Lost braces; missing escapes or markup?
    96 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                             ^
checkRd: (-1) data_generator_loop.Rd:98: Lost braces; missing escapes or markup?
    98 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++},
       |                                                                 ^
checkRd: (-1) data_generator_loop.Rd:99: Lost braces; missing escapes or markup?
    99 |   S_{*+} and PP estimands}
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) ciu.ggplot.col.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
checkRd: (-1) ciu.meta.explain.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
checkRd: (-1) ciu.meta.result.new.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
checkRd: (-1) ciu.textual.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CivisFuture.Rd: Future
  civis_platform.Rd: future, plan
  write_civis_file.Rd: plan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  estimate_ancestral_states.Rd: rerootingMethod, phytools, ace, ape
  find_minimum_spanning_edges.Rd: mst, ape
  fix_root_time.Rd: drop.tip, ape
  map_stochastic_changes.Rd: make.simmap, phytools
  ordinate_cladistic_matrix.Rd: pcoa, ape
  plot_rates_character.Rd: geoscale
  plot_rates_time.Rd: geoscalePlot, geoscale
  plot_rates_tree.Rd: geoscale
  read_nexus_matrix.Rd: read.nexus.data
  safe_taxonomic_reinsertion.Rd: ape, read.tree, read.nexus
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cc01-0-MultiTtest-class.Rd: ExpressionSet-class, matrixT
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  generate_classification_data.Rd: knn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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 ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ClickHouseHTTPConnection-class.Rd: dbConnect
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fitMarkovChain.Rd: Rsolnp
  frequencies.Rd: transactions
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) cf_save_kml.Rd:68: Lost braces
    68 | \code{\link{cf_find_station}} and code{vignette("choose-station")} for
       |                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  liftHurstC.Rd: artificial.levels, Hfrombeta
  liftHurstCC.Rd: artificial.levels, Hfrombeta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  thornthwaite.Rd: daylength, geosphere
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 48.6Mb
  sub-directories of 1Mb or more:
    extdata  48.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clinDR-package.Rd: DoseFinding
  emaxsim.Rd: Mods
  emaxsimB.Rd: Mods
  fitEmaxB.Rd: rstan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) clinsig.Rd:129: Lost braces
   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                   ^
checkRd: (-1) clinsig.Rd:129: Lost braces
   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                                 ^
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  knitPrintListObjects.Rd: knitr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'clock/libs/x64/clock.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) print.clogitL1.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.clogitL1.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.clogitL1.Rd:23: Lost braces in \itemize; meant \describe ?
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cloudml_train.Rd: flags
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
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}
       |                                                                                    ^
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
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.clusEvol.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.clus_lme.Rd: ggexport
  plot.clus_opt_thres3.Rd: ggexport
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clusterabilitytest.Rd: dip.test
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  aucplot.Rd: lattice, xyplot
  cluscomp.Rd: cluster
  clusterCons-package.Rd: cluster, lattice, apcluster
  dkplot.Rd: lattice, xyplot
  expressionPlot.Rd: lattice, xyplot
  membBoxPlot.Rd: lattice, bwplot
  wrappers.Rd: cluster, agnes, pam, diana, apclusterK
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dissmutmatrix.Rd: dissplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) HTKmeans.Rd:62: Lost braces
    62 | \item{centers }{A matrix of cluster centres.}
       |      ^
checkRd: (-1) HTKmeans.Rd:62: Lost braces
    62 | \item{centers }{A matrix of cluster centres.}
       |                ^
checkRd: (-1) HTKmeans.Rd:63: Lost braces
    63 | \item{cluster }{A vector of integers (from 1:\code{k}) indicating the cluster to which each point is allocated.}
       |      ^
checkRd: (-1) HTKmeans.Rd:63: Lost braces
    63 | \item{cluster }{A vector of integers (from 1:\code{k}) indicating the cluster to which each point is allocated.}
       |                ^
checkRd: (-1) HTKmeans.Rd:64: Lost braces
    64 | \item{itnb }{The number of iterations executed until convergence}
       |      ^
checkRd: (-1) HTKmeans.Rd:64: Lost braces
    64 | \item{itnb }{The number of iterations executed until convergence}
       |             ^
checkRd: (-1) HTKmeans.Rd:65: Lost braces
    65 | \item{converged }{Whether the algorithm stopped by converging or through reaching the maximum number of itertions.}
       |      ^
checkRd: (-1) HTKmeans.Rd:65: Lost braces
    65 | \item{converged }{Whether the algorithm stopped by converging or through reaching the maximum number of itertions.}
       |                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kmeansvar.Rd: splitmix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clustvarsel.Rd: mclustModelNames, hc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clusvisMixmod.Rd: MixmodCluster-class
  clusvisVarSelLCM.Rd: VSLCMresults-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cluster_stability.Rd: agnes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
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}
       |                     ^
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File 'CMF/libs/x64/CMF.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mlsei.Rd: solve.QP
  mlsun.Rd: solve.QP
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
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
       |                                  ^
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nested_data_plot.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'tobit1'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cnaOpt.Rd: configTable, rreduce, condTbl, cna
  conCovOpt.Rd: configTable, cna
  conCovOpt_utils.Rd: rreduce, condTbl
  ereduce.Rd: full.ct
  findOutcomes.Rd: configTable, cna, selectCases, full.ct
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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
       |                                                                       ^
Specified C++11: please drop specification unless essential
checkRd: (-1) conversion.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conversion.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conversion.Rd:70-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conversion.Rd:72-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conversion.Rd:75-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:103-104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:105-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:109-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:112-113: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
Package suggested but not available for checking: 'PopGenome'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dic.fit.mcmc.Rd: MCMCmetrop1R
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'disttree'
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CoClust-class.Rd: copula-class
  CoClust.Rd: fitCopula
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package which this enhances but not available for checking: 'rkward'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  envfit.coca.Rd: vectorfit, factorfit, envfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
2c2
< This is vegan 2.6-6.1
---
> This is vegan 2.6-4
Package which this enhances but not available for checking: 'rkward'
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 ?
Package suggested but not available for checking: 'userfriendlyscience'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  create_codemeta.Rd: write_json
  write_codemeta.Rd: write_json
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coefplot.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) kprime.Rd:36: Lost braces; missing escapes or markup?
    36 | kprime is a {p,d,q} set of functions that compute the K-prime distribution. This distribution has many applications,
       |             ^
checkRd: (-1) lsecond.Rd:37: Lost braces; missing escapes or markup?
    37 | lsecond are {p,d,q} functions that compute the Lambda-second (L") distribution. This
       |             ^
checkRd: (-1) pilsecond.Rd:39: Lost braces; missing escapes or markup?
    39 | pilsecond are {p,d,q} functions that compute the prior-informed Lambda-second (L") distribution. This
       |               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  boxesLx.Rd: grViz
  mkratetable.Rd: survival, pyears
  plotcuminc.Rd: survival, pyears
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  subsetPHMM.Rd: derivePHMM
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CoImp-class.Rd: fitCopula, lp, copula-class
  CoImp.Rd: fitCopula, lp
  MAR-class.Rd: lp, copula-class
  MAR.Rd: fitCopula
  MCAR-class.Rd: lp, copula-class
  MCAR.Rd: fitCopula
  NPCoImp-class.Rd: cluster, copula-class
  PerfMeasure-class.Rd: tailIndex, lp, copula-class
  PerfMeasure.Rd: fitCopula, tailIndex
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   2.7Mb
File 'collapse/libs/x64/collapse.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_TRUELENGTH', 'TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
File 'collections/libs/x64/collections.dll':
  Found non-API calls to R: 'PRENV', 'SET_CLOENV'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  roi_select.Rd: imager
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
checkRd: (-1) getHistList.Rd:32: Lost braces; missing escapes or markup?
    32 | ({FALSE})? If a bin is empty, the center of the bin is returned as the
       |  ^
checkRd: (-1) imageClusterPipeline.Rd:82: Lost braces; missing escapes or markup?
    82 | of the bin ({FALSE})? If a bin is empty, the center of the bin is returned
       |             ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_colors_3d.Rd: plotly
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  InterpolateColorFun.Rd: ggplot2
  OrderDataTSP.Rd: TSP
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.0Mb
checkRd: (-1) colour_values.Rd:143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values.Rd:144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values_rgb.Rd:143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values_rgb.Rd:144: Lost braces in \itemize; meant \describe ?
Unexported object imported by a ':::' call: 'crayon:::mypaste'
  See the note in ?`:::` about the use of this operator.
Problems with news in 'NEWS.md':
No news entries found.
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) xsimplex.Rd:6: Lost braces; missing escapes or markup?
     6 |              Generates all points on a {p,n} simplex lattice (i.e. a p-part
       |                                        ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) BMD.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add.risk.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add.risk.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) count_pairs.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) score_log_nonparam.Rd:36: Lost braces; missing escapes or markup?
    36 | {0, 1}.
       | ^
checkRd: (-1) score_log_semiparam.Rd:40: Lost braces; missing escapes or markup?
    40 | values in {0, 1}.
       |           ^
checkRd: (-1) sort_pairs.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    java   6.7Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) hmm.Rd:47-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:56-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:63-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:71-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:79-84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:85-89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:95-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:104-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:108-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:112-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:119-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:130-133: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'CAM'
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}
       |                       ^
checkRd: (-1) atomdeps.Rd:9: Lost braces
     9 |  \item{"tangle"}: {Dihedral angle defined by atoms A-B-C-D as described below. \code{NA}'s represent the free side chain dihedral angles \emph{chi} for that amino acid.}
       |                   ^
checkRd: (-1) atomdeps.Rd:10: Lost braces; missing escapes or markup?
    10 |  \item{"names"}: {The component atoms of the amino acid side chain.  Represents atom D in the dihedral.}
       |                  ^
checkRd: (-1) atomdeps.Rd:11: Lost braces; missing escapes or markup?
    11 |  \item{"matx"}: {The names of atoms A,B,C in the dihedral, with rows corresponding to the atoms in "names".}
       |                 ^
checkRd: (-1) atomdeps.Rd:12: Lost braces; missing escapes or markup?
    12 |  \item{"bangle"}: {Planar bond angle formed between B-C-D}
       |                   ^
checkRd: (-1) atomdeps.Rd:13: Lost braces; missing escapes or markup?
    13 |  \item{"blength"}: {Bond length between C-D}
       |                    ^
checkRd: (-1) keener.Rd:82: Lost braces; missing escapes or markup?
    82 | a_{ij} = (S_ij + 1) / (S_ij + S_ji + 2). This step should make comparing
       |   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rlm.Rd: lqs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  confint.Rd: boot.ci
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  codadendrogram.Rd: histogram
  pairwisePlot.Rd: lmrob
  pwlrPlot.Rd: lmrob
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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
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
       |                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  estimateParCondCopula.Rd: VineCopula
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) KCI.Rd:44: Lost braces
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                ^
checkRd: (-1) KCI.Rd:44: Lost braces
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                      ^
checkRd: (-1) KCI.Rd:44: Lost braces; missing escapes or markup?
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                                    ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cmvnorm.Rd: pmvnorm, dmvnorm, qmvnorm
  condMVN.Rd: pmvnorm, dmvnorm, qmvnorm
  pcmvnorm.Rd: GenzBretz, Miwa, TVPACK, pmvnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pcmvt.Rd: pmvt, GenzBretz
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
run_pipeline_gbq: no visible global function definition for
  'query_exec'
Undefined global functions or variables:
  query_exec
'LazyData' is specified without a 'data' directory
checkRd: (-1) mya.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:22: 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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  loo_conformal.Rd: predictive_interval
  predictive_interval.conformal.Rd: posterior_predict
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  conformal.multidim.full.Rd: future.apply
  conformal.multidim.msplit.Rd: future.apply
  glmnet.funs.Rd: glmnet
  plot_multidim.Rd: ggplot2, gridExtra, hrbrthemes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  km.outcomes.Rd: survfit
  km.pmf.Rd: survfit
  km.support.Rd: survfit
  km.surv.Rd: survfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) binary_class_cm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) NetStats.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DBI.Rd: DBIConnection-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
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.  
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ^
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Set.Rd: set
  deprecated.Rd: set
  dict.table.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) getConvexHull.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getConvexHull.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getConvexHull.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cf_grid.Rd:38: Lost braces; missing escapes or markup?
    38 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
checkRd: (-1) cf_highdim.Rd:58: Lost braces; missing escapes or markup?
    58 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
checkRd: (-1) gcf_grid.Rd:51: Lost braces; missing escapes or markup?
    51 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  curve_cont.Rd: riskRegression
  plot_surv_3Dsurface.Rd: riskRegression
  plot_surv_animated.Rd: riskRegression, facet_wrap
  plot_surv_area.Rd: riskRegression, facet_wrap
  plot_surv_at_t.Rd: riskRegression, facet_wrap
  plot_surv_contour.Rd: riskRegression, ggplot2, facet_wrap
  plot_surv_heatmap.Rd: riskRegression, facet_wrap
  plot_surv_lines.Rd: riskRegression, facet_wrap
  plot_surv_matrix.Rd: riskRegression, facet_wrap
  plot_surv_quantiles.Rd: riskRegression, facet_wrap
  plot_surv_rmst.Rd: riskRegression, facet_wrap
  plot_surv_rmtl.Rd: riskRegression, facet_wrap
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  svylorenz.Rd: oldsvyquantile
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) CovrgPlot.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{plotCI}{a vector of up to 4 numbers out of the set {1,2,3,4}, corresponding to which
       |                                                          ^
Specified C++11: please drop specification unless essential
checkRd: (-1) copCAR.Rd:40: Lost braces
    40 |        item{\code{maxit}}{the maximum number of iterations to be used by \code{\link{optim}} when optimizing the objective function. Defaults to \code{1000}.}
       |            ^
checkRd: (-1) copCAR.Rd:40: Lost braces
    40 |        item{\code{maxit}}{the maximum number of iterations to be used by \code{\link{optim}} when optimizing the objective function. Defaults to \code{1000}.}
       |                          ^
checkRd: (-1) condQestCopC.Rd:45: Lost braces; missing escapes or markup?
    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                          ^
checkRd: (-1) condQestCopC.Rd:45: Lost braces; missing escapes or markup?
    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                                      ^
checkRd: (-1) condQestCopC.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                  ^
checkRd: (-1) condQestCopC.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                              ^
checkRd: (-1) ComputeCope.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:57-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DrawContour.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Draws the contour {f=c}.}
       |                          ^
checkRd: (-1) DrawContour.Rd:20: Lost braces; missing escapes or markup?
    20 | Draws the contour {f=c}.
       |                   ^
checkRd: (-1) cope.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:35: Lost braces in \itemize; meant \describe ?
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.2Mb
    vignette_data   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.2Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cophe.prepare.dat.susie.Rd: runsusie
  cophe.susie.Rd: check_dataset, runsusie
  cophe.susie.lbf.Rd: runsusie
  cophe_heatmap.Rd: pheatmap
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bcalibrate.Rd: kEstimate, pca
  cal_rv.Rd: kEstimate, pca
  gcalibrate.Rd: kEstimate, pca
  plot_estimates.Rd: theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  margins.Rd: ptruncnorm, qtruncnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cloud2-methods.Rd: cloud
  contourplot2-methods.Rd: contourplot
  splom2-methods.Rd: splom
  wireframe2-methods.Rd: wireframe, panel.3dwire
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CopulaREMADA.Rd: meshgrid
  FactorCopulaREMADA.Rd: meshgrid
  VineCopulaREMADA.Rd: meshgrid
  Vuong.Rd: meshgrid
  hybridCopulaREMADA.Rd: meshgrid
  vineVuong.Rd: meshgrid
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  column.Rd: CsparseMatrix-class
  nnzero.Rd: CsparseMatrix-class, RsparseMatrix-class
  submatrix.Rd: CsparseMatrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cordillera.Rd: optics
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CoreCollection.Rd: R6Class
  dot-CoreCollectionClass.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) getSurface.Rd:22: Lost braces
    22 | value \code{getSurface} shortens the output of \code{conv} to remove artificial surface layers. The output is thus a subset of the input, and identical in structure to the /code{conv} output.
       |                                                                                                                                                                                  ^
checkRd: (-1) cvGen.Rd:29: Lost braces
    29 | The function code{gatherFromList} returns a list with components containing elements of the same name.
       |                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getRpartModel.Rd: rpart.object
  plot.CoreModel.Rd: rpart.plot, rpart.object, plot.rpart, pam
  rfClustering.Rd: pam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) CorMID.Rd:54: Lost braces; missing escapes or markup?
    54 |  individual compound containing 2 carbons and observe a vector of {978,22,0}.
       |                                                                   ^
checkRd: (-1) CorMID.Rd:58: Lost braces; missing escapes or markup?
    58 |  The equivalent corMID vector would be {1,0,0}, indicating that the non-labeled
       |                                        ^
Error(s) in re-building vignettes:
--- re-building 'CorMID.Rmd' using rmarkdown
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bbdml.Rd: trust
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) carstats.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:14: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  carstats.Rd: data.table
  rundata.Rd: data.table
  titanic.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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
       |                          ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tCorpus-cash-annotate_rsyntax.Rd: tquery
  tCorpus-cash-subset.Rd: subset.data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  corrarray.Rd: rcorr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) jointprobs.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) jointprobs.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) jointprobs.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) jointprobs.Rd:21: Lost braces; missing escapes or markup?
    21 | \eqn{K+1} categories the arrays will have either \eqn{K+1} or {K} dimensions, depending on whether 
       |                                                               ^
checkRd: (-1) multinom.gen.Rd:46: Lost braces
    46 | For a \emph{K}-variate multinomial, the matrix{m} should have \emph{K-1} columns
       |                                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cor_test.Rd: parameters, winsorize
  correlation.Rd: parameters, winsorize
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggbplot.Rd: bplot
  tally.Rd: bplot, calibrate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.7Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  corrgrapher.Rd: visNetwork
  plot.corrgrapher.Rd: visNetwork
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  polycorr.Rd: polychor
  tetracorr.Rd: polychor
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Invalid citation information in 'inst/CITATION':
  Error in s[[i]]: attempt to select more than one element in vectorIndex
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rplot.Rd: geom_point
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    doc    1.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ctmaAllInvFit.Rd: ctStanFit
  ctmaFit.Rd: ctStanFit, ctsem
  ctmaInit.Rd: ctStanFit, ctsem
  ctmaOptimizeFit.Rd: ctStanFit
  ctmaOptimizeInit.Rd: ctStanFit
  ctmaPlotCtsemMod.Rd: ctsem
  ctmaScaleInits.Rd: ctStanFit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) summary_fitlist.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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}
       |                                                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ml.nb1.Rd: glm.nb
  ml.nb2.Rd: glm.nb
  ml.nbc.Rd: glm.nb
  ml.pois.Rd: glm.nb
  modelfit.Rd: glm.nb
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/coursekata.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   4.7Mb
File 'covr/libs/x64/covr.dll':
  Found non-API calls to R: 'SET_BODY', 'SET_CLOENV', 'SET_FORMALS'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  axis_canvas.Rd: ggplot2, coord_flip
  background_grid.Rd: theme
  draw_line.Rd: geom_path
  draw_text.Rd: geom_label
  ggsave2.Rd: ggsave
  insert_xaxis_grob.Rd: ggplot2
  save_plot.Rd: ggsave
  theme_minimal_grid.Rd: theme_minimal
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coxed.Rd: mgcv, rms
  coxed.gam.Rd: mgcv
  coxed.gam.tvc.Rd: mgcv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.9Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) gen_data.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gen_data.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gen_data.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coxr.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) coxph.RT.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) coxph.RT.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) coxph.RT.Rd:59-71: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coxsei-package.Rd: survival
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CPC.Rd: diana, pam, dbscan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cpi.Rd: lrn, create.second_order
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
'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
checkRd: (-1) sharedat.Rd:23: Lost braces
    23 | \doi{10.7910/DVN/YXMQZM}{Harvard dataverse}
       |                         ^
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
checkRd: (-1) crwPredict.Rd:54-68: Lost braces
    54 | \item("predTime"){
       |                  ^
checkRd: (-1) crwPredict.Rd:59: Lost braces
    59 |  no longer the default (see \item{return.type}). If the original data were 
       |                                  ^
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Source(s) listed in 'build/vignette.rds' but not in package:
  'Introduction.Rmd'
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
checkRd: (-1) normFit.Rd:39: Lost braces; missing escapes or markup?
    39 | {analytes}}
       | ^
checkRd: (-1) normPred.Rd:27: Lost braces
    27 | ode{standards}, \code{analytes}}
       |    ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_multi_silodata.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  crossnma.Rd: jags.model
  netconnection.crossnma.Rd: netconnection
  netconnection.crossnma.model.Rd: netconnection
  netgraph.crossnma.Rd: netgraph.netmeta
  netgraph.crossnma.model.Rd: netgraph.netmeta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  body_add_table_list.Rd: body_add_flextable
  body_add_table_section.Rd: body_add_flextable
  ct_compact.Rd: flextable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  filter_slider.Rd: tag, HTML
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CrossVal.Rd: Modeler, Modeler-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Crossword.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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
       |      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  crrstep.Rd: crr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  crsra_anonymize.Rd: digest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
checkRd: (-1) cruts-package.Rd:21: Lost braces
    21 | section{Dependencies}{
       |        ^
checkRd: (-1) cruts-package.Rd:21-24: Lost braces
    21 | section{Dependencies}{
       |                      ^
checkRd: (-1) cruts-package.Rd:26: Lost braces
    26 | section{Citation}{
       |        ^
checkRd: (-1) cruts-package.Rd:26-28: Lost braces
    26 | section{Citation}{
       |                  ^
checkRd: (-1) cruts-package.Rd:30-32: Lost braces
    30 | references{
       |           ^
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc  11.9Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  alma.Rd: TTR
  assert.Rd: cli
  dema.Rd: TTR
  ema.Rd: TTR
  evwma.Rd: TTR
  fetch.Rd: xts
  get_fgindex.Rd: xts
  get_fundingrate.Rd: xts
  get_lsratio.Rd: xts
  get_openinterest.Rd: xts
  get_quote.Rd: xts
  hma.Rd: TTR
  sma.Rd: TTR
  vwap.Rd: TTR
  wma.Rd: TTR
  zlema.Rd: TTR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) calculate_cell_volume.Rd:16: Lost braces; missing escapes or markup?
    16 | V A real number. The volume (in angstroms^3 or angstroms^{-3})
       |                                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) calculateEffects.Rd:24: Lost braces; missing escapes or markup?
    24 | equals (I-B)^{-1}Gamma. The indirect effect equals the difference between
       |              ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
checkRd: (-1) csvy.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) csvy.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) csvy.Rd:60: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  csvy.Rd: calibrate, plotpersp, incr, decr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Source(s) listed in 'build/vignette.rds' but not in package:
  'CTD_Lab-Exercise.Rmd'
'LazyData' is specified without a 'data' directory
checkRd: (-1) mcmc.fmove.Rd:81: Lost braces; missing escapes or markup?
    81 |   beta ~ N( 0 , tau^2 * QQ^{-1} )
       |                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  akde.Rd: res
  as.telemetry.Rd: fread
  ctmm-FAQ.Rd: zoom
  projection.Rd: CRS
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ctpm.fit.Rd: slouch, plot.variogram
  variogram.Rd: plot.variogram
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ctqr-package.Rd: pchreg
  ctqr.Rd: Surv, pchreg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ctFit.Rd: ctModel
  ctModelFromFit.Rd: ctModel
  ctMultigroupFit.Rd: ctLongToWide, ctModel
  ctPostPredict.Rd: ctPlotArray
  ctRefineTo.Rd: ctModel
  ctsemOMX.Rd: ctModel
  summary.ctsemFit.Rd: ctModel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.7Mb
    libs   7.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cubeViewOutput.Rd: shinyWidgetOutput
  cubeview.Rd: levelplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  jumpoints.Rd: lars
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Survcure.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.8Mb
File 'curl/libs/x64/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Package which this enhances but not available for checking: 'RGtk2'
'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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SparseCCA.Rd: CCA, CCA.permute
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    doc    1.2Mb
    libs   1.2Mb
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  simulate_cycloSurv.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  createCyclopsData.Rd: Matrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata       1.3Mb
    htmlwidgets   1.4Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Cramer_vonMises.Rd: Copula-class
  Cylcop.Rd: Copula-class
  ccylcop.Rd: Copula-class
  cyl_copula-class.Rd: Copula-class
  cyl_rect_combine-class.Rd: Copula-class
  cyl_rect_combine.Rd: Copula-class
  cyl_rot_combine-class.Rd: Copula-class
  cyl_rot_combine.Rd: Copula-class
  fit_cylcop_ml.Rd: Copula-class, fitCopula
  full2half_circ.Rd: circular
  half2full_circ.Rd: circular
  joint.Rd: Copula-class
  numerical_conditional_cop.Rd: Copula-class
  numerical_inv_conditional_cop.Rd: Copula-class
  plot_cop_surf.Rd: Copula-class
  wasserstein.Rd: Copula-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_fan.Rd: aes, aes_, ggplot, fortify, borders, layer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) CytofTree.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RetrievePops.Rd:20-21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RetrievePops.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rnaRaw.Rd: dgCMatrix-class
  rnaVelo.Rd: dgCMatrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ConfMatrix.Rd: R6
  D2MCS.Rd: getModelInfo
  GainRatioHeuristic.Rd: gain.ratio
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  StoragehubManager.Rd: R6Class
  d4storagehub4RLogger.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Found the following HTML validation problems:
saveReportTable.html:80:1 (saveReportTable.Rd:36): Warning: trimming empty <dt>
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DAAGtheme.Rd: theEconomist.theme, standard.theme, simpleTheme,
    custom.theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{  A small, positive scalar that determines when iterations
       |               ^
checkRd: (-1) fpiter.Rd:60-61: Lost braces
    60 |     \code{maxiter}{  An integer denoting the maximum limit on the number of
       |                   ^
checkRd: (-1) fpiter.Rd:63-65: Lost braces
    63 |     \code{trace}{  A logical variable denoting whether some of the intermediate
       |                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  associations.Rd: Assocs
  associations.folder.Rd: Assocs
  kurtosis.folder.Rd: kurtosis
  mdsdd.Rd: Assocs
  plotframes.Rd: xyplot
  skewness.folder.Rd: skewness
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  designGGPlot.Rd: labellers, ggplot, geom_text
  designPlotlabels.Rd: ggplot, geom_text
  interaction.ABC.plot.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) formatScientificTeX.Rd:33: Lost braces; missing escapes or markup?
    33 | function will return  " 3.0\\\\times 10^{2}"
       |                                         ^
Package which this enhances but not available for checking: 'doMC'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DAISIE_ML.Rd: deSolve
  DAISIE_ML1.Rd: deSolve
  DAISIE_ML2.Rd: deSolve
  DAISIE_ML4.Rd: deSolve
  DAISIE_ML_IW.Rd: deSolve
  DAISIE_loglik_integrand.Rd: deSolve
  DAISIE_loglik_integrate.Rd: deSolve
  default_params_doc.Rd: deSolve
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.predict_parts.Rd: break_down, local_attributions,
    local_interactions
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  link_dam_metadata.Rd: data.table
  read_dam_file.Rd: behavr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  factload.Rd: polychor
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  utils.dart2genlight.Rd: adegenet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gl.filter.parent.offspring.Rd: gl.report.rdepth,
    gl.report.reproducibility
  gl.report.parent.offspring.Rd: gl.report.rdepth,
    gl.report.reproducibility
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
checkRd: (-1) gl.filter.maf.Rd:7: Lost braces; missing escapes or markup?
     7 |  {adegenet} object}
       |  ^
checkRd: (-1) gl.pcoa.Rd:68: Lost braces; missing escapes or markup?
    68 | The function is essentially a wrapper for glPca {adegenet} or pcoa \{ape\}
       |                                                 ^
checkRd: (-1) gl.play.history.Rd:17: Lost braces
    17 | code{x2@other$history[c(1,4,5)]}). [optional].}
       |     ^
checkRd: (-1) utils.jackknife.Rd:49: Lost braces
    49 | bold{Note} that when n is very small, jackknife resampling is not recommended.
       |     ^
checkRd: (-1) utils.jackknife.Rd:51: Lost braces
    51 | Parallel computation is implemented. The argument code{n.cores} indicates the 
       |                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gl.genleastcost.Rd: landgenreport, popgenreport, wassermann, lgrMMRR
  utils.dart2genlight.Rd: adegenet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gl.diagnostics.sim.Rd: gl.filter.callrate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gl.spatial.autoCorr.Rd: gl.propShared, gl.dist.ind
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dcr_app.Rd: plotly
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FillIn.Rd: data.table
  slide.Rd: dplyr
  slideMA.Rd: dplyr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) processFlow.Rd:14: Lost braces
    14 | \item{roundDigits}{Integer. If NA, numerics are not rounded before comparison. If /code{roundDigits} is specified, numerics are 
       |                                                                                        ^
checkRd: (-1) processFlow.Rd:15: Lost braces
    15 | rounded to /code{roundDigits} decimal places using \link[base]{round}.}
       |                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) data_edit.Rd:137: Lost braces
   137 | code{data_edit} is a shiny application built on \code{rhandsontable} that is
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  configure_report.Rd: theme
  create_report.Rd: render
  drop_columns.Rd: data.table
  group_category.Rd: data.table
  plotDataExplorer.Rd: theme
  plotDataExplorer.grid.Rd: theme
  plotDataExplorer.multiple.Rd: theme, facet_wrap
  plotDataExplorer.single.Rd: theme
  plot_bar.Rd: geom_bar, theme_gray, theme
  plot_boxplot.Rd: geom_boxplot, geom_jitter, scale_y_continuous,
    theme_gray, theme
  plot_correlation.Rd: geom_text, theme_gray, theme
  plot_density.Rd: geom_density, scale_x_continuous, theme_gray, theme
  plot_histogram.Rd: geom_histogram, scale_x_continuous, theme_gray,
    theme
  plot_intro.Rd: geom_label, theme_gray, theme
  plot_missing.Rd: geom_label, theme_gray, theme
  plot_prcomp.Rd: geom_label, theme_gray, theme
  plot_qq.Rd: geom_qq, geom_qq_line, theme_gray, theme
  plot_scatterplot.Rd: geom_point, geom_jitter, scale_x_continuous,
    scale_y_continuous, theme_gray, theme
  plot_str.Rd: diagonalNetwork, radialNetwork
  set_missing.Rd: data.table
  split_columns.Rd: data.table
  update_columns.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) defaultFactorSummaries.Rd:29: Lost braces
    29 | code{\link{variableType}}, \code{\link{countMissing}}, \code{\link{uniqueValues}},
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  identifyOutliers.Rd: mc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dataone-defunct.Rd: getData, getIdentifier, getFormatId,
    setPublicAccess, canRead, addData
  setPublicAccess.Rd: DataObject-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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"}}
       |                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  aggregate_by_key.Rd: data.table
  build_target_encoding.Rd: data.table
  fast_handle_na.Rd: copy, data.table
  generate_date_diffs.Rd: data.table
  set_col_as_character.Rd: data.table
  set_col_as_date.Rd: data.table
  set_col_as_factor.Rd: data.table
  set_col_as_numeric.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  acc_distributions.Rd: ggplot
  acc_distributions_loc.Rd: ggplot
  acc_distributions_loc_ecdf.Rd: ggplot
  acc_distributions_only.Rd: ggplot
  acc_distributions_only_ecdf.Rd: ggplot
  acc_distributions_prop.Rd: ggplot
  acc_multivariate_outlier.Rd: ggplot2
  acc_robust_univariate_outlier.Rd: ggplot
  acc_shape_or_scale.Rd: ggplot2
  acc_univariate_outlier.Rd: ggplot
  con_contradictions.Rd: ggplot
  con_contradictions_redcap.Rd: ggplot
  con_limit_deviations.Rd: ggplot
  des_scatterplot_matrix.Rd: ggplot
  int_datatype_matrix.Rd: ggplot2
  prep_render_pie_chart_from_summaryclasses_ggplot2.Rd: ggplot2
  pro_applicability_matrix.Rd: ggplot2
  util_heatmap_1th.Rd: ggplot
  util_plot_figure_no_plotly.Rd: ggplot2
  util_plot_figure_plotly.Rd: ggplot2
  util_set_size.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) defaultFactorSummaries.Rd:29: Lost braces
    29 | code{\link{variableType}}, \code{\link{countMissing}}, \code{\link{uniqueValues}},
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  identifyOutliers.Rd: mc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dataStepClass.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'data.table/libs/x64/data_table.dll':
  Found non-API calls to R: 'LEVELS', 'NAMED', 'SETLENGTH',
    'SET_GROWABLE_BIT', 'SET_S4_OBJECT', 'SET_TRUELENGTH',
    'SET_TYPEOF', 'STRING_PTR', 'TRUELENGTH', 'UNSET_S4_OBJECT'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Node.Rd: R6Class
  as.Node.rpart.Rd: rpart, text.rpart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  stat_pde_density.Rd: aes, aes_, ggplot, fortify, layer, borders
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) is_datelife_query.Rd:17: Lost braces; missing escapes or markup?
    17 | First, that \code{input} is of class {datelifeQuery}.
       |                                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clean_taxon_info_children.Rd: taxonomy_taxon_info
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following HTML validation problems:
get_dated_otol_induced_subtree.html:53:1 (get_dated_otol_induced_subtree.Rd:19): Warning: trimming empty <dt>
get_otol_synthetic_tree.html:67:1 (get_otol_synthetic_tree.Rd:29): Warning: trimming empty <dt>
summary_matrix_to_phylo.html:89:1 (summary_matrix_to_phylo.Rd:42): Warning: trimming empty <dt>
Package suggested but not available for checking: 'SASxport'
'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 Rd file(s) with Rd \link{} targets missing package
anchors:
  dbcsp-class.Rd: TSDatabaseDistances, parallelDist
  predict.dbcsp.Rd: predict.lda
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) plot.mleBb.Rd:48: Lost braces
    48 |   \ code{size} is extracted from argument \code{x}.
       |         ^
checkRd: (-1) value_missing_table.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) value_missing_table.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CI_mc.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{i}{the row index of the interest entry X_{i,j}}
       |                                                ^
checkRd: (-1) CI_mc.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{j}{the row index of the interest entry X_{i,j}}
       |                                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DEnvelope.Rd: envelope
  Dhat.Rd: fv.object, plot.fv, Kest, Kcross
  FillEnvelope.Rd: fv.object, envelope
  GlobalEnvelope.Rd: fv.object
  GoFtest.Rd: envelope
  KEnvelope.Rd: envelope
  KdEnvelope.Rd: envelope
  Kdhat.Rd: fv.object, plot.fv
  Khat.Rd: fv.object, plot.fv, Kest, Kcross
  KinhomEnvelope.Rd: density.ppp, envelope
  Kinhomhat.Rd: density.ppp, bw.diggle, fv.object, plot.fv, Kinhom
  KmmEnvelope.Rd: envelope
  Kmmhat.Rd: fv.object, plot.fv, markcorrint
  Ktest.Rd: ppp.object, is.rectangle
  LEnvelope.Rd: envelope
  Lhat.Rd: fv.object, plot.fv
  LmmEnvelope.Rd: envelope
  Lmmhat.Rd: fv.object, plot.fv
  MEnvelope.Rd: envelope
  Mhat.Rd: fv.object, plot.fv
  Smooth.wmppp.Rd: fv.object, Smooth.ppp, bw.scott
  as.Dtable.Rd: ppp
  as.wmppp.Rd: owin.object, ppp, ppp.object
  autoplot.Rd: ggplot
  dbmssEnvelope.Rd: envelope
  envelope.Dtable.Rd: envelope
  gEnvelope.Rd: envelope
  generic.spatstat.Rd: ppp.object, rthin, sharpen.ppp, split.ppp,
    superimpose.ppp, unique.ppp
  ghat.Rd: sewpcf, fv.object, plot.fv
  m_Envelope.Rd: envelope
  m_hat.Rd: fv.object, plot.fv
  paracou16.Rd: ppp.object
  print.dbmssEnvelope.Rd: envelope
  rPopulationIndependenceK.Rd: rshift
  rRandomPositionK.Rd: runifpoint, rpoispp
  summary.dbmssEnvelope.Rd: envelope
  wmppp.Rd: owin.object
  wmppp.object.Rd: ppp, ppp.object
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  arrange.tbl_lazy.Rd: arrange, show_query
  backend-hana.Rd: copy_to
  collapse.tbl_sql.Rd: collapse, compute, collect
  complete.tbl_lazy.Rd: show_query
  copy_inline.Rd: copy_to
  copy_to.src_sql.Rd: copy_to, show_query
  count.tbl_lazy.Rd: count, tally
  db-sql.Rd: copy_to
  dbplyr-slice.Rd: slice_min, slice_max, slice_sample
  distinct.tbl_lazy.Rd: distinct, show_query
  expand.tbl_lazy.Rd: show_query
  filter.tbl_lazy.Rd: show_query
  get_returned_rows.Rd: rows_insert, rows_append, rows_update,
    rows_upsert, rows_delete
  group_by.tbl_lazy.Rd: group_by
  head.tbl_lazy.Rd: show_query
  join.tbl_sql.Rd: join, show_query
  memdb_frame.Rd: !!, !!!, .data, .env
  mutate.tbl_lazy.Rd: mutate, transmute, show_query
  nycflights13.Rd: src_postgres
  pivot_wider.tbl_lazy.Rd: expand
  pull.tbl_sql.Rd: pull
  replace_na.tbl_lazy.Rd: show_query
  rows-db.Rd: rows_insert, rows_append, rows_update, rows_patch,
    rows_upsert, rows_delete, tbl, compute
  select.tbl_lazy.Rd: select, rename, relocate
  summarise.tbl_lazy.Rd: summarise, show_query
  tbl.src_dbi.Rd: compute, collect, show_query, explain, do
  win_over.Rd: group_by, arrange
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dbglm.Rd: daisy
  dblm.Rd: daisy
  dbplsr.Rd: plsr, daisy
  disttoD2.rd: daisy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) data.Rd:11: Lost braces
    11 | \doi{10.1007/s40258-021-00647-3}{DOI}
       |                                 ^
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'BRugs'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dcoptions.Rd: gelman.diag
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) CalcStatClusterGivenCenter.Rd:36: Lost braces; missing escapes or markup?
    36 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) CalcStatClusterGivenCenter.Rd:37: Lost braces; missing escapes or markup?
    37 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) CalcStatsAllClusters.Rd:49: Lost braces; missing escapes or markup?
    49 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) CalcStatsAllClusters.Rd:50: Lost braces; missing escapes or markup?
    50 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) DetectClustersModel.Rd:60: Lost braces; missing escapes or markup?
    60 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) DetectClustersModel.Rd:61: Lost braces; missing escapes or markup?
    61 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) glmAndZIP.iscluster.Rd:34: Lost braces; missing escapes or markup?
    34 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) glmAndZIP.iscluster.Rd:35: Lost braces; missing escapes or markup?
    35 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CalcStatClusterGivenCenter.Rd: glmer
  CalcStatsAllClusters.Rd: glmer
  DetectClustersModel.Rd: glmer, SpatialPolygonsDataFrame, STFDF,
    SpatialPolygons
  glmAndZIP.iscluster.Rd: glmer
  knbinary.Rd: SpatialPolygonsDataFrame
  mergeknclusters.Rd: SpatialPolygonsDataFrame
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dcFit-class.Rd: bugs.fit
  gsFit-class.Rd: bugs.fit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) kernel.assign.Rd:27: Lost braces; missing escapes or markup?
    27 |  {q = [0, 1]}. Kernels are of the Müller-Wang type ("MW"), Müller type ("M")
       |  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dNTD.Rd: plotTensor3D
  dNTF.Rd: plotTensor3D
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CUR.Rd: pcor, spcor
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ddalpha.train.Rd: covMcd, lda, knn, knn.cv
  depth.L2.Rd: covMcd
  depth.Mahalanobis.Rd: covMcd
  depth.betaSkeleton.Rd: covMcd
  depth.potential.Rd: covMcd
  depth.simplicialVolume.Rd: covMcd
  depth.space.Mahalanobis.Rd: covMcd
  depth.space.potential.Rd: covMcd
  depth.space.simplicialVolume.Rd: covMcd
  depth.space.spatial.Rd: covMcd
  depth.spatial.Rd: covMcd
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) detectAgeInterval.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Age}, or code{age}.}
       |                                                                              ^
checkRd: (-1) detectSex.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Sex}, or code{sex}.}
       |                                                                              ^
checkRd: (-1) ggbgetAgesFit.Rd:28: Lost braces
    28 | code{\link{ggbChooseAges}}
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.ddpcr_plate.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ddpcr_plate.Rd:138-139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ddpcr_plate.Rd:140-141: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_cashflow.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  declare_estimator.Rd: lm_robust, estimatr, glance
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'declared/libs/x64/declared.dll':
  Found non-API calls to R: 'ENVFLAGS', 'SET_ENVFLAGS'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  inst.ratio.Rd: pdfDisplay
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) deconv.Rd:85: Lost braces; missing escapes or markup?
    85 |     \code{tg}, std. error of \eqn{g}, \eqn{G} (the cdf of {g}),
       |                                                           ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  recode.variables.Rd: recode
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dedupe_wide.Rd: data.table
  na_move.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  deepforest.Rd: rpart.control
  deeptree.Rd: rpart.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) deepNN-package.Rd:18: Lost braces
    18 | section{Dependencies}{
       |        ^
checkRd: (-1) deepNN-package.Rd:18-21: Lost braces
    18 | section{Dependencies}{
       |                      ^
checkRd: (-1) deepNN-package.Rd:23: Lost braces
    23 | section{Citation}{
       |        ^
checkRd: (-1) deepNN-package.Rd:23-25: Lost braces
    23 | section{Citation}{
       |                  ^
checkRd: (-1) deepNN-package.Rd:27-38: Lost braces
    27 | references{
       |           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) deltaPlot.Rd:28: Lost braces
    28 |  \item{purify}{logical: should item purification be performed? (Default is code{FALSE}). See \bold{Details}.}
       |                                                                                ^
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
checkRd: (-1) kin.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:53-61: Lost braces
    53 | {\itemize{
       | ^
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sim.dpp.modal.fast.Rd: spam
  sim.dpp.modal.fast.seq.Rd: spam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dendro.varcov.Rd: varFunc, varIdent, lmeObject
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    help   2.2Mb
    libs   1.9Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  estim_sigma.Rd: estim_ncp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  denseFLMM.Rd: gamm, mgcv, gam, bam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  density_polygons.Rd: sf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'densityClust/libs/x64/densityClust.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  densregion.Rd: contourplot, levelplot
  densregion.survfit.Rd: survfit
  denstrip.Rd: trellis.par.get
  denstrip.legend.Rd: trellis.par.get
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  start_bot_for_chat.Rd: telegram.bot
  use_ui.Rd: ui_line, ui_todo, ui_done, ui_oops, ui_info,
    ui_code_block, ui_stop, ui_warn, ui_yeah, ui_nope, ui_field,
    ui_value, ui_path, ui_code
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       4.8Mb
    extdata   2.1Mb
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
       |                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  depmix.fit.Rd: solnp
  response-classes.Rd: nnet
  vcov.Rd: nlme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
checkRd: (-1) Deriv.Rd:33: Lost braces
    33 | guessed either from\ code{names(formals(f))} (if \code{f} is a function)
       |                          ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.N' '.Nmiss' '.Q1' '.Q3' '.factorN' '.factorNmiss' '.factorQ1'
  '.factorQ3' '.factormax' '.factormean' '.factormedian' '.factormin'
  '.factorsd' '.max' '.mean' '.median' '.min' '.sd'
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pander.desctable.Rd: pandoc.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'RDCOMClient'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.7Mb
    libs   1.2Mb
checkRd: (-1) alpha.split.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{r}{vector for the proportion for each sub-population, r_1 is 1, r_i>r_{i+1}}
       |                                                                             ^
checkRd: (-1) designCTPB.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{r_set}{the matrix of proportion for each sub-population, r_1 is 1, r_i>r_{i+1}}
       |                                                                                ^
checkRd: (-1) phat.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{r}{vector for the proportion for each sub-population, r_1is 1, r_i>r_{i+1}}
       |                                                                            ^
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.6Mb
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.}
       |                               ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DetLTS.Rd: h.alpha.n
  OGKCStep.Rd: h.alpha.n
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  check.Rd: compiler_flags
  remote-reexports.Rd: ellipsis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MA_estimates.Rd: glmer, lmerControl, glmerControl
  REMB-class.Rd: glmer
  glimem.Rd: glmer, lmerControl, glmerControl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) mtaBin_next.Rd:27: Lost braces
    27 |   \item{s_1}{A function depending on the number of patients included used for adaptive randomization in plateau determination, only used if the estimation method chosen is "MTA-RA". The default function is function(n_cur,n){0.2}.}
       |                                                                                                                                                                                                                                ^
checkRd: (-1) mtaBin_sim.Rd:30: Lost braces
    30 |   \item{s_1}{A function depending on the number of patients included used for adaptive randomization in plateau determination, only used if the estimation method chosen is "MTA-RA". The default function is function(n_cur){0.2}.}
       |                                                                                                                                                                                                                              ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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 ?
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.}
       |                                                                         ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) dHSIC-package.Rd:32: Lost braces
    32 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dHSIC-package.Rd:36: Lost braces
    36 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dHSIC-package.Rd:36: Lost braces
    36 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
checkRd: (-1) dhsic.Rd:84: Lost braces
    84 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dhsic.Rd:88: Lost braces
    88 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dhsic.Rd:88: Lost braces
    88 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
checkRd: (-1) dhsic.test.Rd:124: Lost braces
   124 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dhsic.test.Rd:128: Lost braces
   128 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dhsic.test.Rd:128: Lost braces
   128 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  class_to_regL1.Rd: rq
  class_to_rq.Rd: rq
  forwardSearch_regL1.Rd: lmsreg, rq, rq.fit.br, rq.fit.fnb
  regL1.Rd: rq, rq.fit.br, rq.fit.fnb
  regL1_het.Rd: rq, rq.fit.br, rq.fit.fnb
  summary.regL1.Rd: summary.rq, boot.rq
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  max_qEI.Rd: genoud
  qEGO.nsteps.Rd: genoud
  sampleFromEI.Rd: km
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) DIconvex.Rd:40: Lost braces; missing escapes or markup?
    40 |  {Paul Schneider <paul.schneider@usi.ch>}{}
       |  ^
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) did_imputation.Rd:74: Lost braces; missing escapes or markup?
    74 | form average treatment effects for groups of {it}.
       |                                              ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  diffChr.Rd: style, num_colors
  diffCsv.Rd: style, num_colors
  diffDeparse.Rd: style, num_colors
  diffFile.Rd: style, num_colors
  diffPrint.Rd: style, num_colors
  diffStr.Rd: style, num_colors
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  diffr.Rd: createWidget
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
checkRd: (-1) simulate_diff_tables.Rd:72: Lost braces; missing escapes or markup?
    72 |   {The Sharma-Song test} {\code{\link[DiffXTables]{sharma.song.test}}}
       |   ^
checkRd: (-1) simulate_diff_tables.Rd:74: Lost braces; missing escapes or markup?
    74 |   {The comparative chi-squared test} {\code{\link[DiffXTables]{cp.chisq.test}}}
       |   ^
checkRd: (-1) simulate_diff_tables.Rd:76: Lost braces; missing escapes or markup?
    76 |   {The heterogeneity test} {\code{\link[DiffXTables]{heterogeneity.test}}}
       |   ^
checkRd: (-1) difTID.Rd:185: Lost braces
   185 |  \code{\link[deltaPlotR]{deltaPlot}}, code{\link[deltaPlotR]{diagPlot}}, \code{\link{dichoDif}}
       |                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  itemPar1PL.rd: rasch
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DigitalDLSorter-class.Rd: SingleCellExperiment-class,
    dgCMatrix-class, ZinbModel-class, SummarizedExperiment-class
  ZinbParametersModel-class.Rd: ZinbModel-class
  bulk.simul.Rd: SummarizedExperiment-class
  createDDLSobject.Rd: SingleCellExperiment-class,
    SummarizedExperiment-class
  loadDeconvData.Rd: SummarizedExperiment-class
  simSCProfiles.Rd: SingleCellExperiment-class
  single.cell.real.Rd: SingleCellExperiment-class
  single.cell.simul.Rd: SingleCellExperiment-class
  zinb.params.Rd: ZinbModel-class
  zinbwave.model.Rd: ZinbModel-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) DIME.Rd:272: Lost braces; missing escapes or markup?
   272 | \item{name}{the name of the model {"GNG", "iNUDGE","NUDGE"} where
       |                                   ^
checkRd: (-1) DRR-class.Rd:79: Lost braces; missing escapes or markup?
    79 | n^{1/3} up to sacrificing some accuracy, for details see
       |   ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DirichletRegModel.Rd: update.Formula
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  iact.Rd: multiESS
  mcmcdiag.Rd: multiESS
  metropdir.Rd: multiESS
  metropdir.adapt.Rd: multiESS
  msjd.Rd: multiESS
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  expectreg.aft.Rd: rb, cdf.qp, cdf.bundle, summary.expectreg,
    plot.expectreg, predict.expectreg, resid.expectreg,
    fitted.expectreg, effects.expectreg
  modreg.Rd: control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nelsonaalen_npdf.Rd: survfit
  npdf_cox.Rd: Surv
  plot.npdf.Rd: survfit.formula, plot.survfit
  survfit_npdf.Rd: survfit.formula
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) app_server.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{input, output, session}{Internal parameters for `{shiny}`.
       |                                                        ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  discrim-package.Rd: discrim_flexible
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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)
       |                ^
checkRd: (-1) cIndex.Rd:32: Lost braces; missing escapes or markup?
    32 | [a_{q-1}, a_q) are available.
       |    ^
checkRd: (-1) cIndexCompRisks.Rd:31: Lost braces; missing escapes or markup?
    31 | [a_{q-1}, a_q) are available.
       |    ^
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
checkRd: (-1) estMargProb.Rd:23: Lost braces; missing escapes or markup?
    23 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) estMargProbCompRisks.Rd:24: Lost braces; missing escapes or markup?
    24 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) estSurv.Rd:23: Lost braces; missing escapes or markup?
    23 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) estSurvCompRisks.Rd:24: Lost braces; missing escapes or markup?
    24 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) lifeTable.Rd:21: Lost braces; missing escapes or markup?
    21 | [a_0, a_1), [a_1, a_2), ..., [a_{q-1}, a_q) ("character vector")}
       |                                 ^
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) csv_to_disk.frame.Rd:56: Lost braces; missing escapes or markup?
    56 | strings, and you are encouraged to use {fasttime} to convert the strings to
       |                                        ^
checkRd: (-1) purrr_as_mapper.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{.f}{a normal function or purrr syntax function i.e. `~{ ...code...}`}
       |                                                             ^
checkRd: (-1) mess.Rd:28: Lost braces
    28 | Elith J., M. Kearney M., and S. Phillips, 2010. The art of modelling range-shifting species. \doi{10.1111/j.2041-210X.2010.00036.x}{Methods in Ecology and Evolution 1:330-342}.
       |                                                                                                                                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gbif.Rd: drawExtent, extent
  gmap.Rd: plotRGB
  mess.Rd: writeRaster
  predict.Rd: writeRaster
  randomPoints.Rd: Extent
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
       |                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ds.Rd: AIC.ds, plot.ds
  print.summary.dsmodel.Rd: summary.ds
  summary.dsmodel.Rd: summary.ds, dht
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DistatisR-package.Rd: prettyGraphs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'distcomp/libs/x64/distcomp.dll':
  Found non-API call to R: 'NAMED'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
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: \&
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) dapply.Rd:27-30: Lost braces
    27 | udf <- function(x){
       |                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dists.Rd: betareg
  moments.Rd: betareg, gamlss, bamlss
  plot_dist.Rd: gamlss, bamlss, betareg, ggplot2
  plot_moments.Rd: gamlss, bamlss, betareg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EmpiricalMVDistribution.Rd: DiscreteDistribution
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:31: Lost braces
    31 | \strong{Support}: {x in [0, \eqn{\infty})}
       |                   ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) moranTest.Rd:37: Lost braces; missing escapes or markup?
    37 |   {M(theta)=-(log(y_1-y_0)+log(y_2-y_1)+...+log(y_m-y_m-1))}
       |   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  qqplot.Rd: qqbounds
  returnlevelplot.Rd: qqbounds
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
2c2
< :startupmsg>  Utilities for Start-Up Messages (version 0.9.6.1)
---
> :startupmsg>  Utilities for Start-Up Messages (version 0.9.6)
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dmrcoef-class.Rd: dgCMatrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
2c2
< :startupmsg>  Utilities for Start-Up Messages (version 0.9.6.1)
---
> :startupmsg>  Utilities for Start-Up Messages (version 0.9.6)
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mock-db-methods.Rd: dbConnect, dbListFields, dbWriteTable,
    dbRemoveTable, dbGetInfo, dbQuoteIdentifier
  mockdb.Rd: dbConnect
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  freqPlot.Rd: geom_violin
  scatterHex.Rd: ggrepel
  scatterPlot.Rd: ggrepel
  yPlot.Rd: geom_violin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) fadlad.Rd:30: Lost braces
    30 | \item{diffbin}{\code{(logical)}: Difference-based duration for discreet time (only applicabble to cases when \code{bin} is provided). If set to \code{TRUE}, single-interval taxa will \code{0} durations. Setting this argument to \code{FALSE} will add code{1} to the durations of all taxa.}
       |                                                                                                                                                                                                                                                               ^
checkRd: (-1) slice.Rd:27: Lost braces
    27 | Due to stratigraphic constraints, we can only process deep time data, when it is sliced to discrete bins. It is suggested that you do this separately for most of your analyses. This function is also used by the code{\link{divDyn}} function when \code{age} entries are provided.
       |                                                                                                                                                                                                                        ^
checkRd: (-1) tabinate.Rd:31: Lost braces
    31 | Setting both \code{bin} If \code{bin=NULL} and code{tax=NULL}, will run \code{FUN} on the entire dataset (no effect). Providing either \code{bin} or \code{tax} and keeping the other \code{NULL} will iterate \code{FUN} for every \code{bin} or \code{tax} entry (whichever is presented).
       |                                                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calibrateDepth.Rd: unireg
  labDive-internal.Rd: unireg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  find.mle.Rd: subplex, ace, birthdeath
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'BOLTSSIRR'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cr.Rd: smooth.construct.cr.smooth.spec
  ps.Rd: smooth.construct.ps.smooth.spec
  smooth.construct.cb.smooth.spec.Rd: smooth.construct.ps.smooth.spec,
    smooth.construct.cr.smooth.spec,
    smooth.construct.tensor.smooth.spec
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  compare_category.data.frame.Rd: tbl_df
  compare_numeric.data.frame.Rd: tbl_df
  correlate.data.frame.Rd: grouped_df
  describe.data.frame.Rd: tbl_df, grouped_df, group_by
  describe.tbl_dbi.Rd: group_by
  diagnose.data.frame.Rd: tbl_df, grouped_df
  diagnose_category.data.frame.Rd: tbl_df, grouped_df
  diagnose_numeric.data.frame.Rd: tbl_df, grouped_df
  diagnose_outlier.data.frame.Rd: tbl_df, grouped_df
  diagnose_paged_report.data.frame.Rd: tbl_df
  diagnose_report.data.frame.Rd: tbl_df
  diagnose_sparese.data.frame.Rd: tbl_df
  diagnose_web_report.data.frame.Rd: tbl_df
  eda_paged_report.data.frame.Rd: tbl_df
  eda_report.data.frame.Rd: tbl_df
  eda_web_report.data.frame.Rd: tbl_df
  find_na.Rd: tbl_df
  find_outliers.Rd: tbl_df
  find_skewness.Rd: tbl_df
  imputate_na.Rd: tbl_df
  imputate_outlier.Rd: tbl_df
  normality.data.frame.Rd: tbl_df, group_by
  normality.tbl_dbi.Rd: group_by
  overview.Rd: tbl_df
  plot_bar_category.data.frame.Rd: tbl_df, grouped_df
  plot_box_numeric.data.frame.Rd: tbl_df, grouped_df
  plot_correlate.data.frame.Rd: tbl_df
  plot_hist_numeric.data.frame.Rd: tbl_df, grouped_df
  plot_normality.data.frame.Rd: tbl_df
  plot_outlier.data.frame.Rd: tbl_df
  plot_qq_numeric.data.frame.Rd: tbl_df, grouped_df
  target_by.data.frame.Rd: tbl_df, grouped_df
  target_by.tbl_dbi.Rd: grouped_df
  transformation_paged_report.Rd: tbl_df
  transformation_report.Rd: tbl_df
  transformation_web_report.Rd: tbl_df
  univar_category.data.frame.Rd: tbl_df
  univar_numeric.data.frame.Rd: tbl_df
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}
       |                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot-dmbc_fit-ANY-method.Rd: bayesplot, MCMC-overview
  plot-dmbc_fit_list-ANY-method.Rd: bayesplot, MCMC-overview
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) dca.Rd:24: Lost braces; missing escapes or markup?
    24 | \eqn{neglinks_{ij} = 1} means chunklet \code{i} and chunklet {j}
       |                                                              ^
checkRd: (-1) dca.Rd:26: Lost braces; missing escapes or markup?
    26 | \eqn{neglinks_{ij} = 0} means chunklet \code{i} and chunklet {j}
       |                                                              ^
checkRd: (-1) rca.Rd:57: Lost braces; missing escapes or markup?
    57 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |            ^
checkRd: (-1) rca.Rd:57: Lost braces; missing escapes or markup?
    57 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |                          ^
checkRd: (-1) scale_color_dMod.Rd:10: Lost braces
    10 | \item{...}{arguments goint to code{scale_color_manual()}}
       |                                   ^
checkRd: (-1) scale_fill_dMod.Rd:10: Lost braces
    10 | \item{...}{arguments goint to code{scale_color_manual()}}
       |                                   ^
checkRd: (-1) trust.Rd:103: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:104: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:107-108: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:109-110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:111-112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:113-114: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:115-122: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:123-126: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:127: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:128-131: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:132-133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:134-135: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:136-138: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:139-141: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EstimateDMQ.rd: DEoptim
  fn.DEoptim.Rd: DEoptim
  fn.solnp.Rd: solnp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dm_examine_cardinalities.Rd: as_tibble
  dm_examine_constraints.Rd: as_tibble
  dm_from_con.Rd: src
  dm_zoom_to.Rd: nest_join
  json_nest.Rd: tidyr_tidy_select
  json_pack.Rd: tidyr_tidy_select
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tractography.Rd: rgl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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) 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
       |                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kNN.Rd: knn, knn1, knn.cv
  rpartXse.Rd: rpart, prune.rpart
  rt.prune.Rd: rpart, prune.rpart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) setCPT.O.Rd:85: Lost braces; missing escapes or markup?
    85 | statespace {0,1,2}, which this is *not* checked anywhere. Thus, if
       |            ^
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  deepAFT.Rd: survreg
  deepSurv.Rd: survreg
  dnn-package.Rd: coxph, survival
  print.Rd: survreg
  survfit.deepAFT.Rd: survfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
checkRd: (-1) beetle.Rd:13: Lost braces; missing escapes or markup?
    13 |     \item{\code{x}}{dose (log base 10 CS2mgl^{-1})}
       |                                              ^
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  to_miniature.Rd: image_border, pdf_convert, image_read
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  checks.Rd: rcmdcheck
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   1.7Mb
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  corrPlot.Rd: levelplot
  fac.design.Rd: factorize
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package which this enhances but not available for checking: 'gurobi'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  functionsFromDoEbase.Rd: DoE.base
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) rsmformula.Rd:96: Lost braces
    96 |       URL{http://www.jstatsoft.org/v32/i07/}.
       |          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rsmformula.Rd: rsm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  doFuture.Rd: foreach, future
  grapes-dofuture-grapes.Rd: %dopar%
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bootAverageDominanceAnalysis.Rd: boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) py_select_interpreter.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Tell {reticulate} to use Python Conda version available on Domino Data Lab.}
       |             ^
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    data      1.9Mb
    extdata   2.3Mb
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.
       |                                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  redisDelete.Rd: hiredis
  redisGet.Rd: hiredis
  redisSet.Rd: hiredis
  registerDoRedis.Rd: foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New features
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  doRNG-package.Rd: RNGseq
  grapes-dorng-grapes.Rd: foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'gurobi'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dosresmeta-package.Rd: mvmeta, mvmeta-package, mvmeta.fit, blup
  dosresmeta.Rd: mvmeta.fit, mvmeta
  dosresmeta.control.Rd: mvmeta.control
  dosresmetaObject.Rd: mvmetaObject
  mlprof.fun.Rd: mvmeta.control, mvmeta.fit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'dotCall64/libs/x64/dotCall64.dll':
  Found non-API call to R: 'NAMED'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) dot.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sha_url.Rd: digest
  source_url.Rd: digest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.2Mb
checkRd: (-1) downscale.Rd:9: Lost braces; missing escapes or markup?
     9 | \item{occupancies}{Either a data frame containing two columns or an object of class \code{"upgrain"} from the \code{\link{upgrain}} function. If using a data frame the first column must be the grain sizes (cell area in squared units e.g. km^{2}). The second column is the proportion of occupancies at each grain size.}
       |                                                                                                                                                                                                                                                  ^
checkRd: (-1) ensemble.downscale.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
checkRd: (-1) hui.downscale.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{new.areas}{vector of grain sizes as cell area (in same units as cell.width but squared e.g. km^{2}) at fine scales for model prediction.}
       |                                                                                                      ^
checkRd: (-1) predict.downscale.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  downscale.Rd: mpfr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  correlationTest.Rd: phylo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'dparser/libs/x64/dparser.dll':
  Found non-API call to R: 'SET_TYPEOF'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  chron.ci.Rd: boot, boot.ci
  latexify.Rd: captureOutput
  pass.filt.Rd: butter, cheby1, filtfilt
  rasterPlot.Rd: readPNG
  uuid.gen.Rd: digest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'dplR/libs/x64/dplR.dll':
  Found non-API call to R: 'SET_TYPEOF'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
File 'dplyr/libs/x64/dplyr.dll':
  Found non-API calls to R: 'LEVELS', 'PRVALUE',
    'R_shallow_duplicate_attr', 'SET_PRCODE', 'SET_PRENV',
    'SET_PRVALUE'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  datapackage_init.Rd: toJSON, export
  datapackage_install.Rd: import
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EmpiricalRiskMinimizationDP.KST.Rd: nloptr
  LinearRegressionDP.Rd: nloptr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dnt.Rd: dntJKBf, getPrec, mpfr-class
  pbetaD94.Rd: pbetaI
  pnormLU.Rd: mpfr
  utils.Rd: mpfr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  chebyshevPoly.Rd: polyn.eval
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
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: \&
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  new_cache.Rd: storr_rds
  recover_cache.Rd: storr_environment
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gompertz.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) hatvalues.drc.Rd:43: Lost braces
    43 |   emph{Generalized Linear Models}, 
       |       ^
checkRd: (-1) hatvalues.drc.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) llogistic.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) modelFit.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) weibull1.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) excalibur.Rd:18: Lost braces; missing escapes or markup?
    18 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
checkRd: (-1) festuca.Rd:16: Lost braces; missing escapes or markup?
    16 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ED.drcte.Rd: drm
  drmte.Rd: LL.4, LL.5, W1.4, getMeanFunctions, drmc
  drmteControl.Rd: drm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) logistic2_fn.Rd:34: Lost braces; missing escapes or markup?
    34 | This function allows values other than {0, 1, -1} for \code{alpha} and \code{delta} but
       |                                        ^
checkRd: (-1) loglogistic2_fn.Rd:35: Lost braces; missing escapes or markup?
    35 | This function allows values other than {0, 1, -1} for \code{alpha} and \code{delta} but
       |                                        ^
checkRd: (-1) generate_individual_graphs.Rd:11: Lost braces
    11 | code{\link[DrDimont]{compute_correlation_matrices}}}
       |     ^
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).}
       |                                              ^
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.drf.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:44: Lost braces in \itemize; meant \describe ?
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  findRoots.Rd: nleqslv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   3.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RNAseqdata.Rd: rlog, vst
  itemselect.Rd: lmFit, eBayes, topTable, DESeqDataSetFromMatrix,
    DESeq, results
  microarraydata.Rd: normalizeBetweenArrays
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) popsize.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dr.weights.Rd: cov.rob
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DR.SC.Rd: Seurat
  drscPlot.Rd: DimPlot
  readscRNAseq.Rd: ReadMtx
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/DRviaSPCN.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Survey.LT-class.Rd: make.design
  Survey.PT-class.Rd: make.design
  dsims-package.Rd: make.region, make.design
  make.density.Rd: make.region
  make.ds.analysis.Rd: ds
  make.population.description.Rd: make.region
  make.simulation.Rd: make.design, make.region
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DSLiteConnection-class.Rd: DSConnection-class
  DSLiteDriver-class.Rd: DSDriver-class
  DSLiteResult-class.Rd: DSResult-class
  getDSLiteData.Rd: DSConnection-class
  setupCNSIMTest.Rd: datashield.login
  setupDASIMTest.Rd: datashield.login
  setupDATASETTest.Rd: datashield.login
  setupDISCORDANTTest.Rd: datashield.login
  setupDSLiteServer.Rd: datashield.login
  setupSURVIVALTest.Rd: datashield.login
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'dsBaseClient'
checkRd: (-1) dsm_varprop.Rd:67: Lost braces
    67 | parameter uncertainty. See Wood, Pya & S{\"a}fken (2016) for more
       |                                         ^
checkRd: (-1) dsm_varprop.Rd:100: Lost braces
   100 | Wood, S.N., Pya, N. and S{\"a}fken, B. (2016) Smoothing parameter and model
       |                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  check.cols.Rd: mrds
  dsm.cor.Rd: residuals.gam
  dsm_cor.Rd: residuals.gam
  dsm_varprop.Rd: gamObject
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  OpalConnection-class.Rd: DSConnection-class
  OpalDriver-class.Rd: DSDriver-class
  OpalResult-class.Rd: DSResult-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Voss.density.Rd: dLBA, ddiffusion, dwiener
  estDstarM.Rd: DEoptim.control, DEoptim
  estND.Rd: DEoptim.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Onoue.Friberg.Rd: pomp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) DTDAcif.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) efron.petrosian.Rd:22: Lost braces
    22 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
checkRd: (-1) lynden.Rd:21: Lost braces
    21 |    \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                                ^
checkRd: (-1) shen.Rd:24: Lost braces
    24 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) extract-methods.Rd:105: Lost braces
   105 |   argument \code{what}.  For code{"["} the cutted object.
       |                                  ^
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  arrange.dtplyr_step.Rd: arrange
  count.dtplyr_step.Rd: count
  distinct.dtplyr_step.Rd: distinct
  filter.dtplyr_step.Rd: arrange
  group_by.dtplyr_step.Rd: group_by, ungroup
  group_modify.dtplyr_step.Rd: group_map, group_modify
  intersect.dtplyr_step.Rd: union_all
  lazy_dt.Rd: collect, pull, select
  left_join.dtplyr_step.Rd: left_join, right_join, inner_join,
    full_join, anti_join, semi_join
  mutate.dtplyr_step.Rd: mutate
  relocate.dtplyr_step.Rd: relocate
  rename.dtplyr_step.Rd: rename, rename_with
  select.dtplyr_step.Rd: select
  slice.dtplyr_step.Rd: slice
  summarise.dtplyr_step.Rd: summarise
  transmute.dtplyr_step.Rd: transmute
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Mena.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) count_subgroup.Rd:29: Lost braces; missing escapes or markup?
    29 | {.subgroup} for the subgroup column name and \{.name\} for the subgroup
       | ^
checkRd: (-1) p_count_subgroup.Rd:29: Lost braces; missing escapes or markup?
    29 | {.subgroup} for the subgroup column name and \{.name\} for the subgroup
       | ^
Found the following HTML validation problems:
p_mutate.html:56:1 (p_mutate.Rd:17): Warning: trimming empty <dt>
p_rename.html:56:1 (p_rename.Rd:17): Warning: trimming empty <dt>
p_select.html:56:1 (p_select.Rd:17): Warning: trimming empty <dt>
p_transmute.html:56:1 (p_transmute.Rd:17): Warning: trimming empty <dt>
p_ungroup.html:56:1 (p_ungroup.Rd:21): Warning: trimming empty <dt>
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.4Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dataTableOutput.Rd: shinyWidgetOutput
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
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
'LazyData' is specified without a 'data' directory
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DurgaPlot.Rd: RColorBrewer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  familias2dvir.Rd: readFam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: replacing previous import 'Matrix::det' by 'SparseM::det' when loading 'DWDLargeR'
See 'd:/Rcompile/CRANpkg/local/4.5/DWDLargeR.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cfaHB.Rd: lavaan, cfa, model.syntax
  cfaOne.Rd: lavaan, cfa, model.syntax
  equivTest.Rd: lavaan
  exactFit.Rd: lavaan, cfa, model.syntax
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'cmdstanr'
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    data   9.3Mb
Package unavailable to check Rd xrefs: 'cmdstanr'
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.
       |                             ^
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.dynaTree.Rd:107: Lost braces
   107 |   For \code{coef} a new \R{XXc} field is created so as not to trample
       |                           ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lle'
'LazyData' is specified without a 'data' directory
checkRd: (-1) generate_kinetics.Rd:57: Lost braces; missing escapes or markup?
    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                          ^
checkRd: (-1) generate_kinetics.Rd:57: Lost braces; missing escapes or markup?
    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                                                     ^
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.}
       |                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  new_fmt_layout.Rd: crayon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
'LazyData' is specified without a 'data' directory
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
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.4Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dynr.cook.Rd: autoplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dynsimGG.Rd: scale_colour_brewer, discrete_scale
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mapdf.Rd: map
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   1.7Mb
checkRd: (-1) monitor_long_1d.Rd:33: Lost braces
    33 | If \code{side="upward"}{apply control charts that aim to detect upward shifts.} \cr
       |                        ^
checkRd: (-1) monitor_long_1d.Rd:34: Lost braces
    34 | If \code{side="downward"}{apply control charts that aim to detect downward shifts.} \cr
       |                          ^
checkRd: (-1) monitor_long_1d.Rd:35: Lost braces
    35 | If \code{side="both"}{apply control charts that aim to detect shifts in both sides}}
       |                      ^
checkRd: (-1) monitor_long_1d.Rd:38: Lost braces
    38 | If \code{chart="CUSUM"}{apply CUSUM charts.} \cr
       |                        ^
checkRd: (-1) monitor_long_1d.Rd:39: Lost braces
    39 | If \code{chart="EWMA"}{apply EWMA charts.}}
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  matchControls.Rd: daisy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    bin       3.0Mb
    extdata   1.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) AM.Rd:95-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:99-102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:123-125: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:126-133: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:134-135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:163-165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:166-173: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:174-176: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:177-178: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:179-180: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:55-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:75: Lost braces; missing escapes or markup?
    75 | From the initial values, \code{B0} and {S0}, \code{\link{MHLS}} draws \code{beta} and \code{subgrad} samples.
       |                                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
    34 | if (require(incidence)) {
       |                         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) surrogates_ews.Rd:31: Lost braces
    31 | \item{span}{parameter that controls the degree of smoothing (numeric between 0 and 100, Default 25). see more on loess{stats}}
       |                                                                                                                       ^
checkRd: (-1) surrogates_ews.Rd:33: Lost braces
    33 | \item{degree}{the degree of polynomial to be used for when loess fitting is applied, normally 1 or 2 (Default). see more on loess{stats}}
       |                                                                                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  earth.Rd: rlm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'earth/libs/x64/earth.dll':
  Found non-API call to R: 'SET_TYPEOF'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_earthtones.Rd: get_map, pam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cens_margin_to.Rd: group_by, summarize
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
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 ?
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EasyData.Rd: SSBtoolsData
  PTwrap.Rd: runArgusBatchFile, createArgusInput
  ProtectTable.Rd: GaussSuppression, protectTable,
    protect_linked_tables, primarySuppression, FindDimLists,
    FindTableGroup, Stack, AutoSplit, runArgusBatchFile,
    createArgusInput
  ProtectTable1.Rd: FindTableGroup, protectTable,
    protect_linked_tables, runArgusBatchFile, primarySuppression,
    makeProblem, HierarchicalGroups, FactorLevCorr, FindDimLists,
    FindCommonCells
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'gurobi'
checkRd: (-1) write_spss.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:35-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:46: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  boot.Rd: paircomp
  envirosound.Rd: paircomp
  soundquality.Rd: paircomp
  winetaste.Rd: paircomp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cumhaz_splines.Rd: msfit
  ebmstate-package.Rd: survival, mstate
  msfit_generic.Rd: msfit, mstate
  probtrans_ebmstate.Rd: probtrans
  probtrans_fft.Rd: probtrans
  probtrans_mstate.Rd: probtrans, mstate
  unique_paths.Rd: transMat, msprep
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) OCC1950.Rd:64: Lost braces
    64 |     \doi{10.18128/D010.V10.0}{IPUMS USA: Version 10.0 [dataset]. Minneapolis, MN: IPUMS}. 
       |                              ^
checkRd: (-1) Oil.Rd:45: Lost braces
    45 |       code{pt-pt-1} on a constant
       |           ^
checkRd: (-1) breaches.Rd:70-74: Lost braces
    70 |     \code{breach_end}{
       |                      ^
checkRd: (-1) breaches.Rd:75-78: Lost braces
    75 |     \code{year}{
       |                ^
checkRd: (-1) nuclearWeaponStates.Rd:82-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:93-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:104-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:128-140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:141-150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:151-161: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:162-172: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:173-191: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:192-219: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  USFinanceIndustry.Rd: readNIPA
  USstateAbbreviations.Rd: readUSstateAbbreviations,
    grepNonStandardCharacters, subNonStandardCharacters
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BoxCox.Rd:266-269: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BoxCox.Rd:270-275: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BoxCox.Rd:276-284: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BoxCox.Rd:285-293: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Newdata.Rd:88-91: Lost braces
    88 |   {replace \code{newDat[, x2]}:  
       |   ^
checkRd: (-1) interpPairs.Rd:120: Lost braces
   120 |     environment / list to use with code{object},
       |                                        ^
checkRd: (-1) matchQuote.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) matchQuote.Rd:75-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) matchQuote.Rd:81-88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) matchQuote.Rd:89-94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simulate.bic.glm.Rd:81-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.bic.glm.Rd:92-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.bic.glm.Rd:104-108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.glm.Rd:79-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.glm.Rd:84-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.glm.Rd:96-100: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  logVarCor.Rd: pdLogChol
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) e_pictorial.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) e_pictorial.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nesting.Rd:48: Lost braces
    48 | `{itemStyle: {color: 'red', fontBold: 'bold'}}`.
       |  ^
checkRd: (-1) nesting.Rd:48: Lost braces; missing escapes or markup?
    48 | `{itemStyle: {color: 'red', fontBold: 'bold'}}`.
       |              ^
checkRd: (-1) nesting.Rd:51: Lost braces; missing escapes or markup?
    51 | `{symbolSize: 4}`.
       |  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  echartsNJSON.Rd: jsonlite
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  navigation.hac.Rd: bearingRhumb, distVincentyEllipsoid
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ecipex.Rd: count.elements
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EBVstats.Rd: cellStats
  gaugeIndicator.Rd: list_lsm, calculate_lsm
  plot.EBVstats.Rd: tibble
  plot.Indicator.Rd: tibble
  sampleIndicator.Rd: list_lsm, sample_lsm
  tabuleRaster.Rd: rasterDT
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cgr.Rd: glasso
  plot.cgr.Rd: gplot
  stackedsdm.Rd: mvabund
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coalesc_abc.Rd: abc
  plot_comm.Rd: ggplot2-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calcres.Rd: ode
  ecosim-package.Rd: calc.stoich.coef, ode
  process-class.Rd: calc.stoich.coef
  system-class.Rd: ode
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  glenan.Rd: envelope
  glomel.Rd: envelope
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coef.ecpc.Rd: Surv
  cv.ecpc.Rd: Surv
  ecpc.Rd: Surv
  postSelect.Rd: Surv
  predict.ecpc.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) transformFitness.Rd:25: Lost braces; missing escapes or markup?
    25 | minimization (most others). This function computes a factor from {-1, 1} for
       |                                                                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) sd_map.Rd:33-34: Lost braces
    33 | the map. \itemize{ \item{\code{elem} {displays elementary and unified
       |                                      ^
checkRd: (-1) sd_map.Rd:34: Lost braces; missing escapes or markup?
    34 | districts}} \item{\code{secon} {displays secondary and unified districts}}}
       |                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  filter_case_condition.Rd: dplyr_data_masking
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  eval_posterior_eDITH.Rd: aggregate_river
  posterior_pred_sim_eDITH.Rd: aggregate_river, DHARMa
  run_eDITH_BT.Rd: aggregate_river, river_to_AEM, runMCMC,
    createBayesianSetup, dtrunc, MAP, getCredibleIntervals,
    gelmanDiagnostics
  run_eDITH_BT_joint.Rd: aggregate_river, river_to_AEM, runMCMC,
    createBayesianSetup, dtrunc, MAP, getCredibleIntervals,
    gelmanDiagnostics
  run_eDITH_optim.Rd: aggregate_river, river_to_AEM
  run_eDITH_optim_joint.Rd: aggregate_river, river_to_AEM
  run_eDITH_single.Rd: aggregate_river
  sampling_strategy_direct.Rd: aggregate_river
  sampling_strategy_eDNA.Rd: paths_river
  wigger.Rd: extract_river
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.lp.mip.Rd: make.lp
  editrules.plotting.Rd: as.igraph
  editrules_package.Rd: as.igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  USData.Rd: xts
  USRecessions.Rd: zoo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) edm2psd.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{D}{A matrix in the set D_{n}^{-}.}
       |                                ^
checkRd: (-1) edm2psd.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{D}{A matrix in the set D_{n}^{-}.}
       |                                    ^
checkRd: (-1) items_ordered_eclsk_atl.Rd:23: Lost braces; missing escapes or markup?
    23 | \item \code{P4SRS10}: Keep working at something until {he/she} is finished?
       |                                                       ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EEAaq_idw_map.Rd: idw, leaflet, addProviderTiles
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  eegfilter.Rd: butter, fir1, filtfilt, freqz_plot
  eegpsd.Rd: imagebar
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  eem_biological_index.Rd: interp2
  eem_coble_peaks.Rd: interp2
  eem_fluorescence_index.Rd: interp2
  eem_humification_index.Rd: interp2
  eem_peaks.Rd: interp2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  crosstabplot.Rd: mosaic
  gelmansim.Rd: sim
  moves_calc.Rd: data.table
  profpoly.Rd: geom_polygon
  profpoly.data.Rd: geom_polygon
  theme_dpi.Rd: theme_bw
  theme_dpi_map.Rd: theme_bw
  theme_dpi_map2.Rd: theme_bw
  theme_dpi_mapPNG.Rd: theme_bw
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EESPCACV.Rd: PMA
  RifleInit.Rd: rifle
  RiflePCACV.Rd: rifle, PMA
  TpowerPCACV.Rd: PMA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  OMEGA.Rd: schmid
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  regex.search.Rd: read.fasta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  effCoef.Rd: get_parameters
  effect.Rd: gls, multinom, polr, lmer, glmer, svyglm, xyplot,
    densityplot, barchart
  effectsTheme.Rd: trellis.device, trellis.par.set
  plot.effect.Rd: sequential_hcl, lattice, xyplot, densityplot,
    print.trellis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  efs_eval.Rd: roc.test
  ensemble_fs.Rd: randomForest, cforest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EBICglasso.qgraph.Rd: qgraph
  EGA.Rd: igraph
  EGA.estimate.Rd: igraph
  EGA.fit.Rd: igraph
  EGAnet-plot.Rd: GGally, ggplot2
  LCT.Rd: igraph
  bootEGA.Rd: igraph
  community.consensus.Rd: igraph
  community.detection.Rd: igraph
  compare.EGA.plots.Rd: qgraph
  convert2igraph.Rd: igraph
  dynEGA.Rd: igraph
  dynEGA.ind.pop.Rd: igraph
  hierEGA.Rd: igraph
  igraph2matrix.Rd: igraph
  invariance.Rd: igraph
  network.generalizability.Rd: igraph
  riEGA.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  acor.Rd: zoo
  egcm-package.Rd: adf.test, pp.test
  egcm.Rd: zoo, rlm, adf.test, pp.test
  egcm.set.default.i1test.Rd: adf.test, pp.test
  pgff.test.Rd: adf.test
  ur_power.Rd: adf.test, pp.test
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'eggCountsExtra'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotCounts.Rd: xyplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as_tibble.egor.Rd: tbl_svy, as_tibble, as_survey
  egor.Rd: as_tibble, tibble, tbl_svy
  rowlist.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotFluxHistBoot.Rd: printFluxUnitCheatSheet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Constants.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Constants.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Constants.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxConcMonth.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{las}{numeric in {0,1,2,3}; the style of axis labels, see ?par}
       |                       ^
checkRd: (-1) boxQTwice.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{las}{numeric in {0,1,2,3}; the style of axis labels, see ?par}
       |                       ^
checkRd: (-1) boxResidMonth.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{las}{numeric in {0,1,2,3}; the style of axis labels}
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  eha-package.Rd: coxph
  plot.coxreg.Rd: survival
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  join_vars_to_ontol.Rd: tidygraph
  metavariable_agg.Rd: tidygraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc       5.1Mb
    extdata   5.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EHyClus.Rd: smooth.terms
  generate_indices.Rd: smooth.terms
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lr_ancova.Rd: jags
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  to_as4wrf.Rd: sf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) fit_mean.Rd:54: Lost braces
    54 | \code{t_optims}{optimal parametrizations}
       |                ^
checkRd: (-1) fit_mean.Rd:55: Lost braces
    55 | \code{G_optims}{optimal rotations}
       |                ^
checkRd: (-1) fit_mean.Rd:56: Lost braces
    56 | \code{b_optims}{optimal scalings}
       |                ^
checkRd: (-1) fit_mean.Rd:57: Lost braces
    57 | \code{n_optims}{optimal re-normalization}
       |                ^
checkRd: (-1) fit_mean.Rd:58: Lost braces
    58 | \code{n_iter}{number of iterations until convergence}
       |              ^
checkRd: (-1) docs_delete_by_query.Rd:47: Lost braces; missing escapes or markup?
    47 | as a document at .tasks/task/${taskId}. This is yours to keep or remove
       |                               ^
checkRd: (-1) docs_update_by_query.Rd:48: Lost braces; missing escapes or markup?
    48 | as a document at .tasks/task/${taskId}. This is yours to keep or remove
       |                               ^
'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: \_
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dirichlet_tree.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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)
       |                                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_aws_terrain.Rd: st_crs
  get_elev_point.Rd: st_crs
  get_elev_raster.Rd: st_crs
  get_opentopo.Rd: st_crs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) prepareInitsLM.Rd:21-23: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  elisa_batch-class.Rd: nls.lm
  elisa_batch.Rd: nls.lm
  elisa_plate-class.Rd: nls.lm
  elisa_plate.Rd: nls.lm
  elisa_run-class.Rd: nls.lm
  elisa_run.Rd: nls.lm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'ellipsis/libs/x64/ellipsis.dll':
  Found non-API calls to R: 'PRVALUE', 'Rf_findVarInFrame3'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) elliptic-package.Rd:92: Lost braces
    92 |     J. Kotus and M. Urb\'{a}nski 2003.  \emph{Hausdorff dimension and Hausdorff
       |                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) elo.run.Rd:80: Lost braces
    80 | \code{\link{score}}, \link{elo.run.helpers}{elo.run helpers}, \code{\link{elo.calc}},
       |                                            ^
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
GNU make is a SystemRequirements.
checkRd: (-1) Emas.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EMAS.manhattan.Rd: manhattan
  Emas.parallel.Rd: sem, lavaan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  step_collapse_cart.Rd: selections, bake, prep, tidy.recipe
  step_collapse_stringdist.Rd: selections, prep, tidy.recipe
  step_discretize_cart.Rd: selections, tidy.recipe
  step_discretize_xgb.Rd: selections, tidy.recipe
  step_embed.Rd: tidy.recipe
  step_feature_hash.Rd: tidy.recipe
  step_lencode_bayes.Rd: tidy.recipe
  step_lencode_glm.Rd: tidy.recipe
  step_lencode_mixed.Rd: tidy.recipe
  step_pca_sparse.Rd: selections, prep, tidy.recipe
  step_pca_sparse_bayes.Rd: selections, prep, tidy.recipe
  step_pca_truncated.Rd: prep, step_center, step_scale, tidy.recipe,
    case_weights
  step_umap.Rd: prep, bake, tidy.recipe
  step_woe.Rd: selections, step_discretize, tidy.recipe
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) NEWS.Rd:194: Lost braces; missing escapes or markup?
   194 |             \item added {d,r}betabinom
       |                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  apply2d.Rd: create_progress_bar
  curve3d.Rd: create_progress_bar
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  write.excel.Rd: openxlsx
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  em.prec.Rd: glassoFast
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hfit.Rd: maxLik
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) minimize.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:33: Lost braces in \itemize; meant \describe ?
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 }
       |                                                            ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  write_eml.Rd: write_xml
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EMMA.Rd: rotations, nnls
  GUI.Rd: runApp
  test.robustness.Rd: rotations
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) macacaModels.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) macacaModels.Rd:10-11: Lost braces in \itemize; meant \describe ?
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
checkRd: (-1) medal.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) medal.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) medal.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WRegTest.Rd:43: Lost braces
    43 | For ordinary least squares estimator, \code{psifun} should be the identity function psifun <- function(t){t}.
       |                                                                                                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  empChurn.Rd: prediction
  empCreditScoring.Rd: prediction
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) em.Rd:25: Lost braces
    25 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.clogit.Rd:65: Lost braces
    65 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.default.Rd:65: Lost braces
    65 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.fitdist.Rd:49: Lost braces
    49 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.glmerMod.Rd:50: Lost braces
    50 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.panelmodel.Rd:49: Lost braces
    49 |  \code{terms} the code{terms} object used.
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_trackdata.Rd: wrasspOutputInfos, tibble
  query.Rd: tibble
  requery_hier.Rd: tibble
  requery_seq.Rd: tibble
  serve.Rd: stopAllServers, httpuv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.
       |                                                                                                                                                                                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  APR.Feature.Rd: DNAStringSet
  Bayes.Feature.Rd: DNAStringSet
  Density.Feature.Rd: DNAStringSet
  MM1.Feature.Rd: DNAStringSet
  MM2.Feature.Rd: DNAStringSet
  MN.Fdtf.Feature.Rd: DNAStringSet
  Maldoss.Feature.Rd: DNAStringSet
  PN.Fdtf.Feature.Rd: DNAStringSet
  POS.Feature.Rd: DNAStringSet
  Predoss.Feature.Rd: DNAStringSet
  SAE.Feature.Rd: DNAStringSet
  Sparse.Feature.Rd: DNAStringSet
  Trint.Dist.Feature.Rd: DNAStringSet
  WAM.Feature.Rd: DNAStringSet
  WMM.Feature.Rd: DNAStringSet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 Rd file(s) with Rd \link{} targets missing package
anchors:
  genkeys.Rd: openssl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  endoSwitch.Rd: maxLik
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) enetLTS-package.Rd:41: Lost braces; missing escapes or markup?
    41 |   \code{family="binomial"} should be a factor with two levels which is coded as \code{0} and {1}.
       |                                                                                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotEnrich.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) CTN.Rd:22: Lost braces; missing escapes or markup?
    22 | less memory. Genetic data consists of nucleotide data {A,T,C,G} and are usually saved
       |                                                       ^
checkRd: (-1) ALL.Regression.Config-class.Rd:39: Lost braces
    39 |     \item{code{shrinkage}:}{Object of class \code{"numeric"}, defining the shrinkage parameter applied to each tree in expansion.}
       |               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Regression.Select.MinAvgErr.Config-class.Rd: Instance.List-class,
    Regression.Select.Config-class
  Regression.Select.MinAvgErr.FitObj-class.Rd:
    Regression.Select.Config-class, RegressionSelectPred-class,
    Regression.Select.FitObj-class
  ecv.regression.Rd: Instance.List-class,
    Regression.CV.Batch.FitObj-class, Regression.Batch.FitObj-class
  ecv.regression.baselearner.control.Rd: rmse.error
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Regression.Integrator.PCR.SelMin.Config-class.Rd:
    Regression.Integrator.Config-class
  Regression.Integrator.PCR.SelMin.FitObj-class.Rd:
    Regression.Integrator.FitObj-class
  epcreg.Rd: Instance.List-class, Regression.CV.Batch.FitObj-class,
    Regression.Batch.FitObj-class
  epcreg.baselearner.control.Rd: rmse.error
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Regression.Integrator.PenReg.SelMin.Config-class.Rd:
    Regression.Integrator.Config-class
  Regression.Integrator.PenReg.SelMin.FitObj-class.Rd:
    Regression.Integrator.FitObj-class
  epenreg.Rd: Instance.List-class, Regression.CV.Batch.FitObj-class,
    Regression.Batch.FitObj-class
  epenreg.baselearner.control.Rd: rmse.error
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AllenH.Rd: phylo
  AlphaDiversity.Rd: phylo
  AlphaEntropy.Rd: phylo
  BetaDiversity.Rd: phylo
  BetaEntropy.Rd: phylo
  ChaoPD.Rd: phylo
  DivEst.Rd: phylo, ggarrange
  DivPart.Rd: phylo
  DivProfile.Rd: phylo, ggarrange
  GammaDiversity.Rd: phylo
  GammaEntropy.Rd: phylo
  GenSimpson.Rd: GenSimp.z
  PDFD.Rd: phylo
  PPtree.Rd: phylo
  Paracou618.Taxonomy.Rd: phylo
  PhyloApply.Rd: phylo
  PhyloBetaEntropy.Rd: phylo
  PhyloDiversity.Rd: phylo
  PhyloEntropy.Rd: phylo
  Preprocess.Tree.Rd: phylo
  RAC.Rd: fisher.alpha
  Rao.Rd: phylo
  SpeciesDistribution.Rd: fisher.alpha
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  envcpt.Rd: cpt-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'enviPat/libs/x64/enviPat.dll':
  Found non-API call to R: 'SETLENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  envi-package.Rd: sparr, spatstat.geom, sf, terra, future, doFuture,
    doRNG, foreach
  lrren.Rd: future, doFuture, doRNG, foreach
  perlrren.Rd: future, doFuture, doRNG, foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) metrics.Rd:124: Lost braces
   124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
       |                                  ^
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    help   3.6Mb
checkRd: (-1) Olympic.NH4.df.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) eqpois.Rd:200: Lost braces
   200 |   \code{\link{epois}}, \link[stats]{Poisson}, code{\link{estimate.object}}.
       |                                                   ^
checkRd: (-1) plotPredIntLnormAltSimultaneousTestPowerCurve.Rd:77: Lost braces
    77 |   positive integer between \code{1} and code{r} specifying the number of future 
       |                                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  eoa3.Rd: ppersist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
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},
       |                                                        ^
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    help   2.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clean_admin_names.Rd: countrycode
  clean_names_strings.Rd: janitor
  consistency_check.Rd: ggplot2
  export.Rd: rio
  import.Rd: rio
  missing_plot.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
checkRd: (-1) estimate_R.Rd:59-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:64-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:70-72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:76-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:79-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:84-86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:48-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:56-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  estimate_R.Rd: incidence
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sub-.epiflows.Rd: [.epicontacts
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DiscreteCovariatesToOneHot.Rd: dplyr_tidy_select
  charlson_score.Rd: dplyr_data_masking
  flatten_date_intervals.Rd: dplyr_tidy_select, dplyr_data_masking
  lms.Rd: dplyr_data_masking
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.epictmcmc.Rd: mcmc, plot.mcmc
  summary.epictmcmc.Rd: mcmc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  epimcmc.Rd: MCMC, adaptMCMC
  plot.epimcmc.Rd: mcmc, plot.mcmc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'epidict'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   2.8Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.network.transmat.Rd: network
  as.phylo.transmat.Rd: phylo
  brewer_ramp.Rd: brewer.pal, RColorBrewer
  control.dcm.Rd: ode
  netdx.Rd: control.simulate.formula.tergm
  netest.Rd: control.tergm
  plot.dcm.Rd: RColorBrewer, brewer.pal.info
  plot.netsim.Rd: plot.network
  plot.transmat.Rd: plot.network
  print.netdx.Rd: effectiveSize
  tedgelist_to_toggles.Rd: as.data.frame.networkDynamic
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) runSim.Rd:111: Lost braces
   111 | \ifelse{html}{\out{<i>r</i><sub>1</sub> = 1}}{{\eqn{r_1 = 1}}{r_1 = 1}} while the individual with the lowest phenotypic value
       |                                                              ^
checkRd: (-1) runSim.Rd:112: Lost braces
   112 | is given the rank \ifelse{html}{\out{<i>r<sub>n</sub></i> = <i>n</i>}}{{\eqn{r_n = n}}{r_n = n}}), the probability of an individual
       |                                                                                       ^
checkRd: (-1) runSim.Rd:120-122: Lost braces
   120 | }{
       |  ^
Package suggested but not available for checking: 'cmdstanr'
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   2.3Mb
    libs      6.6Mb
Package unavailable to check Rd xrefs: 'cmdstanr'
GNU make is a SystemRequirements.
checkRd: (-1) getAgeGender.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAgeGender.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAgeGender.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAgeGender.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getMap.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getMap.Rd:46-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getMap.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTableByMS.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTableByMS.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTableByMS.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTrend.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTrend.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAgeGender.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAgeGender.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAgeGender.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTS12MAvg.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTS12MAvg.Rd:28: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getAgeGender.Rd: ggplot2, officer
  getMap.Rd: officer
  getSeason.Rd: ggplot2, officer
  getTableByMS.Rd: flextable, officer
  getTrend.Rd: ggplot2, officer
  plotAge.Rd: ggplot2
  plotAgeGender.Rd: ggplot2
  plotBar.Rd: ggplot2
  plotBarGrouped.Rd: ggplot2
  plotBarGroupedH.Rd: ggplot2
  plotBarH.Rd: ggplot2
  plotPie.Rd: ggplot2
  plotSeasonality.Rd: ggplot2
  plotTS.Rd: ggplot2
  plotTS12MAvg.Rd: ggplot2
  plotTSGrouped.Rd: ggplot2
  shapeECDCFlexTable.Rd: set_header_df, flextable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  boot.bias.Rd: boot
  plot.episensr.booted.Rd: boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fit_disc_gamma.Rd: distcrete
  gamma_tools.Rd: distcrete
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'epiworldR/libs/x64/epiworldR.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  epoc.Rd: lassoshooting
  epoc.survival.Rd: survdiff
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Cmip6Dict.Rd: data.table
  summary_database.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  multiec.Rd: modIRT
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  renderEq.Rd: shiny
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  equiv.boot.Rd: boot
  equivalence.xyplot.Rd: xyplot
  rtost.Rd: yuen.t.test
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Binomial-ergmReference-cdff43a4.Rd: ergmTerm, ergmReference
  CMB-ergmTerm-5a51afe9.Rd: ergmTerm
  CMP-ergmTerm-4d501174.Rd: ergmTerm
  Disc-ergmProposal-b6c6e5ca.Rd: DiscUnif-ergmReference, ergmProposal
  DiscTNT-ergmProposal-c3c2e8cb.Rd: DiscUnif-ergmReference,
    ergmProposal, TNT-ergmProposal
  Geometric-ergmReference-1ee5c5ac.Rd: sum-ergmTerm, ergmReference
  Poisson-ergmReference-40df5ec8.Rd: ergmTerm, ergmReference
  ZIPoisson-ergmProposal-bba55a81.Rd: ergmProposal
  ergm.count-package.Rd: ergm-package, ergmReference, ergmTerm, ergm,
    control.ergm
  zach.Rd: network
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EgoStat-internal.Rd: egor
  as.egor.egodata.Rd: egor
  as.egor.network.Rd: network, egor
  control.ergm.ego.Rd: network
  degreedist.egor.Rd: egor
  ergm.ego-terms.Rd: egor
  ergm.ego.Rd: egor
  gof.ergm.ego.Rd: control.gof.formula, control.gof.ergm
  mixingmatrix.egor.Rd: egor
  nodal_attributes-API.Rd: check.ErgmTerm, egor, network
  simulate.ergm.ego.Rd: network, ergm, simulate.ergm
  summary_formula.egor.Rd: egor
  template_network.Rd: egor, tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  simEGP.Rd: network
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nvertex.Rd: network
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AlterSwap-ergmProposal-7e827ae4.Rd: ergmProposal
  CompleteOrder-ergmReference-f40141c3.Rd: ergmReference
  ergm.rank-package.Rd: ergm-package, ergm
  rankdeference-ergmTerm-73181c43.Rd: ergmTerm
  rankedgecov-ergmTerm-5905bc22.Rd: ergmTerm
  rankinconsistency-ergmTerm-b232ab56.Rd: network, ergmTerm
  ranknodeicov-ergmTerm-856bed59.Rd: ergmTerm
  ranknonconformity-ergmTerm-a4593778.Rd: ergmTerm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  approx.hotelling.diff.test.Rd: mcmc.list
  call.ErgmTerm.Rd: network
  control.ergm.Rd: mcmc.list
  degreedist.Rd: network
  ergm-errors.Rd: abort, warn, inform
  ergm.Rd: network, %v%, %n%
  ergm.design.Rd: network
  ergm.estfun.Rd: mcmc, mcmc.list
  ergm.geodistdist.Rd: network
  ergm.getnetwork.Rd: network
  ergm.godfather.Rd: network, mcmc
  ergmConstraint.Rd: network
  ergmMPLE.Rd: network
  ergmReference.Rd: network
  ergmTerm.Rd: network, %v%, %n%
  ergm_MCMC_sample.Rd: mcmc.list
  ergm_dyadgen_select.Rd: network
  ergm_model.Rd: term_list
  ergm_plot.mcmc.list.Rd: mcmc.list
  ergm_preprocess_response.Rd: network
  ergm_proposal.Rd: term_list
  ergm_state.Rd: network, tibble, edgelist
  ergm_symmetrize.Rd: network, tibble
  ergmlhs.Rd: network
  get.node.attr.Rd: network
  geweke.diag.mv.Rd: mcmc, mcmc.list
  gof.Rd: network
  is.valued.Rd: edgelist, network
  network.list.Rd: network
  nvattr.copy.network.Rd: network, network.initialize,
    set.vertex.attribute, set.network.attribute
  rlebdm.Rd: tibble, edgelist, network, as.edgelist
  samplk.Rd: network
  sampson.Rd: network
  san.Rd: network
  simulate.ergm.Rd: network, mcmc, mcmc.list, edgelist
  spectrum0.mvar.Rd: spectrum0.ar
  summary.ergm_model.Rd: network
  summary.formula.Rd: network
  summary_formula.Rd: network
  to_ergm_Cdouble.Rd: network
  update.network.Rd: network
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'ergm/libs/x64/ergm.dll':
  Found non-API call to R: 'SET_TYPEOF'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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,
       |                                                                                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  elastic.Rd: glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  errorist_init.Rd: searcher
  shims.Rd: searcher
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MipRules-class.Rd: validator
  errorlocate-package.Rd: validate
  errorlocation.Rd: values
  is_linear.Rd: validator
  replace_errors.Rd: validator
  translate_mip_lp.Rd: lp.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) enp.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enp.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evolat.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evolat.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psns.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psns.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc  13.3Mb
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gui_models.Rd: runApp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) festRidge.Rd:80: Lost braces; missing escapes or markup?
    80 | \item{XtXlamIinv}{explicit value of (X'X + diag(penalty))^{-1}.  Useful
       |                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) USA_state_N.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) USA_state_N.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) confirmed.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) confirmed.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) death.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) death.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recovered.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recovered.Rd:11: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'essentials/libs/x64/essentials.dll':
  Found non-API call to R: 'UNSET_S4_OBJECT'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) momento.central.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{orden}{Es un valor numérico que representa el orden del momento central (orden = {1,2,3,4,...})}
       |                                                                                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) aic.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:64: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  W_sampler.Rd: R6Class
  beta_sampler.Rd: R6Class
  rho_sampler.Rd: R6Class
  sigma_sampler.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) integration.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) integration.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) integration.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) integration.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loess.options.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loess.options.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maxlogLreg.Rd:138: Lost braces; missing escapes or markup?
   138 | $j^{th}$ for all the observations.
       |    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  maxlogL.Rd: DEoptim
  maxlogLreg.Rd: DEoptim, DEoptim.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  simulate_background_earthquakes.Rd: etas
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  catalog.Rd: inside.owin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dbWipe.Rd: DBIConnection-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) data_cls.Rd:24: Lost braces
    24 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability 0.10 for
       |                    ^
checkRd: (-1) data_cls.Rd:24: Lost braces
    24 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability 0.10 for
       |                            ^
checkRd: (-1) data_reg.Rd:21: Lost braces
    21 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability given by
       |                    ^
checkRd: (-1) data_reg.Rd:21: Lost braces
    21 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability given by
       |                            ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  map_non_standard_calendar.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  set_key.Rd: setkey
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  freq_binom_one_simons_twostage.Rd: ph2simon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}"
       |                                                       ^
checkRd: (-1) dist.evaluate.core.Rd:26: Lost braces; missing escapes or markup?
    26 | the \code{names} column in {data} as labels. If \code{NULL} (default),
       |                            ^
'LazyData' is specified without a 'data' directory
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) colplot.Rd:52: Lost braces
    52 | \item{legend}{should a legend be added? Defaults to code{FALSE}}
       |                                                         ^
checkRd: (-1) colplot.Rd:56: Lost braces
    56 | \item{legend.pretty}{logical: should the legend values produced by \[base]{pretty}? Othewrwise they are exact. Defaults to \code{TRUE}}
       |                                                                           ^
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})}.
       |                                                                                                                               ^
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
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
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MantelCor.Rd: mantel
  MantelModTest.Rd: mantel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Almer.Rd: lme4, lmer, merMod
  Almer_SE.Rd: lmer, merMod
  Almer_sim.Rd: simulate.merMod
  rate_gls.Rd: phylo
  simulate_rate.Rd: phylo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ShapeDist.Rd:18: Lost braces; missing escapes or markup?
    18 | Procrustes distance provides a measure of coincidence of two point sets {xi} and {yi}, i=1..N. For this purpose the variance of point deviations is calculated at the optimal superposition of the sets. It allows to characterize the shape proximity of a given simplex to shape of a reference one.
       |                                                                         ^
checkRd: (-1) ShapeDist.Rd:18: Lost braces; missing escapes or markup?
    18 | Procrustes distance provides a measure of coincidence of two point sets {xi} and {yi}, i=1..N. For this purpose the variance of point deviations is calculated at the optimal superposition of the sets. It allows to characterize the shape proximity of a given simplex to shape of a reference one.
       |                                                                                  ^
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.6Mb
    extdata   2.4Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clockrate_dens_plot.Rd: facet_wrap, geom_density
  clockrate_reg_plot.Rd: geom_smooth, geom_point
  plot_treerates_sgn.Rd: scale_color_steps2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  power2x2.Rd: uniroot.integer, ss.nonadh
  unirootGrid.Rd: uniroot.integer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  powerBinom.Rd: uniroot.integer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: 'ExactData'
Running 'spelling.R' [0s]
  Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(exampletestr)
  > 
  > get_os <- function() {
  +   sysinf <- Sys.info()
  +   if (!is.null(sysinf)) {
  +     os <- sysinf["sysname"]
  +     if (os == "Darwin") {
  +       os <- "osx"
  +     }
  +   } else { ## mystery machine
  +     os <- .Platform$OS.type
  +     if (grepl("^darwin", R.version$os)) {
  +       os <- "osx"
  +     }
  +     if (grepl("linux-gnu", R.version$os)) {
  +       os <- "linux"
  +     }
  +   }
  +   if (os == "osx") os <- "mac"
  +   tolower(os)
  + }
  > 
  > if (get_os() != "mac" || Sys.getenv("NOT_CRAN") == "true") {
  +   test_check("exampletestr")
  + }
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-example-extraction.R:15:3'): `extract_examples()` works ──────
  `extract_examples("detect", tempdir(check = TRUE))` threw an error with unexpected message.
  Expected match: "Path .+ does not appear to be inside a project or package."
  Actual message: "✖ Path 'D:/temp/RtmpKiFNzm/' does not appear to be inside a project or\n  package.\nℹ Read more in the help for `usethis::proj_get()`."
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test-example-extraction.R:15:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─exampletestr:::extract_examples("detect", tempdir(check = TRUE))
    7.   └─usethis::local_project(path = pkg_dir, quiet = TRUE)
    8.     └─usethis::proj_set(path = path, force = force)
    9.       └─usethis:::ui_abort(...)
   10.         └─cli::cli_abort(...)
   11.           └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
  Error: Test failures
  Execution halted
checkRd: (-1) exams2sakai.Rd:152: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  exams2sakai.Rd: xexams, exams_eval, exams2html
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    exiftool  14.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: '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
       |       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  expectreg-package.Rd: BayesX-package, mboost-package
  india.bnd.Rd: BayesX-package
  northger.bnd.Rd: BayesX-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ExplainPrediction-package.Rd: CORElearn, CoreModel, predict.CoreModel
  explanation.Rd: CoreModel, discretize, semiArtificial-package,
    CORElearn, predict.CoreModel, attrEval
  wrap4Explanation.Rd: nnet, CORElearn-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  expm.Higham08.Rd: sparseMatrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  graph2office.Rd: emf
  table2office.Rd: tidy
  table2spreadsheet.Rd: tidy
  table2tex.Rd: tidy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  epGraphs.Rd: prettyGraphs, createColorVectorsByDesign, prettyPlot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mrset.Rd: text_expand
  vars.Rd: text_expand
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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) 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.}
       |                                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cox.adapt.Rd: coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ci.fevd.Rd: ci
  datagrabber.Rd: datagrabber
  decluster.Rd: datagrabber
  distill.fevd.Rd: distill
  fevd.Rd: ci, distill, datagrabber
  findpars.Rd: distill
  xbooter.Rd: booter
  xtibber.Rd: tibber, booter
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  distLquantile.Rd: quantileMean
  distLweights.Rd: dist.list
  plotLexBoot.Rd: ciBand
  plotLextreme.Rd: logAxis
  plotLfit.Rd: logAxis
  printL.Rd: rainbow2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'exuberdata'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  autoplot.ds_radf.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) read_edf.Rd:32: Lost braces
    32 | code{TRUE}}
       |     ^
checkRd: (-1) read_edf.Rd:35: Lost braces
    35 | code{TRUE}}
       |     ^
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: \#
Package suggested but not available for checking: 'doMC'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ezCutoffs.Rd: boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
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
checkRd: (-1) ez-package.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:33: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mable.Rd: !!, !!!, .data, .env
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pspline.Rd: gam, mgcv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) fmCov.Rd:37: Lost braces; missing escapes or markup?
    37 | where, \code{alpha(i)} is the intercept, \code{f(t)} is a {K x 1} vector of 
       |                                                           ^
checkRd: (-1) plot.ffm.Rd:82: Lost braces; missing escapes or markup?
    82 | \item{las}{one of {0, 1, 2, 3} to set the direction of axis labels, same as
       |                   ^
checkRd: (-1) summary.ffm.Rd:39: Lost braces; missing escapes or markup?
    39 | Returned object is of class {summary.ffm}.
       |                             ^
checkRd: (-1) fviz_nbclust.Rd:75: Lost braces; missing escapes or markup?
    75 | (2001) proposed: "the smallest k such that gap(k) >= gap(k+1) - s_{k+1}". 
       |                                                                   ^
checkRd: (-1) fviz_nbclust.Rd:77: Lost braces; missing escapes or markup?
    77 | SE.factor*s_{k+1}" where SE.factor is a numeric value which can be 1
       |             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Investigate.Rd: CA
  classif.Rd: HCPC
  description.Rd: CA
  factoGraph.Rd: CA
  graphHab.Rd: CA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  HCPC.Rd: agnes
  plotellipses.Rd: xyplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    minor changes
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  factorplot.Rd: glht, summary.glht
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CAshiny.Rd: CA, plot.CA
  FAMDshiny.Rd: FAMD, plot.FAMD
  HCPCshiny.Rd: HCPC, plot.HCPC
  MCAshiny.Rd: MCA, dimdesc, plot.MCA
  MFAshiny.Rd: PCA, plot.PCA
  PCAshiny.Rd: PCA, plot.PCA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SMART.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) FADPclust.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) happy.Rd:14: Lost braces
    14 |                  code{Pretty happy} <  \code{Very happy}}
       |                      ^
checkRd: (-1) fra_sf.Rd:22: Lost braces; missing escapes or markup?
    22 | A map of France as {sf} object. Can be used as dataset or for maps
       |                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getFormula.Rd: createLipidDB, assignDB
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    help   1.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  famos.Rd: future
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) pi0FAMT.Rd:18: Lost braces
    18 | \code{pi0}{The estimated proportion \code{pi0} of null hypotheses.}}
       |           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.FAMTdata.Rd: impute.knn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kmPredictWrapper.Rd: predict.km, fast99
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'fansi/libs/x64/fansi.dll':
  Found non-API call to R: 'R_nchar'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  robustMD.Rd: cov.rob
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  farm.select.Rd: ncvreg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    doc    9.2Mb
    help   1.8Mb
    libs   2.0Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    images   3.1Mb
    libs     1.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    1.1Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ica.c:100:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  ica.c:100:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.5/fastICA.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fastJT-package.Rd: Rcpp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'coxKM'
checkRd: (-1) KITdesign.Rd:36: Lost braces; missing escapes or markup?
    36 |  \item{trait}{One of {'c','d','s',NULL} indicating the type
       |                      ^
checkRd: (-1) KITkernel.Rd:51: Lost braces; missing escapes or markup?
    51 |  \item{trait}{One of {'c','d','s',NULL} indicating the type
       |                      ^
checkRd: (-1) geno.Rd:19: Lost braces; missing escapes or markup?
    19 |                 Must be one of {'ibs', 'linear', 'quadratic'}.
       |                                ^
checkRd: (-1) geno.Rd:31: Lost braces; missing escapes or markup?
    31 |                      {'add', 'dom', 'rec'} indicating additive,
       |                      ^
checkRd: (-1) nongeno.Rd:14: Lost braces; missing escapes or markup?
    14 |                 Must be one of {'interactive', 'linear', 'quadratic'}.
       |                                ^
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.2Mb
checkRd: (-1) eigen_compute_single_entry_of_diagonal_matrix.Rd:17: Lost braces; missing escapes or markup?
    17 | The value of m^{-1}_{j,j}
       |                ^
checkRd: (-1) eigen_compute_single_entry_of_diagonal_matrix.Rd:17: Lost braces; missing escapes or markup?
    17 | The value of m^{-1}_{j,j}
       |                     ^
'LazyData' is specified without a 'data' directory
File 'fastmatch/libs/x64/fastmatch.dll':
  Found non-API calls to R: 'NAMED', 'SETLENGTH', 'SET_NAMED',
    'STRING_PTR', 'VECTOR_PTR'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
File 'fastMatMR/libs/x64/fastMatMR.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SSplot.Rd: rand
  col.fastR.Rd: trellis.par.set, show.settings
  maxLik2.Rd: maxLik
  plot.maxLik2.Rd: maxLik
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  directed_erdos_renyi.Rd: Matrix
  directed_factor_model.Rd: Matrix
  erdos_renyi.Rd: Matrix
  undirected_factor_model.Rd: Matrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) update_nhl_db.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_nhl_db.Rd:54-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_phf_db.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_phf_db.Rd:54-57: Lost braces in \itemize; meant \describe ?
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    Rcgi      2.6Mb
    cgi-bin   2.5Mb
.run: no visible binding for global variable 'init'
.run: no visible global function definition for 'init'
.run: no visible binding for global variable 'run'
Undefined global functions or variables:
  init run
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  WebPlot.Rd: Cairo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fat2Lpoly.Rd: kinship
  fat2Lpoly.withinR.Rd: kinship
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Error-Classes.Rd:107-119: Lost braces
   107 |   \item \code{do_verbose(response, template)} {
       |                                               ^
checkRd: (-1) Error.Rd:33-45: Lost braces
    33 |   \item \code{do(response, mssg)} {
       |                                   ^
checkRd: (-1) fh_bounds.Rd:14: Lost braces
    14 | \item{params1}{Arguments to pass to the r{dist} function for distribution 1}
       |                                          ^
checkRd: (-1) fh_bounds.Rd:16: Lost braces
    16 | \item{params2}{Arguments to pass to the r{dist} function for distribution 2}
       |                                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  stats-rowStats.Rd: colStats
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) fbad_copy_ad.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_ad.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) fbad_copy_adset.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_adset.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) fbad_copy_campaign.Rd:31: Lost braces; missing escapes or markup?
    31 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_campaign.Rd:33: Lost braces; missing escapes or markup?
    33 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) plot.fbroc.conf.Rd:5: Lost braces
     5 | \title{Plots function for object of class{fbroc.conf}}
       |                                          ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) fcr-package.Rd:15: Lost braces; missing escapes or markup?
    15 | Let $y_{ij}$ denote some outcome measured at
       |        ^
checkRd: (-1) fcr-package.Rd:16: Lost braces; missing escapes or markup?
    16 | $t_{ij}$ on the functional domain (e.g. time) for subject $i$ at observation
       |    ^
checkRd: (-1) fcr-package.Rd:29: Lost braces; missing escapes or markup?
    29 | Initially, a model is fit without $b_i(t_{ij})$. Using the residuals from this initial fit,
       |                                          ^
checkRd: (-1) fcr.Rd:13: Lost braces; missing escapes or markup?
    13 | The formula should only include terms not associated with the random function intercept b_i(t_{ij}). See Examples.}
       |                                                                                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fcr.Rd: gam, bam, face.sparse
  plot.fcr.Rd: plot.gam
  predict.fcr.Rd: predict.gam, predict.bam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    1.5Mb
    help   2.1Mb
    libs   1.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FPCAdens.Rd: FPCA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) simulation_model9.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                              ^
checkRd: (-1) simulation_model9.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                                           ^
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
GNU make is a SystemRequirements.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
checkRd: (-1) NASAtemp.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NASAtemp.Rd:15: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LMDC.select.Rd: gam
  PCvM.statistic.Rd: fd
  classif.DD.Rd: lda, qda
  classif.ML.Rd: pca.fd, create.basis, rpart
  classif.glm.Rd: pca.fd, create.basis
  classif.gsam.Rd: pca.fd, create.basis
  fda.usc-package.Rd: gam
  fdata.deriv.Rd: Data2fd, deriv.fd
  fdata2fd.Rd: Data2fd
  flm.test.Rd: create.basis
  fregre.basis.Rd: create.bspline.basis
  fregre.basis.fr.Rd: linmod, create.bspline.basis
  fregre.glm.Rd: pca.fd, create.basis
  fregre.gls.Rd: corStruct, corClasses, varFunc, varFixed, varClasses,
    glsControl, glsObject
  fregre.gsam.Rd: s, te, gam, pca.fd, create.basis, summary.gam
  fregre.gsam.vs.Rd: s, te, gam, summary.gam
  fregre.lm.Rd: pca.fd, create.basis
  norm.fdata.Rd: fd, inprod
  plot.fdata.Rd: bifd
  predict.fregre.lm.Rd: gam
  semimetric.basis.Rd: create.bspline.basis, Data2fd, deriv.fd
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following HTML validation problems:
GCCV.S.html:87:32 (GCCV.S.Rd:47): Warning: trimming empty <code>
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FDboost.Rd: mboost
  FDboostLSS.Rd: Families, GaussianLSS, boost_control
  bootstrapCI.Rd: cvrisk
  cvrisk.FDboostLSS.Rd: cvrisk.mboostLSS
  predict.FDboost_fac.Rd: predict.mboost
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) plot.dma.Rd:46: Lost braces; missing escapes or markup?
    46 | If {x} comes from estimation of Dynamic Model Selection (DMS) or Median Probability Model (MED), after executing \code{plot} the User is asked to choose
       |    ^
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/fdrDiscreteNull.Rcheck/00install.out' for details.
checkRd: (-1) p.fdr.Rd:30: Lost braces
    30 | \item{adjust.method}{A string used to identify the p-value and false discovery rate adjustment method. Defaults to \code{BH}. Options are \code{BH}, \code{BY}, code{Bon},\code{Holm}, \code{Hoch}, and \code{Sidak}.}
       |                                                                                                                                                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fast.Discrete.Rd: fisher.pvalues.support
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 Rd file(s) with Rd \link{} targets missing package
anchors:
  CSCMatrix-class.Rd: dgCMatrix-class
  hashed.model.matrix.Rd: dgCMatrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'FeatureHashing/libs/x64/FeatureHashing.dll':
  Found non-API call to R: 'HASHTAB'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  features.Rd: glkerns
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) mutlicol_terminator.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New Stuff
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CFUN.rd: na.count
  Extract.ff.rd: maxindex
  Extract.ffdf.rd: virtual, physical
  LimWarn.rd: maxindex
  as.ff.bit.rd: bit
  as.ff.rd: clone
  as.hi.rd: rlepack
  chunk.ffdf.rd: chunk, ri
  clone.ffdf.rd: clone
  ff.rd: clone, bit, is.sorted, na.count
  ffapply.rd: bbatch, repfromto
  ffdfsort.rd: ramsort, ramorder
  ffindexorder.rd: bbatch
  fforder.rd: ramorder, na.count
  ffsort.rd: is.sorted, na.count, ramsort
  getset.ff.rd: na.count
  hi.rd: rlepack, intrle, maxindex, poslength
  is.sorted.rd: intisasc, clone, na.count
  length.ff.rd: na.count, is.sorted
  length.hi.rd: poslength, maxindex
  maxlength.rd: maxindex
  na.count.rd: is.sorted
  physical.ff.rd: physical, is.sorted, na.count
  ramorder.default.rd: ramsort
  ramsort.default.rd: ramorder
  readwrite.ff.rd: na.count
  regtest.fforder.rd: ramsort
  repnam.rd: repfromto
  update.ff.rd: clone
  vt.rd: clone
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  classtable.Rd: confusionMatrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  abundance.Rd: group_by
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  type_vft.Rd: read_delim
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) contemParametros.Rd:19: Lost braces
    19 | \item{exclui3pontos}{verify por ... ? in f<-function(a, ...){ }}
       |                                                             ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fic.survreg.Rd: survreg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R         4.7Mb
    doc       2.3Mb
    extdata   2.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Rcpp_CmbTable-class.Rd: C++Object-class
  Rcpp_RunningStats-class.Rd: C++Object-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  instrument.auto.Rd: setSymbolLookup
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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 Rd file(s) with Rd \link{} targets missing package
anchors:
  collect_predictions.Rd: collect_metrics, tune
  show_best.Rd: show_best
  tune_sim_anneal.Rd: tune_grid, tune_bayes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) fun-igraph_financial.Rd:34: Lost braces; missing escapes or markup?
    34 | The same result for both \code{igraph} and {igraph_financial} objects
       |                                            ^
checkRd: (-1) igraph_E_iterators.Rd:31: Lost braces; missing escapes or markup?
    31 | The same result for both \code{igraph} and {igraph_financial} objects
       |                                            ^
checkRd: (-1) igraph_v_iterators.Rd:29: Lost braces; missing escapes or markup?
    29 | The same result for both \code{igraph} and {igraph_financial} objects
       |                                            ^
checkRd: (-1) plot_igraph-methods.Rd:22: Lost braces
    22 | Methods to extend code{igraph}'s plotting functions to \code{igraph_financial} objects
       |                       ^
checkRd: (-1) plot_igraph-methods.Rd:19: Lost braces; missing escapes or markup?
    19 | For both \code{igraph} and {igraph_financial} objects, returns NULL invisibly. It is called to print the graph to any R device. (see method and \href{https://rdrr.io/cran/igraph/man/plot.igraph.html}{igraph::plot.igraph})
       |                            ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) FiSh-package.Rd:19: Lost braces
    19 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
checkRd: (-1) FiSh-package.Rd:32: Lost braces
    32 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
checkRd: (-1) SEP_FIM.Rd:46: Lost braces
    46 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    extdata   3.8Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  convert.rMR.Rd: DO.unit.convert
  convert.respirometry.Rd: conv_o2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    lib    3.0Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
checkRd: (-1) fitConic.Rd:66-73: Lost braces
    66 | \code{parA }{vector of the six "ABCDEF" coefficients
       |             ^
checkRd: (-1) fitConic.Rd:67: Lost braces
    67 | \code{RSS }{'root sum square' figure of merit describing the relative fit quality}
       |            ^
checkRd: (-1) fitConic.Rd:68: Lost braces
    68 | \code{iters }{number of iterations at convergence}
       |              ^
checkRd: (-1) fitConic.Rd:69-71: Lost braces
    69 | \code{exitCode }{1 means ellipse, 2 means hyperbola, 3 means parabola.
       |                 ^
checkRd: (-1) rotateA.Rd:59: Lost braces; missing escapes or markup?
    59 | For \code{xyrot} {a Nx2 array of the x,y coordinates of the rotated data set. }
       |                  ^
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'gridlayout'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fitode-class.Rd: mle2-class
  fitode.Rd: ode, ginv, mle2
  fitodeMCMC.Rd: ode
  logLik.sensitivity.Rd: ode
  ode.sensitivity.Rd: ode
  summary-fitodeMCMC-method.Rd: effectiveSize, gelman.diag
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fitplc.Rd: nlme, lme, intervals.lme, deltaMethod
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
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'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fpAnova.Rd: anovaBF
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    3.6Mb
    libs   1.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  feNmlm.Rd: jacobian, genD
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
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
checkRd: (-1) convertInitDesignToGrid.Rd:11: Lost braces; missing escapes or markup?
    11 | The initial design, consisting of \code{d + 1} columns ({d} dimensions and
       |                                                         ^
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   1.2Mb
checkRd: (-1) ModelMixHMM-class.Rd:31: Lost braces; missing escapes or markup?
    31 |         \code{smoothed} of class {StatMixHMM}).
       |                                  ^
checkRd: (-1) ModelMixHMMR-class.Rd:31: Lost braces; missing escapes or markup?
    31 |         \code{smoothed} of class {StatMixHMMR}).
       |                                  ^
checkRd: (-1) summary.flamcv.rd:8: Lost braces
     8 | This function summarizes a call to code{\link{flamCV}} and identifies the tuning parameter chosen by cross-validation.
       |                                        ^
'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: \&
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.
       |                            ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_top_level_commits.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) flex_dashboard.Rd:96: Lost braces; missing escapes or markup?
    96 | the `{.storyboard}` attribute to individual pages rather than using the
       |      ^
'LazyData' is specified without a 'data' directory
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)
       |                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FLXMRnlm.Rd: gnm, flexmix
  flexmixNL-package.Rd: flexmix, gnm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AICc.Rd: gam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FlexParamCurve-package.Rd: nlsList, nlme
  SSposnegRichards.Rd: nlsList, nlme
  extraF.Rd: nlsList
  logist.data.Rd: nlme
  pn.mod.compare.Rd: nlsList
  pn.modselect.step.Rd: nlsList
  posneg.data.Rd: nlme
  posnegRichards.calls.Rd: nlsList
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FlexReg-package.Rd: rstan
  WAIC.Rd: loo, loo_compare, waic
  convergence.diag.Rd: check_hmc_diagnostics
  convergence.plot.Rd: ggplot2
  curve.density.Rd: stat_function
  flexreg.Rd: sampling
  flexreg_binom.Rd: sampling
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  flexsurvcure.Rd: Surv, flexsurvreg, survreg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Source(s) listed in 'build/vignette.rds' but not in package:
  'flexsurv.Rnw'
  'flexsurv-examples.Rnw'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  augment.flexsurvreg.Rd: tibble, Surv
  flexsurvmix.Rd: Surv, survreg
  flexsurvreg.Rd: Surv, survreg
  flexsurvrtrunc.Rd: survreg
  flexsurvspline.Rd: Surv
  glance.flexsurvreg.Rd: tibble
  msfit.flexsurvreg.Rd: coxph
  plot.flexsurvreg.Rd: plot.survfit
  plot_survtrunc.Rd: plot.survfit, lines.survfit
  pmatrix.fs.Rd: ode, deSolve
  predict.flexsurvreg.Rd: tibble
  tidy.flexsurvreg.Rd: tibble
  totlos.fs.Rd: ode, deSolve
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  add_latex_dep.Rd: knit_meta_add
  as_flextable.tabular.Rd: fp_par
  as_flextable.tabulator.Rd: fp_border
  border_inner.Rd: fp_border
  border_inner_h.Rd: fp_border
  border_inner_v.Rd: fp_border
  border_outer.Rd: fp_border
  footers_flextable_at_bkm.Rd: prop_section
  fp_border_default.Rd: fp_border
  fp_text_default.Rd: fp_text
  gen_grob.Rd: hyperlink_ftext
  headers_flextable_at_bkm.Rd: prop_section
  hline.Rd: fp_border
  hline_bottom.Rd: fp_border
  hline_top.Rd: fp_border
  htmltools_value.Rd: div, HTML
  rtf_add.flextable.Rd: rtf_add, rtf_doc
  save_as_docx.Rd: prop_section
  save_as_rtf.Rd: prop_section
  set_caption.Rd: fp_par
  vline.Rd: fp_border
  vline_left.Rd: fp_border
  vline_right.Rd: fp_border
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  scramblase_assay_plot.Rd: facet_wrap, ggplot, nlsLM, geom_line,
    geom_segment, geom_point
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc   9.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
checkRd: (-1) flow_embed.Rd:30: Lost braces; missing escapes or markup?
    30 | \item Don't forget to add {flow} to Suggests in your DESCRIPTION file.
       |                           ^
checkRd: (-1) flowdata.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{Flow}{Water flow, in m^{3}/s}
       |                              ^
checkRd: (-1) to_flow.Rd:110-117: Lost braces
   110 | \strong{Behaviour:}{
       |                    ^
checkRd: (-1) to_flowdef.Rd:111-115: Lost braces
   111 | {
       | ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  whisker_render.Rd: whisker.render
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Malformed Description field: should contain one or more complete sentences.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addPredictions.Rd: crosspred
  metaFluMoDL.Rd: mvmeta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CurrencyPair.Rd: JointCalendar, USNYCalendar
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  generate_schedule.Rd: Period-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  obsplot.Rd: print.deSolve, ode, deSolve
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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) FMP.Rd:30: Lost braces; missing escapes or markup?
    30 | \eqn{m(\theta) = b_0 + b_1 \theta + b_2 \theta^2 + b_3 \theta^3}. Acceptable values of k = {0,1,2,3}. According to 
       |                                                                                            ^
checkRd: (-1) autoFMradio.Rd:46: Lost braces; missing escapes or markup?
    46 | Step 1 (regularized correlation matrix estimation) is performed using the \code{X}, \code{t}, and {fold} arguments.
       |                                                                                                   ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Estable.Rd:40: Lost braces
    40 |   \code{dEstable}{ gives the density function;}
       |                  ^
checkRd: (-1) Estable.Rd:41: Lost braces
    41 |   \code{pEstable}{ gives the distribution function or its complement;}
       |                  ^
checkRd: (-1) Estable.Rd:42: Lost braces
    42 |   \code{qEstable}{ gives quantiles;}
       |                  ^
checkRd: (-1) Estable.Rd:43-56: Lost braces
    43 |   \code{tailsEstable}{ returns a list with the following components
       |                      ^
checkRd: (-1) FMstable.Rd:50: Lost braces
    50 |   \code{dFMstable}{ gives the density function;}
       |                   ^
checkRd: (-1) FMstable.Rd:51: Lost braces
    51 |   \code{pFMstable}{ gives the distribution function or its complement;}
       |                   ^
checkRd: (-1) FMstable.Rd:52: Lost braces
    52 |   \code{qFMstable}{ gives quantiles;}
       |                   ^
checkRd: (-1) FMstable.Rd:53-66: Lost braces
    53 |   \code{tailsFMstable}{  returns a list with the following components
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  moment_fmx.Rd: moment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) navbar_page.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) navbar_page.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) navbar_page.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  foodingraph.Rd: igraph, ggraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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: 'doMC'
checkRd: (-1) foreca.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:78-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:84-87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:88-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:91-92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) initialize_weightvector.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:64-65: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  comb_EIG2.Rd: accuracy
  comb_SA.Rd: accuracy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cvts.Rd: forecast
  fitted.hybridModel.Rd: accuracy
  plot.hybridModel.Rd: autoplot
  plotFitted.Rd: autoplot
  plotModelObjects.Rd: autoplot
  residuals.hybridModel.Rd: accuracy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  analyze.windanomaly.Rd: lpacf.plot
  forecastlpacf.Rd: lpacf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) errorMetricFunctions.Rd:48: Lost braces
    48 |         The metric MdAE is obtained using code{type = "AE"} and  \code{statistic = "Md"}
       |                                               ^
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
checkRd: (-1) species_bw.Rd:23: Lost braces
    23 | between trees." \doi{10.1371/journal.pone.0229930}{PLOS One 15: e0229930}.
       |                                                   ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) process_pcl.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{pavd}{logical input to include Plant Area Volume Density Plot from {plot_pavd},
       |                                                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) depth.Rd:17: Lost braces; missing escapes or markup?
    17 |   \item {file} : {filename}
       |                  ^
checkRd: (-1) depth.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item {z_depth} : {measured focus range depth (z)}}
       |                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bio.volume.Rd: volume
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    help   1.0Mb
    libs   1.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  correlations.Rd: saveWidget
  distance.sampling.Rd: ds
  normalize.Rd: classify_ground, grid_terrain, normalize_height
  optimize.plot.design.Rd: saveWidget
  relative.bias.Rd: saveWidget
  simulations.Rd: vroom
  tree.detection.several.plots.Rd: vroom_write
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fwdlm.Rd: lmsreg
  fwdsco.Rd: lmsreg
  lmsglm.Rd: lmsreg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) FGf.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FourgameteP.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ancoord.Rd: cov.rob
  awcoord.Rd: cov.rob
  clustatsum.Rd: silhouette
  cluster.stats.Rd: silhouette
  cqcluster.stats.Rd: silhouette
  fixmahal.Rd: cov.rob
  kmeansCBI.Rd: isoMDS, sammon, pam
  mahalanofix.Rd: cov.rob
  mvdcoord.Rd: cov.rob
  ncoord.Rd: cov.rob
  valstat.object.Rd: silhouette
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
2711,2714c2711,2714
<   1  3  0  0  2  0  0  0
<   2 10  9  8  0  5  0  0
<   3  0  0  0  0  0  0  1
<   4  1  0  0  4  0  3  4
---
>   1  4  0  0  0  1  0  0
>   2 10  9  8  5  0  0  0
>   3  0  0  1  0  0  0  0
>   4  0  0  0  0  4  3  5
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot_lines.Rd:66: Lost braces
    66 | moderator. By default it is equal to \8code{c(19, 17, 15, 8, 5, 4, 3, 1)}.}
       |                                            ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |     ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                        ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                              ^
checkRd: (-1) Fpop.Rd:9: Lost braces; missing escapes or markup?
     9 | m_{i+1}), where the indicator function I counts the number of
       |   ^
Package suggested but not available for checking: 'RandomFields'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) emfrail_control.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:55-57: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    help   2.7Mb
    libs   3.6Mb
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fr_emdII.Rd: mle2
  fr_flexp.Rd: mle2
  fr_flexpnr.Rd: mle2
  fr_hassIII.Rd: mle2
  fr_hassIIInr.Rd: mle2
  fr_hollingsII.Rd: mle2
  fr_rogersII.Rd: mle2
  fr_typeI.Rd: mle2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) summary.frbs.Rd:32: Lost braces
    32 |                           \code{"GAUSSIAN"}, code{"TRIANGLE"}, \code{"TRAPEZOID"}, \code{"SIGMOID"}, and \code{"BELL"}.
       |                                                  ^
checkRd: (-1) summary.frbs.Rd:60: Lost braces; missing escapes or markup?
    60 |          {4.0, 0.23, 0.43, 0.53, 0.73} on its column. It means that the label a.2 of variable v.1 
       |          ^
checkRd: (-1) grade.Rd:57: Lost braces
    57 |   \code{freealg} object comprising terms of grade code{n}.
       |                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  checkmnc-methods.Rd: checkimg
  fs_cmd.Rd: readnii
  readmgz.Rd: readnii
  readmnc.Rd: readnii
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fts.freqdom.Rd: freqdom
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) maximin.Rd:197: Lost braces
   197 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Catalogues.Rd: FrF2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FrF2Large.Rd: Letters
  makecatlg.Rd: Letters
  pb.Rd: generalized.word.length, length3, length4
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  read_resource.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) NEWS.Rd:234: Escaped LaTeX specials: \_
checkRd: (-1) NEWS.Rd:257: Escaped LaTeX specials: \_ \_
checkRd: (-1) NEWS.Rd:258: Escaped LaTeX specials: \_ \_
checkRd: (-1) NEWS.Rd:259: Escaped LaTeX specials: \_
checkRd: (-1) NEWS.Rd:262: Escaped LaTeX specials: \_
checkRd: (-1) NEWS.Rd:265: Escaped LaTeX specials: \_
Package suggested but not available for checking: 'dggrids'
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.8Mb
    libs  12.8Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
checkRd: (-1) FSelector-package.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-information_gain.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-information_gain.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) information_gain.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) information_gain.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  feature_search.Rd: foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) report.Rd:18: Lost braces; missing escapes or markup?
    18 |         \item{las}{numeric in {0,1,2,3}; the style of axis labels (see \code{\link{par}}).}
       |                               ^
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  check_file.Rd: checkimg
  fast.Rd: readnii
  flirt.Rd: readnii
  flirt_apply.Rd: readnii
  fnirt.Rd: readnii
  fnirt_with_affine.Rd: readnii
  fnirt_with_affine_apply.Rd: readnii
  fsl_anat.Rd: checkimg
  fsl_applywarp.Rd: readnii
  fsl_biascorrect.Rd: readnii
  fsl_cluster.Rd: readnii
  fsl_deface.Rd: readnii
  fsl_resample.Rd: readnii
  fslabs.Rd: readnii
  fslacos.Rd: readnii
  fsladd.Rd: readnii
  fslasin.Rd: readnii
  fslatan.Rd: readnii
  fslbet.Rd: readnii
  fslbin.Rd: readnii
  fslbinv.Rd: readnii
  fslchfiletype.Rd: readnii
  fslcmd.Rd: readnii
  fslcos.Rd: readnii
  fslcpgeom.Rd: readnii
  fsldilate.Rd: readnii
  fsldiv.Rd: readnii
  fsledge.Rd: readnii
  fslepi_reg.Rd: readnii
  fslerode.Rd: readnii
  fslexp.Rd: readnii
  fslfill.Rd: readnii
  fslfill2.Rd: readnii
  fslhd.Rd: checkimg
  fslindex.Rd: readnii
  fsllog.Rd: readnii
  fslmask.Rd: readnii
  fslmaths.Rd: readnii
  fslmerge.Rd: readnii
  fslmul.Rd: readnii
  fslnan.Rd: readnii
  fslnanm.Rd: readnii
  fslor.Rd: readnii
  fslorient.Rd: readnii
  fslrand.Rd: readnii
  fslrandn.Rd: readnii
  fslrange.Rd: checkimg
  fslrecip.Rd: readnii
  fslrem.Rd: readnii
  fslreorient2std.Rd: readnii
  fslrobustfov.Rd: readnii
  fslroi.Rd: readnii
  fslsin.Rd: readnii
  fslslicetimer.Rd: readnii
  fslsmooth.Rd: readnii
  fslsplit.Rd: readnii
  fslsqr.Rd: readnii
  fslsqrt.Rd: readnii
  fslstats.Rd: checkimg
  fslsub.Rd: readnii
  fslsub2.Rd: readnii
  fslswapdim.Rd: readnii
  fsltan.Rd: readnii
  fslthresh.Rd: readnii
  fslval.Rd: checkimg
  fslview.Rd: checkimg
  fslvol.Rd: voxdim
  fslxor.Rd: readnii
  getForms.Rd: checkimg
  mcflirt.Rd: readnii
  melodic.Rd: checkimg
  mni_img.Rd: nifti
  readrpi.Rd: readnii
  susan.Rd: readnii
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fso.Rd: dsvdis
  mfso.Rd: dsvdis
  plot.mfso.Rd: dsvdis
  step.mfso.Rd: dsvdis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File 'fstcore/libs/x64/fstcore.dll':
  Found non-API calls to R: 'Rf_NonNullStringMatch', 'SET_S4_OBJECT'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  farforecast.Rd: fds
  long_run_covariance_estimation.Rd: fts
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'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.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  promaxQ.Rd: GPForth
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  funky_heatmap.Rd: ggsave
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) plot.fd.Rd:69-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.fd.Rd:72-77: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.fd.Rd: lines.fd, plotfit.fd
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nbrOfWorkers.batchtools.Rd: plan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Fuzzy_DBScan.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) misspellings.Rd:18: Lost braces
    18 | This is a code{tbl_df} mapping misspellings of their words, compiled by
       |               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  regex_join.Rd: str_detect
  stringdist_join.Rd: stringdist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                             ^
checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                                                     ^
checkRd: (-1) genmf.Rd:26: Lost braces; missing escapes or markup?
    26 | \item 'gbellmf' is c(\code{a, b, c}), where \code{a} denotes the width, \code{b} is usually positive and {c} locates the center of the curve.
       |                                                                                                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  prevalence.Rd: mod2obspred
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fuzzyStationaryProb.Rd: DEoptim.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following HTML validation problems:
FuzzyNumberList.html:76:1 (FuzzyNumberList.Rd:285): Warning: trimming empty <ul>
TrapezoidalFuzzyNumberList.html:118:1 (TrapezoidalFuzzyNumberList.Rd:572): Warning: trimming empty <ul>
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   4.6Mb
File 'gafit/libs/x64/gafit.dll':
  Found non-API calls to R: 'FRAME', 'HASHTAB'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) min_hpd_inc_area_df.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) min_hpd_inc_area_df.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) min_hpd_inc_area_df.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) vza_mean_and_var_rasters.Rd:20: Lost braces
    20 | of the paper on Wilson's warbler, this function computes $tilde{T}^{(mu)}$ (returned as
       |                                                                ^
checkRd: (-1) vza_mean_and_var_rasters.Rd:20: Lost braces; missing escapes or markup?
    20 | of the paper on Wilson's warbler, this function computes $tilde{T}^{(mu)}$ (returned as
       |                                                                    ^
checkRd: (-1) vza_mean_and_var_rasters.Rd:21: Lost braces; missing escapes or markup?
    21 | list component \code{mean.raster}) and $R^{(sigma^2)}$ (returned as list component
       |                                           ^
checkRd: (-1) stabsel.mboostLSS.Rd:44: Lost braces
    44 |     always use code{"none"}.}
       |                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.families.Rd: Family, mboost
  cvrisk.Rd: cv, cvrisk.mboost
  families.Rd: Family
  gamboostLSS-package.Rd: stabsel, mboost
  mboostLSS.Rd: mboost, boost_control, glmboost, gamboost, blackboost,
    mboost_fit, stabsel
  methods.Rd: boost_control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gamboostMSM-package.Rd: mboost
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CVgam.Rd: gam
  addhlines.Rd: rpart, predict.rpart
  gamRF.Rd: gam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BiCopEta2Par.Rd: BiCopPar2Tau, BiCopTau2Par
  BiCopPar2Eta.Rd: BiCopPar2Tau, BiCopTau2Par
  EDF.gamBiCop-methods.Rd: gamObject
  RVM2GVC.Rd: RVineMatrix
  formula.gamBiCop-methods.Rd: gam, formula.gam
  gamBiCop-class.Rd: gamObject, gam
  gamBiCop.Rd: gamObject, gam
  gamBiCopCDF.Rd: predict.gam
  gamBiCopFit.Rd: gam, formula.gam, gam.models
  gamBiCopPDF.Rd: predict.gam
  gamBiCopPredict.Rd: predict.gam
  gamBiCopSelect.Rd: BiCopSelect, gam
  gamBiCopSimulate.Rd: predict.gam
  gamCopula-package.Rd: VineCopula
  gamVine-class.Rd: RVineMatrix
  gamVine.Rd: RVineMatrix
  gamVineCopSelect.Rd: BiCopSelect, gam
  gamVinePDF.Rd: predict.gam
  gamVineSeqFit.Rd: gam
  gamVineStructureSelect.Rd: BiCopSelect
  plot.gamBiCop-methods.Rd: plot.gam
  plot.gamVine-methods.Rd: plot.gam
  summary.gamBiCop-methods.Rd: summary.gam
  summary.gamVine-methods.Rd: summary.gam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) naref.Rd:13: Lost braces
    13 | \details{ For every \code{factor} or \code{character} column in \code{x}, \code{naref} sets \code{NA} as the reference level for a \code{factor} variable. Columns coded as \code{character} class are first converted to factors via \R{factor(x)}.  If \code{impute=TRUE} then the numeric columns are converted to two columns, one appended \code{.x} that contains imputed values and another appended \code{.miss} which is a binary variable indicating whether the original value was missing.  Numeric columns are returned without change if \code{impute=FALSE} or if they do not contain any missing values.  
       |                                                                                                                                                                                                                                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  centilesTwo.Rd: centiles
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  KIBNB.Rd: gamlss.family
  KIDEL.Rd: gamlss.family
  KIDPO.Rd: gamlss.family
  KIGEOM.Rd: gamlss.family
  KIGEOMo.Rd: gamlss.family
  KIGPO.Rd: gamlss.family
  KILG.Rd: gamlss.family
  KINBF.Rd: gamlss.family
  KINBI.Rd: gamlss.family
  KINBII.Rd: gamlss.family
  KIPIG.Rd: gamlss.family
  KIPO.Rd: gamlss.family
  KISI.Rd: gamlss.family
  KISICHEL.Rd: gamlss.family
  KIWARING.Rd: gamlss.family
  KIYULE.Rd: gamlss.family
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) pc.Rd:17: Lost braces
    17 | The functions \code{gamlss.pcr()} and \code{gamlss.pc()} are supporting functions. The  are not intended to be called directly by users. The function \code{gamlss.pc()} is using the linear model function \code{lm()} to fit the first principal components while the function code{gamlss.pcr()} uses \code{fitPCR()}.
       |                                                                                                                                                                                                                                                                                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  family_pdf.Rd: gamlss
  fitted_cdf.Rd: gamlss
  fitted_devianceIncr.Rd: gamlss
  model_pca.Rd: gamlss
  resid_plot.Rd: gamlss, plot.gamlss
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) term.plotZadj.Rd:6: Lost braces
     6 |  \ This is a wrapper to function \code{\link[gamlss]{term.plot}}. code{term.plotZadj} produces term plots for a specified parameter from a    
       |                                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  centiles.Inf0to1.Rd: gamlss, centiles.split, centiles.com
  gamlssInf0to1.Rd: gamlss, gen.Family, gamlss.family, BEINF, BE, BEo,
    BEZI, BEOI
  gamlssZadj.Rd: gamlss, gen.Family, gamlss.family, ZAGA, ZAIG
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LR.test.Rd: dropterm
  gamlss.ps.Rd: ridge
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MRF.Rd: mrf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gamm4.Rd: lmer, glmer, lmerControl, glmerControl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Gapfill.Rd:66-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:69-70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:71-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ndvi.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ndvi.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ndvi.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ndvi.Rd:13: Lost braces in \itemize; meant \describe ?
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    doc   31.8Mb
    libs   1.2Mb
checkRd: (-1) glag.Rd:7: Lost braces; missing escapes or markup?
     7 | Similar to the \code{\link{lag}} function from the \code{stats} package, but \code{glag} enables padding (e.g. {NA}s or 0s) of the lost entries. Contrary to the \code{\link{lag}} function in the stats package, however, the default in \code{glag} is to pad (with \code{NA}s). The \code{glag} is particularly suited for \code{\link{zoo}} objects, since their indexing is retained
       |                                                                                                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coef.garchx.Rd: zoo
  garchx.Rd: zoo, na.trim
  garchxSim.Rd: zoo
  gdiff.Rd: zoo
  glag.Rd: zoo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gargle_oauth_client_from_json.Rd: oauth_app
  request_make.Rd: httr
  request_retry.Rd: httr
  response_process.Rd: httr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) read.ctable.Rd:19: Lost braces; missing escapes or markup?
    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                      ^
checkRd: (-1) read.ctable.Rd:19: Lost braces; missing escapes or markup?
    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                                      ^
checkRd: (-1) read.ctable.Rd:29: Lost braces; missing escapes or markup?
    29 | output array, {row,col}.names are not necessary \code{dimnames[[1]]} and
       |               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Goals.Rd: zoo
  MultiGASFit.Rd: hessian
  UniGASFit.Rd: hessian
  cpichg.Rd: xts
  fn.solnp.Rd: solnp
  sp500ret.Rd: xts
  sp500rv.Rd: xts
  usunp.Rd: xts
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) simulate_gastempt.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{tempt_mean, tempt_std}{Mean and between record standard deviation of parameter $t_{empt}$, typically in minutes.}
       |                                                                                         ^
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.9Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gateR-package.Rd: sparr, spatstat.geom, terra
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Cubic.Rd: R6Class
  Exponential.Rd: R6Class
  FactorKernel.Rd: R6Class
  GauPro_Gauss.Rd: R6Class
  GauPro_Gauss_LOO.Rd: R6Class
  GauPro_base.Rd: R6Class
  GauPro_kernel.Rd: R6Class
  GauPro_kernel_beta.Rd: R6Class
  GauPro_kernel_model.Rd: R6Class
  GauPro_kernel_model_LOO.Rd: R6Class
  GauPro_trend.Rd: R6Class
  Gaussian.Rd: R6Class
  GowerFactorKernel.Rd: R6Class
  IgnoreIndsKernel.Rd: R6Class
  LatentFactorKernel.Rd: R6Class
  Matern32.Rd: R6Class
  Matern52.Rd: R6Class
  OrderedFactorKernel.Rd: R6Class
  Periodic.Rd: R6Class
  PowerExp.Rd: R6Class
  RatQuad.Rd: R6Class
  Triangle.Rd: R6Class
  White.Rd: R6Class
  kernel_product.Rd: R6Class
  kernel_sum.Rd: R6Class
  trend_0.Rd: R6Class
  trend_LM.Rd: R6Class
  trend_c.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Sim.Markov.Chain.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{eta0}{inital value in {1,...,r}.}
       |                             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) CompoundDensPlot.Rd:18: Lost braces
    18 |   \item{shape1, scale ,shape2, shape3}{numeric; positive parameters of the GB2 distribution. On the plot they are denotes as \code{a}, code{b}, \code{p}, \code{q} and \code{pl0} respectively.}
       |                                                                                                                                            ^
checkRd: (-1) CompoundVarest.Rd:58: Lost braces
    58 | \code{scoreU.cgb2} returns a \eqn{N \times (L-1)} matrix of scores <code{U}.
       |                                                                         ^
checkRd: (-1) Fisk.Rd:26: Lost braces
    26 | \value{\code{fisk} and \code{fiskh} return vectors of length 4 containing the estimated parameters \eqn{a}, eqn{b}, as well as \eqn{p=1} and \eqn{q=1}. 
       |                                                                                                                ^
checkRd: (-1) MLfullGB2.Rd:23: Lost braces
    23 |   \item{method}{numeric; the method to be used by \code{optim}. By default, code{method = }1 and the used method is BFGS. If \code{method = }2, method L-BFGS-B is used.}
       |                                                                                 ^
checkRd: (-1) MLprofGB2.Rd:16: Lost braces
    16 |   \item{method}{numeric; the method to be used by \code{optim}. By default, code{method = }1 and the used method is BFGS. If \code{method = }2, method L-BFGS-B is used.}
       |                                                                                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CompoundAuxVarest.Rd: survey
  CompoundVarest.Rd: survey
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) gbm.auto.Rd:208: Lost braces; missing escapes or markup?
   208 | \item Error in if (n.trees > x$n.trees) { : argument is of length zero}. LR or BF probably too low
       |                                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gbm.auto.Rd: n
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'paleofire'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gcite.Rd: GET
  gcite_author_info.Rd: GET
  gcite_citation_index.Rd: GET
  gcite_citation_page.Rd: GET
  gcite_cite_over_time.Rd: GET
  gcite_graph.Rd: GET
  gcite_main_graph.Rd: GET
  gcite_paper_df.Rd: GET
  gcite_papers.Rd: GET
  gcite_user_info.Rd: GET
  gcite_username.Rd: GET
  gcite_wordcloud_spec.Rd: wordcloud
  set_cookies_txt.Rd: set_cookies
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) listInverseBlocks.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                           ^
checkRd: (-1) listInverseBlocks.Rd:17: Lost braces; missing escapes or markup?
    17 | List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                    ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ac.Rd: agnes, silhouette
  cparcoord.Rd: parcoord
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) matern.cormat.Rd:17: Lost braces; missing escapes or markup?
    17 | value of the shape parameter of the Matern correlation class. The default {alpha = 0.5} corresponds to an exponential correlation model. 
       |                                                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cluster.cormat.Rd: nlme
  gcmr.Rd: betareg, Formula
  gs.marg.Rd: betareg
  plot.gcmr.Rd: qqPlot
  summary.gcmr.Rd: bread, estfun, sandwich
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) gconsensus.Rd:48-54: Lost braces
    48 | {\code{display.signif.digits} an integer representing the number of significant digits to be obtained in the adaptative approach of the Monte Carlo simulation,
       | ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cabbage_exp.Rd: cabbages
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) GCTF.Rd:56: Lost braces; missing escapes or markup?
    56 |   U : A matrix which has N-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) GCTF.Rd:57: Lost braces; missing escapes or markup?
    57 |   V : A matrix which has M-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) GCTF.Rd:58: Lost braces; missing escapes or markup?
    58 |   J : The number of dimension (J < {N, M}).
       |                                    ^
installed size is 107.3Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    gdal     3.0Mb
    libs    92.4Mb
    proj     8.4Mb
installed size is 104.9Mb
  sub-directories of 1Mb or more:
    gdal   3.0Mb
    libs  91.0Mb
    proj   8.4Mb
checkRd: (-1) nearblack.Rd:30: Lost braces
    30 | code{infile=}, indicating that the input file should be
       |     ^
checkRd: (-1) is.what.Rd:23-24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) is.what.Rd:25: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) is.what.Rd:26-27: Lost braces in \enumerate; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  angles.csa.Rd: MCA
  dimdescr.Rd: dimdesc
  medoids.Rd: cluster, pam
  modif.rate.Rd: MCA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) GMSCDM.Rd:25: Lost braces; missing escapes or markup?
    25 | representing restricted GMS-DINA and GMS-DINO models where delta_{jm1} are equal for all strategies. Note that only a single model can be used
       |                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Transition-classes.Rd: Raster-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) GDSARM.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) GDSARM.Rd:10: Lost braces
    10 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
checkRd: (-1) GDS_givencols.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) GDS_givencols.Rd:10: Lost braces
    10 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
checkRd: (-1) dantzig.delta.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) dantzigS.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) dataCompoundExt.Rd:6: Lost braces
     6 | \title{Compound Extraction experiment of Dopico-Garc{\' i}a et al. (2007)}
       |                                                     ^
checkRd: (-1) dataCompoundExt.Rd:35: Lost braces
    35 | An analytical experiment conducted by Dopico-Garc{\' i}a et al. (2007) to
       |                                                  ^
checkRd: (-1) dataCompoundExt.Rd:22: Lost braces
    22 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gfontHtmlDependency.Rd: htmlDependency
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'gdxrrw'
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geelm.Rd: geese
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  QIC.Rd: ginv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) dental.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gelnet.logreg.obj.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{y}{n-by-1 binary response vector sampled from {0,1}}
       |                                                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) parkinson.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parkinson.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parkinson.Rd:11: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.2Mb
    libs      1.0Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_raster_single.Rd: raster
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'genderdata'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  robust.g.test.Rd: rlm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) GeneF-internal.Rd:40: Lost braces; missing escapes or markup?
    40 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
checkRd: (-1) flexorhtest.Rd:57: Lost braces; missing escapes or markup?
    57 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
checkRd: (-1) flexorhtest.pvalue.Rd:57: Lost braces; missing escapes or markup?
    57 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggm.estimate.pcor.Rd: dyn.pcor, pcor.shrink
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  summary.hyperblm.Rd: tsHessian
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  factory-mleFactory.Rd: optimParallel
  factory-optimFactory.Rd: optimParallel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geneSLOPE.Rd: SLOPE, bigmemory
  selectionResult.Rd: SLOPE
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) cpm.Rd:70: Lost braces; missing escapes or markup?
    70 | covariates included in \code{formula_l} or {formula_s} (required).}
       |                                            ^
checkRd: (-1) LD.Rd:37-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:47-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:66-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:82-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:84-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:86-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:48-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:59-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:78-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:93-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:95-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:97-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:124: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:126-128: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:129: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
checkRd: (-1) simulate_admixture.Rd:36: Lost braces
    36 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
checkRd: (-1) simulate_ancestry.Rd:49: Lost braces
    49 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
checkRd: (-1) simulate_ancestry_migration.Rd:59: Lost braces
    59 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
checkRd: (-1) simulate_sequence.Rd:51: Lost braces
    51 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
checkRd: (-1) simulate_sequence_migration.Rd:58: Lost braces
    58 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) barto.Rd:15-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) barto.Rd:19-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) barto.Rd:23-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chrY_subseg.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chrY_subseg.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mauve_bbone.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mauve_bbone.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) three_genes.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) three_genes.Rd:19-20: Lost braces in \itemize; meant \describe ?
Problems with news in 'NEWS.md':
No news entries found.
File 'GenSA/libs/x64/GenSA.dll':
  Found non-API call to R: 'SET_TYPEOF'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
checkRd: (-1) cfunc.new.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gensvm.grid.Rd:125: Lost braces
   125 | "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                                ^
checkRd: (-1) gensvm.grid.Rd:125: Lost braces
   125 | "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                                    ^
checkRd: (-1) gensvm.grid.Rd:127: Lost braces
   127 | GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                    ^
checkRd: (-1) gensvm.grid.Rd:127: Lost braces
   127 | GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                        ^
checkRd: (-1) gensvm.grid.Rd:129: Lost braces
   129 | section "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more 
       |                                        ^
checkRd: (-1) gensvm.grid.Rd:129: Lost braces
   129 | section "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more 
       |                                            ^
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geoarrow_handle.Rd: as_nanoarrow_array
  infer_geoarrow_schema.Rd: as_nanoarrow_schema
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) calvaria.Rd:8: Lost braces; missing escapes or markup?
     8 | A named list containing \code{x} {a vector containing the ages}
       |                                  ^
checkRd: (-1) calvaria.Rd:9: Lost braces; missing escapes or markup?
     9 |   \code{y} {a matrix where each column is a preshape.} The 23rd, 101st,
       |            ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geoGAM.Rd: grpreg, cv.grpreg, gamboost, mboost, cvrisk, gam, polr,
    cv, mgcv
  methods.geoGAM.Rd: summary.gam, plot.gam, gam, predict.gam
  predict.geoGAM.Rd: predict.gam, gam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   3.5Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'geomarocdata'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  comb_EIG2.Rd: accuracy
  comb_SA.Rd: accuracy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    R         9.5Mb
    extdata   2.5Mb
    help      2.6Mb
File 'geometries/libs/x64/geometries.dll':
  Found non-API call to R: 'STRING_PTR'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following HTML validation problems:
extprod3d.html:24:32 (extprod3d.Rd:24): Warning: trimming empty <code>
extprod3d.html:29:32 (extprod3d.Rd:27): Warning: trimming empty <code>
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GNAbstractManager.Rd: R6Class
  GNLegacyAPIManager.Rd: R6Class, XMLInternalNode-class
  GNManager.Rd: R6Class
  GNOpenAPIManager.Rd: R6Class, XMLInternalNode-class
  GNPrivConfiguration.Rd: R6Class
  GNRESTRequest.Rd: R6Class
  GNUtils.Rd: R6Class
  GNVersion.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.geonetwork.Rd: plot_sf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GeoNodeManager.Rd: R6Class
  GeoNodeUtils.Rd: R6Class
  GeoNodeVersion.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lgnpp.Rd: SpatialPolygonsDataFrame
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  idw.cv.Rd: idw
  network.design.Rd: krige, spsample, krige.cv, point.in.polygon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'RandomFields'
Malformed Description field: should contain one or more complete sentences.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GeotopRasterBrick-class.Rd: Raster-class
  KML-methods.Rd: projectRaster
  bondone.Rd: zoo
  brick-methods.Rd: RasterBrick-class, raster
  brick.decimal.formatter.Rd: raster, RasterBrick-class
  brickFromOutputSoil3DTensor.Rd: RasterLayer-class, RasterBrick-class,
    Raster-class
  geotopbrick.Rd: RasterBrick-class
  get.geotop.inpts.keyword.value.Rd: Raster-class, raster, zoo
  get.geotop.points.Rd: sf
  get.geotop.recovery.state.Rd: raster
  read.ascii.vectorized.brick.Rd: raster, RasterBrick-class
  read.raster.from.url.Rd: raster
  read.vectorized.geotop.recovery.Rd: raster
  write.ascii.vectorized.brick.Rd: RasterBrick-class, writeRaster
  write.vectorized.geotop.recovery.Rd: writeRaster
  writeRasterxGEOtop.Rd: writeRaster, RasterBrick-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geoTS-package.Rd: reclassify
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coef.geovol.Rd: zoo
  geovol.Rd: zoo
  geovolObj.Rd: zoo
  geovolSim.Rd: zoo
  geovolTest.Rd: zoo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) gesso.cv.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gesso.cv.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gesso.cv.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gesso.cv.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gesso.cv.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gestMultiple.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestMultiple.Rd:81-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestMultiple.Rd:84-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestMultiple.Rd:87-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestSingle.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestSingle.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestSingle.Rd:79-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestSingle.Rd:81-84: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fclustering.Rd: pam
  geom_central_region.Rd: geom_ribbon, geom_line
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  extract_gfc.Rd: writeRaster
  scale_by_pixel_area.Rd: dataType
  scale_toar.Rd: writeRaster
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'RGtk2'
checkRd: (-1) QANOVA.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) QANOVA.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) QANOVA.Rd:64-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) QANOVA.Rd:67: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) gfonts.Rd:8: Lost braces; missing escapes or markup?
     8 | Download Google fonts and generate CSS to use in {rmarkdown} documents and
       |                                                  ^
checkRd: (-1) gfonts.Rd:9: Lost braces; missing escapes or markup?
     9 | {shiny} applications. Some popular fonts are included and ready to use.
       | ^
checkRd: (-1) use_pkg_gfont.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Use a Google Font included in {gfonts}}
       |                                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  glag.Rd: zoo, lag.zoo
  gsummary.Rd: vcovHC, NeweyWest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_bkde.Rd: aes, aes_, ggplot, fortify, borders, layer,
    geom_histogram, geom_freqpoly, geom_violin
  geom_bkde2d.Rd: aes, aes_, ggplot, fortify, borders, layer,
    stat_contour, geom_contour, stat_sum
  geom_cartogram.Rd: aes, aes_, ggplot, fortify, layer, borders
  geom_dumbbell.Rd: aes, aes_, ggplot, fortify, layer, borders
  geom_lollipop.Rd: aes, aes_, ggplot, fortify, layer, borders
  geom_stateface.Rd: aes, aes_, ggplot, fortify, layer, borders
  geom_xspline.Rd: aes, aes_, ggplot, fortify, borders, layer
  geom_xspline2.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_ash.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_stepribbon.Rd: aes, aes_, ggplot, fortify, borders, layer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_arrowsegment.Rd: geom_segment
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_arrow.Rd: aes_position, aes_colour_fill_alpha, aes_group_order,
    aes_linetype_size_shape
  geom_arrow_chain.Rd: aes_position, aes_colour_fill_alpha,
    aes_group_order, aes_linetype_size_shape
  geom_arrow_curve.Rd: aes_position, aes_colour_fill_alpha,
    aes_group_order, aes_linetype_size_shape
  geom_arrow_segment.Rd: aes_position, aes_colour_fill_alpha,
    aes_group_order, aes_linetype_size_shape
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  stat_automap.Rd: cartographer
  stat_automap_coords.Rd: cartographer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_quasirandom.Rd: geom_boxplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggblend-package.Rd: ggplot
  layer_list.Rd: ggplot2
  partition.Rd: vars
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
    libs      1.0Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  brick.Rd: aes, ggplot, fortify, borders
  waffle.Rd: aes, ggplot, fortify, borders
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggca.Rd: ggplot2, ggiraph
  ggmca.Rd: ggplot2, ggiraph
  ggmca_initial_dims.Rd: ggiraph
  ggmca_with_base_ref.Rd: ggiraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_spline.Rd: geom_smooth, aes, aes_string
  gf_ash.Rd: aes, aes_, facet_wrap, facet_grid, geom_histogram
  gf_bar.Rd: facet_wrap, facet_grid
  gf_bin2d.Rd: facet_wrap, facet_grid
  gf_blank.Rd: facet_wrap, facet_grid
  gf_boxplot.Rd: facet_wrap, facet_grid
  gf_col.Rd: facet_wrap, facet_grid
  gf_contour.Rd: facet_wrap, facet_grid
  gf_count.Rd: facet_wrap, facet_grid
  gf_crossbar.Rd: facet_wrap, facet_grid
  gf_curve.Rd: facet_wrap, facet_grid
  gf_density.Rd: facet_wrap, facet_grid
  gf_density_2d.Rd: facet_wrap, facet_grid
  gf_dotplot.Rd: facet_wrap, facet_grid
  gf_facet_grid.Rd: facet_wrap, facet_grid
  gf_fitdistr.Rd: facet_wrap, facet_grid
  gf_freqpoly.Rd: facet_wrap, facet_grid
  gf_hex.Rd: facet_wrap, facet_grid
  gf_histogram.Rd: facet_wrap, facet_grid
  gf_jitter.Rd: facet_wrap, facet_grid
  gf_line.Rd: facet_wrap, facet_grid
  gf_point.Rd: facet_wrap, facet_grid
  gf_polygon.Rd: facet_wrap, facet_grid
  gf_qq.Rd: facet_wrap, facet_grid
  gf_quantile.Rd: facet_wrap, facet_grid
  gf_raster.Rd: facet_wrap, facet_grid
  gf_rect.Rd: facet_wrap, facet_grid
  gf_rug.Rd: facet_wrap, facet_grid
  gf_segment.Rd: facet_wrap, facet_grid
  gf_sf.Rd: facet_wrap, facet_grid
  gf_sina.Rd: facet_wrap, facet_grid
  gf_smooth.Rd: facet_wrap, facet_grid
  gf_spline.Rd: facet_wrap, facet_grid
  gf_spoke.Rd: facet_wrap, facet_grid
  gf_step.Rd: facet_wrap, facet_grid
  gf_text.Rd: facet_wrap, facet_grid
  gf_theme.Rd: theme_minimal
  gf_tile.Rd: facet_wrap, facet_grid
  gf_violin.Rd: facet_wrap, facet_grid
  ggformula-ggproto.Rd: stat_qq
  ggformula.Rd: facet_wrap, facet_grid
  stat_qqline.Rd: aes, aes_string
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) render_context.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{xmin, ymin, xmax, ymax}{Boundaries of the area in pixels. {0,0} is the
       |                                                                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  object_support.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  identify_data.Rd: fortify
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  guide_axis_logticks.Rd: rel
  guide_axis_minor.Rd: rel
  guide_axis_nested.Rd: element_line, element_text
  theme_extensions.Rd: element_line, element_text, rel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggheatmap_theme.Rd: theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_debug_panel.Rd: aes_
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   7.3Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggjoy.Rd: ggridges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_leg.Rd: geom_segment
  inset.Rd: annotation_custom
  legs2route.Rd: geom_path
  qmplot.Rd: facet_wrap, facet_grid
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  theme_mice.Rd: mice, ggplot2
  theme_minimice.Rd: mice, ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
':::' call which should be '::': 'scales:::censor'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'productplots:::bound'
  See the note in ?`:::` about the use of this operator.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AG.Rd: igraph
  MAG.Rd: igraph
  MRG.Rd: igraph
  MSG.Rd: igraph
  MarkEqMag.Rd: igraph
  MarkEqRcg.Rd: igraph
  Max.Rd: igraph
  RG.Rd: igraph
  RepMarBG.Rd: igraph
  RepMarDAG.Rd: igraph
  RepMarUG.Rd: igraph
  SG.Rd: igraph
  ggm.Rd: cliques
  grMAT.Rd: igraph
  msep.Rd: igraph
  null.Rd: Null
  plotGraph.Rd: igraph, tkplot, plot.igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_density_.Rd: geom_density
  geom_hist_.Rd: geom_histogram
  position_dodge_.Rd: position_dodge
  position_stack_.Rd: position_stack
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_edgetext.Rd: geom_text, geom_label
  geom_edgetext_repel.Rd: geom_text_repel, geom_label_repel
  theme_blank.Rd: theme
  theme_facet.Rd: theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_normalviolin.Rd: aes, aes_, ggplot, fortify, borders, layer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_edge.Rd: layer, geom_segment
  geom_edge_label.Rd: geom_label
  geom_node_label.Rd: ggplot, fortify, borders
  geom_node_plot.Rd: facet_wrap
  ggparty.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) geom_from_path.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:87-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_from_path.Rd:91-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_lines.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_lines.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_lines.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_lines.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_lines.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_lines.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_lines.Rd:83: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_lines.Rd: geom_hline, geom_vline
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  draw_key_polygon_pattern.Rd: layer
  scale_pattern_alpha_continuous.Rd: continuous_scale, binned_scale,
    discrete_scale
  scale_pattern_colour_brewer.Rd: discrete_scale, continuous_scale,
    binned_scale
  scale_pattern_colour_viridis_d.Rd: discrete_scale, continuous_scale,
    binned_scale
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) pcp_scale.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:54-55: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggdonut.Rd: geom_text_repel
  ggnestedpie.Rd: geom_text_repel
  ggpie.Rd: geom_text_repel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    2.3Mb
    help   1.2Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggplot2-ggproto.Rd: gtable
  ggplot_gtable.Rd: gtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggplotly_histogram.Rd: ggplot, fortify, aes, aes_, layer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  stat_summaries_hex.Rd: aes, aes_, ggplot, fortify, layer, borders
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.4Mb
    testdata   4.8Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  n_pages.Rd: facet_wrap_paginate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_pointdensity.Rd: aes, aes_, ggplot, fortify, layer, borders
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_polypath.Rd: geom_polygon, geom_map, geom_path, geom_ribbon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_bracket.Rd: layer
  geom_pwc.Rd: layer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  stat_QC.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_QC_CAPA.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_QC_cap_hlabels.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_QC_cap_hlines.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_QC_cap_summary.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_QC_cap_vlabels.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_QC_cap_vlines.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_QC_labels.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_mR.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_pareto.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_qc_violations.Rd: aes, aes_, ggplot, fortify, borders, layer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  stat_km.Rd: trans_new
  stat_kmticks.Rd: trans_new, plot.survfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggplot2-ggproto.Rd: geom_jitter, geom_count, geom_bin2d, layer,
    geom_smooth, geom_quantile, geom_density_2d, geom_boxplot,
    geom_hex, geom_density2d
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
File 'ggraph/libs/x64/ggraph.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  StatCityRoad.Rd: aes
  StatDistrict.Rd: aes
  StatDistrictCoordinates.Rd: aes
  StatPlaces.Rd: aes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_density_line.Rd: geom_density
  geom_density_ridges.Rd: aes, aes_, ggplot, layer, stat_density
  geom_ridgeline.Rd: aes, aes_, ggplot, layer
  geom_ridgeline_gradient.Rd: aes, aes_, ggplot, layer
  geom_vridgeline.Rd: aes, aes_, ggplot, layer
  position_points_jitter.Rd: position_jitter
  scale_cyclical.Rd: discrete_scale
  scale_point.Rd: scale_discrete_manual
  scale_vline.Rd: scale_discrete_manual
  stat_density_ridges.Rd: stat_density, aes, aes_, ggplot, layer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggsdc.Rd: seas
  stat_decomp.Rd: aes, aes_, ggplot, fortify, borders
  stat_index.Rd: aes, aes_, ggplot, fortify, borders
  stat_rollapplyr.Rd: aes, aes_, ggplot, fortify, borders
  stat_seas.Rd: aes, aes_, ggplot, fortify, borders, seas
  stat_stl.Rd: aes, aes_, ggplot, fortify, borders
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    * Changes all data options to .data to decrease possibility of column naming overlap
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggseqlogo.Rd: facet_wrap
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_xsideabline.Rd: aes
  ggside-ggproto-facets.Rd: ggplot2
  xside.Rd: ggplot2
  yside.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) pitch_opta.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pitch_opta.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pitch_opta.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pitch_opta.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pitch_opta.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pitch_opta.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pitch_opta.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pitch_opta.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pitch_opta.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pitch_opta.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pitch_opta.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pitch_opta.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pitch_opta.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pitch_opta.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pitch_opta.Rd:69: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  layer_spatial.Raster.Rd: geom_raster
  layer_spatial.SpatRaster.Rd: geom_raster
  layer_spatial.stars.Rd: geom_raster
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_student.Rd: aes, aes_, ggplot, fortify, borders
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  annotation_raster_tern.Rd: geom_raster
  approved_layers.Rd: geom_point, geom_path, geom_line, geom_label,
    geom_text, geom_jitter, geom_polygon, geom_segment, geom_count,
    geom_curve, geom_blank, geom_rect, stat_identity, stat_sum,
    stat_unique, position_identity
  coord_tern.Rd: geom_segment
  geom_Xline.Rd: geom_hline, geom_vline
  geom_confidence_tern.Rd: ilr, stat_contour
  geom_hex_tern.Rd: aes_position, aes_colour_fill_alpha,
    aes_group_order, aes_linetype_size_shape
  geom_mean_ellipse.Rd: compositions, stat_contour
  geom_tri_tern.Rd: aes_position, aes_colour_fill_alpha,
    aes_group_order, aes_linetype_size_shape
  ggplot_build.Rd: benchplot
  ggplot_gtable.Rd: gtable
  ggtern_labels.Rd: xlab, ylab, latex2exp
  ggtern_package.Rd: proto
  kde2d.weighted.Rd: kde2d
  theme_elements.Rd: element_rect
  theme_latex.Rd: latex2exp, TeX
  theme_showgrid.Rd: element_line, element_blank
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_tufteboxplot.Rd: stat_boxplot, geom_boxplot
  scale_color_tableau.Rd: discrete_scale
  scale_colour_canva.Rd: discrete_scale
  theme_solid.Rd: theme
  theme_tufte.Rd: geom_rug
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
checkRd: (-1) MODFIT.Rd:33: Lost braces; missing escapes or markup?
    33 |   {chisq_i = sum( (O_iz - E_iz)^2 / E_iz; z = 0, ..., C ), }
       |   ^
checkRd: (-1) probs.GGUM.Rd:27: Lost braces; missing escapes or markup?
    27 |   GUM-based probabilities just constrain alpha to a unit vector of length {I}
       |                                                                           ^
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    9.5Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ghapps.Rd: gh
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ancsvm.Rd: svm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    Giac  18.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   2.5Mb
checkRd: (-1) gigg.Rd:70-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) significantTau.Rd:48-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) significantTau.Rd:52-53: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  monthlyComposite.Rd: stackApply, writeRaster
  oldNaming.Rd: writeFormats, ncvar_get, nc_open
  qualityControl.Rd: overlay, writeRaster
  rasterizeGimms.Rd: writeRaster
  significantTau.Rd: zyp.trend.vector, writeRaster, beginCluster,
    MannKendall
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GiNA-package.Rd: EBImage
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following HTML validation problems:
sample_income_data.html:37:1 (sample_income_data.Rd:8): Warning: trimming empty <h4>
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gh_install_packages.Rd: install_github
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) gjamCensorY.Rd:27: Lost braces; missing escapes or markup?
    27 |   \item{\code{y}}{n by S matrix updated with censored {values} substituted for
       |                                                       ^
checkRd: (-1) gjamFillMissingTimes.Rd:32: Lost braces
    32 | Missing times in the data occur where there are gaps in \code{timeCol} column of \code{xdata} and the initial time \code{0} for each sequence.  New versions of the data have \code{NA} (\code{xdata}) or prior values with appropriate weight (\code{ydata}).  Missing times are filled in \code{xdata, ydata, edata}, including a time \code{0} which serves as a prior mean for \code{ydata} for time code{1}.  The group and time indices in columns \code{groupCol} and \code{timeCol} of \code{xdata} reference the time for a given time series.  Missing values in the columns \code{groupVars} of \code{xdata} are filled automatically filled in.  This assumes that values for these variables are fixed for the group.  If \code{FILLMEANS}, the missing  values in \code{ydata} are filled with means for the group and given a low weight specified in \code{missingEffort}.
       |                                                                                                                                                                                                                                                                                                                                                                                                              ^
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  initial.Rd: glm.nb
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'doMC'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gd_api.Rd: GET
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fun.class.regime.bi.Rd: pam, fanny
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) GeneralisedLambdaDistribution.Rd:60: Lost braces; missing escapes or markup?
    60 |   \code{gpd} uses GPD parameterisation, see {van Staden and Loots (2009)}
       |                                             ^
checkRd: (-1) gld.lmoments.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gld.lmoments.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gld.lmoments.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gld.lmoments.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gld.moments.Rd:14: Lost braces
    14 |   {\eqn{\lambda_1}{lambda 1} location parameter}
       |   ^
checkRd: (-1) gld.moments.Rd:15: Lost braces
    15 |   {\eqn{\lambda_2}{lambda 2} - scale parameter}
       |   ^
checkRd: (-1) gld.moments.Rd:16: Lost braces
    16 |   {\eqn{\lambda_3}{lambda 3} - first shape parameter}
       |   ^
checkRd: (-1) gld.moments.Rd:17: Lost braces
    17 |   {\eqn{\lambda_4}{lambda 4} - second shape parameter}
       |   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GLD.lm.Rd: fun.RMFMKL.ml.m, fun.RMFMKL.ml, fun.RMFMKL.lm,
    fun.RPRS.ml.m, fun.RPRS.ml, fun.RPRS.lm
  GLD.lm.full.Rd: fun.RMFMKL.ml.m, fun.RMFMKL.ml, fun.RMFMKL.lm,
    fun.RPRS.ml.m, fun.RPRS.ml, fun.RPRS.lm
  GLD.lm.full.surv.Rd: fun.RMFMKL.ml.m, fun.RMFMKL.ml, fun.RPRS.ml.m,
    fun.RPRS.ml
  GLD.lm.surv.Rd: fun.RMFMKL.ml.m, fun.RMFMKL.ml, fun.RPRS.ml.m,
    fun.RPRS.ml
  qqgld.default.Rd: qqplot.gld, qqplot.gld.bi
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.2Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gllvm.Rd: nloptr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) NEWS.Rd:16: Lost braces; missing escapes or markup?
    16 |         \item Now \code{AICc == Inf} when {n <= p + 1}.
       |                                           ^
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
checkRd: (-1) glmc.control.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) glmc.control.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) summarylr.Rd:34: Lost braces
    34 | \item{method}{NULL or character vector of length 0, 1 or 2; may be code{"LRT"} or \code{"Rao"} or \code{c("LRT", "Rao")} to compute specified P-values.
       |                                                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  glmglrt.Rd: p_value.default
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) glmmSimData.Rd:4: Lost braces; missing escapes or markup?
     4 | \description{Section 4.1.2 of the refence below descries a simulation study with data generated from a probit mixed model with six fixed effects parameters and a bivariate random effects vector having a 2 by 2 symmetric positive definite covariance matrix. The function simulates a data set from this model with 2500 groups and the number of observation in each group being a random draw from {20,21,...,30}.}
       |                                                                                                                                                                                                                                                                                                                                                                                                          ^
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  optimControl.Rd: lme4
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RRglmer.Rd: glmer, lmerControl, glmerControl, lme4
  residuals.RRglmerMod.Rd: residuals.glmResp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  glmmRefit.Rd: glmmTMB
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc             1.3Mb
    libs            4.4Mb
    test_data       2.3Mb
    vignette_data   1.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  confint.glmmTMB.Rd: tmbprofile
  getXReTrms.Rd: mkReTrms
  profile.glmmTMB.Rd: tmbprofile
  ranef.glmmTMB.Rd: ranef.merMod
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  glmnetcr.Rd: glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'glmnet/libs/x64/glmnet.dll':
  Found non-API call to R: 'SET_TYPEOF'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) ccancer.Rd:16: Lost braces
    16 |                          a factor with levels either \\code{F} (female) or code{M} (male)}
       |                                                            ^
checkRd: (-1) ccancer.Rd:16: Lost braces
    16 |                          a factor with levels either \\code{F} (female) or code{M} (male)}
       |                                                                                ^
checkRd: (-1) galapagos.Rd:4: Lost braces
     4 | \title{{Gal\'{a}pagos} Island species data}
       |              ^
checkRd: (-1) galapagos.Rd:6: Lost braces
     6 |   The number of species on the {Gal\'{a}pagos} Islands
       |                                ^
checkRd: (-1) galapagos.Rd:6: Lost braces
     6 |   The number of species on the {Gal\'{a}pagos} Islands
       |                                      ^
checkRd: (-1) galapagos.Rd:40: Lost braces
    40 |    {Gal\'{a}pagos} (the endemics). 
       |    ^
checkRd: (-1) galapagos.Rd:40: Lost braces
    40 |    {Gal\'{a}pagos} (the endemics). 
       |          ^
checkRd: (-1) galapagos.Rd:44: Lost braces
    44 |   Species number and endemism: The {Gal\'{a}pagos} Archipelago revisited.
       |                                          ^
checkRd: (-1) glmtrans.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glmtrans.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glmtrans.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glmtrans.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glmtrans.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.glmtrans.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.glmtrans.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.glmtrans.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.glmtrans.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) consensus.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) getfit.Rd:14: Lost braces
    14 |   \item{object}{A fitted model object, of class \code{glm}, \code{lm} or code{glm.nb}}
       |                                                                              ^
checkRd: (-1) getfit.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-methods.Rd:14: Lost braces
    14 | code{glmulti} finds what are the \code{n} best models (the confidence set of models) among all possible models (the candidate set, as specified by the user).
       |     ^
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
372c372
< Classes and Methods for R originally developed in the
---
> Classes and Methods for R developed in the
375,377c375,377
< Stanford University (2002-2015),
< by and under the direction of Simon Jackman.
< hurdle and zeroinfl functions by Achim Zeileis.
---
> Stanford University
> Simon Jackman
> hurdle and zeroinfl functions by Achim Zeileis
Malformed Description field: should contain one or more complete sentences.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  globalsOf.Rd: codetools
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) getRiiGLPK.Rd:35: Lost braces; missing escapes or markup?
    35 |   Returns the current scale factor $r_{ii}$ for row \code{i} of the specified
       |                                       ^
checkRd: (-1) getSjjGLPK.Rd:35: Lost braces; missing escapes or markup?
    35 |   Returns the current scale factor $s_{jj}$ for column \code{j} of the
       |                                       ^
checkRd: (-1) setRiiGLPK.Rd:28: Lost braces; missing escapes or markup?
    28 |     Scale factor $r_{ii}$.
       |                     ^
checkRd: (-1) setSjjGLPK.Rd:28: Lost braces; missing escapes or markup?
    28 |     Scale factor $s_{jj}$.
       |                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) rtheta.Rd:50-76: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gmChangePassword.Rd: shiny
  gmConnectServer.Rd: dbConnect, RMySQL
  gmSQL.Rd: dbSendQuery
  gmSQLValues.Rd: dbEscapeStrings
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Maf.data.frame.Rd:65: Lost braces
    65 | the lag distance to take. \%For other options see code{getEmpVariogramSlice}.}
       |                                                       ^
checkRd: (-1) NGSAustralia.Rd:114: Lost braces; missing escapes or markup?
   114 | \item{MRB}{obtained from simplifying the major crustal boundaries of {Korsch2015a, Korsch2015b}}
       |                                                                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Maf.data.frame.Rd: cdt, princomp.acomp
  coloredBiplot.genDiag.Rd: coloredBiplot
  gsi.EVario2D.Rd: variogram
  gsi.EVario3D.Rd: variogram
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  descGetMissing.Rd: txtInt
  describeFactors.Rd: txtInt
  describeMean.Rd: txtInt
  describeMedian.Rd: txtInt
  describeProp.Rd: txtInt
  mergeDesc.Rd: htmlTable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'doMC'
checkRd: (-1) ATEgel.Rd:24: Lost braces
    24 | \item{g}{A formula as \code{y~z}, where code{y} is the response and
       |                                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bwWilhelm.Rd: kernHAC, bwAndrews
  estfun.Rd: kernHAC, vcovHAC, sandwich
  gel.Rd: kernHAC, bwAndrews, bwNeweyWest
  gmm.Rd: kernHAC
  smoothG.Rd: weightsAndrews
  sysGmm.Rd: kernHAC, bwAndrews, bwNeweyWest
  vcov.Rd: kernHAC
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotTitleTeX3D.Rd: bbox3d
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) GNE.ceq.Rd:50: Lost braces
    50 | (KKT) system denoted by \eqn{H(z)=0}, for \eqn{z \in \Omega} where eqn{z} is formed by the players strategy 
       |                                                                       ^
checkRd: (-1) GNE.nseq.Rd:76: Lost braces
    76 | (KKT) system denoted by \eqn{\Phi(z)=0}{Phi(z)=0}, where eqn{z} is formed by the players strategy 
       |                                                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GNE.fpeq.Rd: fpiter, squarem
  GNE.nseq.Rd: nleqslv
  eqsolve.depr.Rd: nleqslv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FNN.Rd: layer_dropout
  rPrior.Rd: rCopula
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gofArchmChisq.Rd: gofTstat
  gofArchmGamma.Rd: gofTstat
  gofArchmSnB.Rd: gofTstat
  gofArchmSnC.Rd: gofTstat
  gofCvM.Rd: gofTstat
  gofKS.Rd: gofTstat
  gofRosenblattChisq.Rd: gofTstat
  gofRosenblattGamma.Rd: gofTstat
  gofRosenblattSnB.Rd: gofTstat
  gofRosenblattSnC.Rd: gofTstat
  plot.gofCOP.Rd: pirateplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  glmMLE.Rd: glm2
  testGLMGamma.Rd: glm2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) BVDWSTOXX.Rd:14: Escaped LaTeX specials: \&
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checkRd: (-1) BVDWSTOXX.Rd:16: Escaped LaTeX specials: \& \&
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checkRd: (-1) BVDWSTOXX.Rd:34: Escaped LaTeX specials: \&
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Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  defineNodes.Rd: tbl_df
  examine.Rd: changepoint
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) create_golem.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{package_name}{Package name to use. By default, {golem} uses
       |                                                      ^
checkRd: (-1) fill_desc.Rd:42: Lost braces; missing escapes or markup?
    42 | The {desc} object, invisibly.
       |     ^
checkRd: (-1) get_sysreqs.Rd:23: Lost braces; missing escapes or markup?
    23 | {dockerfiler}.
       | ^
checkRd: (-1) golem_opts.Rd:80: Lost braces; missing escapes or markup?
    80 | \item{config_file}{path to the {golem} config file}
       |                                ^
checkRd: (-1) install_dev_deps.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {golem} dev dependencies}
       |                ^
checkRd: (-1) project_hook.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{package_name}{Package name to use. By default, {golem} uses
       |                                                      ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gar_auth.Rd: Token-class
  gar_auto_auth.Rd: Token-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) GitHubEventsConfig.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{x}{The repository in format {owner}/{repo} e.g. MarkEdmondson1234/googleCloudRunner}
       |                                   ^
checkRd: (-1) GitHubEventsConfig.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{x}{The repository in format {owner}/{repo} e.g. MarkEdmondson1234/googleCloudRunner}
       |                                           ^
checkRd: (-1) cr_buildstep_targets.Rd:27: Lost braces
    27 | \item{id}{The id of the buildstep.  In link{cr_buildstep_targets_multi} this is used along with \code{waitFor} to determine the order of execution}
       |                                            ^
checkRd: (-1) cr_setup_service.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{account_email}{The service account email e.g. \code{accountId@projectid.iam.gserviceaccount.com} or {12345678@cloudbuild.gserviceaccount.com}}
       |                                                                                                           ^
Found the following HTML validation problems:
cr_run.html:115:1 (cr_run.Rd:57): Warning: trimming empty <dt>
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  makeDockerClusterPSOCK.Rd: as.cluster
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  request_make.Rd: httr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) gl_nlp.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gl_auth.Rd: gar_attach_auto_auth
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cell-specification.Rd: cellranger
  request_make.Rd: httr
  sheets_id.Rd: googledrive
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) google_find_place.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) google_find_place.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) google_find_place.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) google_map.Rd:54: Lost braces; missing escapes or markup?
    54 | of `{sf}` objects).}
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  orgls.Rd: varClasses, corClasses, solve.QP
  orglsSet.Rd: varClasses, corClasses
  orlm.Rd: solve.QP
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) compute_lower_bound_1tree.Rd:31: Lost braces; missing escapes or markup?
    31 | instance from vertex 1.  Internally, it creates the graph Kn-{v1}
       |                                                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  apply_incidence_map.Rd: as_edgelist
  compute_cut_weight.Rd: as_edgelist
  compute_lower_bound_1tree.Rd: mst, igraph
  dfs_tree.Rd: bfs, dfs
  dijk.Rd: shortest_paths, igraph
  generate_fundamental_cycles.Rd: as_edgelist
  gor.Rd: igraph
  is_cover.Rd: as_edgelist
  shave_cycle.Rd: as_edgelist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  createListModularCode.Rd: codeCheck
  createListSimpleCode.Rd: codeCheck
  goxygen.Rd: codeCheck
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gpairs.Rd: splom, bwplot, barcode
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  00.GPArotateDF.Rd: NormalizingWeight
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  trait.posterior.Rd: pcubature
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.Rd: wireframe, levelplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) solve_game.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) solve_game.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) solve_game.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) solve_game.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) solve_game.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
Found the following HTML validation problems:
exponential_anisotropic3D_alt.html:70:1 (exponential_anisotropic3D_alt.Rd:34): Warning: trimming empty <h3>
'LazyData' is specified without a 'data' directory
checkRd: (-1) barplot2.Rd:219: Escaped LaTeX specials: \_
checkRd: (-1) colorpanel.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) qqnorm.aov.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) venn.Rd:21: Lost braces
    21 |     in code{data} not in this list will be ignored. Use \code{NA} to
       |            ^
checkRd: (-1) venn.Rd:59: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
checkRd: (-1) Auxil.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Auxil.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Auxil.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Auxil.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Predict.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Predict.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Predict.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LR_GradientConjugate_gpumatrix.Rd: Matrix-class
  gpu.matrix-class.Rd: Matrix-class
  gpu.matrix.Rd: Matrix-class
  matrix-product.Rd: %&%
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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) grade-package.Rd:51-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:58-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:72-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:79-81: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gradientPickerD3.Rd: htmlwidgets, shiny
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    help   5.2Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_3d_point_sd.Rd: facet_wrap
  plot_3d_scatterbar.Rd: facet_wrap
  plot_3d_scatterbox.Rd: facet_wrap, geom_boxplot
  plot_3d_scatterviolin.Rd: facet_wrap, geom_boxplot, geom_violin
  plot_4d_point_sd.Rd: facet_wrap, stat_summary, geom_point
  plot_4d_scatterbar.Rd: facet_wrap, stat_summary, geom_point
  plot_4d_scatterbox.Rd: facet_wrap, geom_boxplot
  plot_4d_scatterviolin.Rd: facet_wrap, geom_boxplot, geom_violin
  plot_befafter_box.Rd: facet_wrap, geom_line, geom_point
  plot_befafter_colours.Rd: facet_wrap, geom_line, geom_point
  plot_befafter_shapes.Rd: facet_wrap, geom_line, geom_point
  plot_density.Rd: geom_density, facet_wrap
  plot_dotbar_sd.Rd: facet_wrap, geom_dotplot
  plot_dotbox.Rd: facet_wrap, geom_boxplot, geom_dotplot
  plot_dotviolin.Rd: facet_wrap, geom_boxplot, geom_dotplot,
    geom_violin
  plot_histogram.Rd: geom_histogram, facet_wrap
  plot_logscale.Rd: scale_y_continuous, scale_x_continuous
  plot_point_sd.Rd: facet_wrap, stat_summary
  plot_qqline.Rd: ggplot2, facet_wrap
  plot_qqmodel.Rd: ggplot2
  plot_scatterbar_sd.Rd: facet_wrap
  plot_scatterbox.Rd: facet_wrap, geom_boxplot
  plot_scatterviolin.Rd: facet_wrap, geom_boxplot, geom_point,
    geom_violin
  plot_xy_CatGroup.Rd: facet_wrap
  plot_xy_NumGroup.Rd: facet_wrap
  posthoc_Levelwise.Rd: emmeans
  posthoc_Pairwise.Rd: emmeans
  posthoc_vsRef.Rd: emmeans
  theme_grafify.Rd: theme_classic
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  grafzahl.Rd: corpus, docvars
  predict.grafzahl.Rd: corpus
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MPG.Rd: igraph, projectRaster
  corridor.Rd: SpatialPoints
  distance.Rd: SpatialPoints
  export.Rd: writeFormats
  ggGS.Rd: ggplot
  goc-class.Rd: igraph
  grainscape-deprecated.Rd: SpatialPolygonsDataFrame, SpatialPoints
  patchFilter.Rd: clump
  plot.Rd: ggplot
  point.Rd: SpatialPoints
  theme_grainscape.Rd: ggplot2, ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  grand.Rd: igraph
  grand.table.Rd: igraph
  grand.text.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'grandR/libs/x64/grandR.dll':
  Found non-API call to R: 'SETLENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) Granger.inference.difference.Rd:65: Lost braces; missing escapes or markup?
    65 |         least one root larger than one) on bootstrapped \verb{x} and {y}.
       |                                                                      ^
checkRd: (-1) Granger.inference.difference.Rd:68: Lost braces; missing escapes or markup?
    68 |         least one root larger than one) on bootstrapped \verb{x} and {z}.
       |                                                                      ^
checkRd: (-1) Granger.inference.difference.Rd:71: Lost braces; missing escapes or markup?
    71 |         least one root larger than one) on bootstrapped \verb{x}, \verb{y} and {z}.
       |                                                                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) crdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) descApp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) layoutApp.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) rbdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) ttApp.Rd:43: Escaped LaTeX specials: \&
'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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.0Mb
    libs   1.2Mb
Specified C++11: please drop specification unless essential
File 'grattanInflators/libs/x64/grattanInflators.dll':
  Found non-API call to R: 'STRING_PTR'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  propagate.gRaven.Rd: propagate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.7Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fit-doc.Rd: fit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gmmpairs.Rd: ggplot2
  plot-DcLbmFit-missing-method.Rd: ggplot2
  plot-DcLbmPath-missing-method.Rd: ggplot2
  plot-DcSbmFit-missing-method.Rd: ggplot2
  plot-DiagGmmFit-missing-method.Rd: ggplot2
  plot-GmmFit-missing-method.Rd: ggplot2
  plot-IclPath-missing-method.Rd: ggplot2
  plot-LcaFit-missing-method.Rd: ggplot2
  plot-MoMFit-missing-method.Rd: ggplot2
  plot-MultSbmFit-missing-method.Rd: ggplot2
  plot-SbmFit-missing-method.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) MinimiseEPL.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MinimiseEPL.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MinimiseEPL.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MinimiseEPL.Rd:20: Lost braces in \itemize; meant \describe ?
Found the following HTML validation problems:
summary_greek.html:58:1 (summary_greek.Rd:22): Warning: trimming empty <dt>
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  caDescribeOpts.Rd: describeMean, describeFactors
  prGetStatistics.Rd: describeMean, describeFactors
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) covFun.Rd:89-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:91-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:93-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:96-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:98-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:100-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:104-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:110-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:114-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:116-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:23: Lost braces in \itemize; meant \describe ?
accrualReport: multiple local function definitions for 'gg' with
  different formal arguments
checkRd: (-1) setgreportOption.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:24: Lost braces
    24 | \item{code{figpos}:}{LaTeX figure environment position; default is \code{"htb!"}}
       |           ^
checkRd: (-1) setgreportOption.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) iterate_matrix.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iterate_matrix.Rd:34-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iterate_matrix.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iterate_matrix.Rd:39-41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iterate_matrix.Rd:42-44: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: 'doMC'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   2.6Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  agopenTrue.Rd: agopen
  graphWidth.Rd: Ragraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) NEWS.Rd:669: Lost braces; missing escapes or markup?
   669 |     parameters are rounded so they belong to one of {0, 0.5, 1}. (Simon)
       |                                                     ^
checkRd: (-1) gradients.Rd:96-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gradients.Rd:100-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gradients.Rd:104-107: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  readCoordsJS.Rd: fromJSON
  readMappingsJS.Rd: fromJSON
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs                     1.3Mb
    supplementary_material   3.1Mb
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  covrob.Rd: scaleTau2
  delete.intercept.Rd: mvr, model.matrix.mvr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
checkRd: (-1) predict.Rd:30: Lost braces
    30 | resp. code{'exponential'} or \code{'no_lag'} for \code{fit_easylinear}.}
       |           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cost.Rd: modCost
  fit_growthmodel.Rd: modFit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Birthwt.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:35-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:40-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:14-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:36-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) matches.Rd:33: Lost braces; missing escapes or markup?
    33 | be set to an index value of \code{length+1}.  If {indexes=FALSE}, they will
       |                                                  ^
File 'grr/libs/x64/grr.dll':
  Found non-API call to R: 'STRING_PTR'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) runGRM.Rd:24: Lost braces
    24 |    from \code{\link{mirt}} or code{\linkS4class{lavaan}} from from
       |                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ESplot.Rd: scale_color_viridis_d, ggplot
  FSplot.Rd: ggplot
  ICCplot.Rd: scale_color_viridis_d, ggplot
  genLavSyn.Rd: lavaan
  infoPlot.Rd: scale_color_viridis_d, ggplot
  runGRM.Rd: lavaan, SingleGroupClass-class, mirt, lavaan-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) GRS.Powerfunc.Rd:22: Lost braces
    22 | {Power: }{Matrix of power values plotted}
       |          ^
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
checkRd: (-1) qdb.p.correct.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{refpts}{a numeric vector used as a reference point to determine the correct side of the \code{qdb} for classifying \code{x}. The \code{length(refpts)} should be equal to {ncol(x)}. Default to \code{colMeans(x)}. }
       |                                                                                                                                                                                 ^
checkRd: (-1) crossval.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
Found the following HTML validation problems:
gsheet2tbl.html:31:5 (gsheet2tbl.Rd:20): Warning: trimming empty <p>
gsheet2tbl.html:31:1 (gsheet2tbl.Rd:20): Warning: trimming empty <li>
checkRd: (-1) besselap.Rd:58: Lost braces
    58 | Thomas Sailer, email{t.sailer@alumni.ethz.ch}.\cr Conversion to R by
       |                     ^
checkRd: (-1) diric.Rd:25: Lost braces; missing escapes or markup?
    25 | evaluated at the elements of the input array {x}.
       |                                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  poly.Rd: roots
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) lisiecki2005.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lisiecki2005.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lisiecki2005.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:29: Lost braces in \itemize; meant \describe ?
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) jura.Rd:29: Lost braces; missing escapes or markup?
    29 |         \item{Cd}{ mg cadmium kg^{-1} topsoil }
       |                                  ^
checkRd: (-1) jura.Rd:30: Lost braces; missing escapes or markup?
    30 |         \item{Co}{ mg cobalt kg^{-1} topsoil }
       |                                 ^
checkRd: (-1) jura.Rd:31: Lost braces; missing escapes or markup?
    31 |         \item{Cr}{ mg chromium kg^{-1} topsoil }
       |                                   ^
checkRd: (-1) jura.Rd:32: Lost braces; missing escapes or markup?
    32 |         \item{Cu}{ mg copper kg^{-1} topsoil }
       |                                 ^
checkRd: (-1) jura.Rd:33: Lost braces; missing escapes or markup?
    33 |         \item{Ni}{ mg nickel kg^{-1} topsoil }
       |                                 ^
checkRd: (-1) jura.Rd:34: Lost braces; missing escapes or markup?
    34 |         \item{Pb}{ mg lead kg^{-1} topsoil }
       |                               ^
checkRd: (-1) jura.Rd:35: Lost braces; missing escapes or markup?
    35 |         \item{Zn}{ mg zinc kg^{-1} topsoil }
       |                               ^
checkRd: (-1) variogramST.Rd:49: Lost braces; missing escapes or markup?
    49 |   time lag $t$, the pseudo cross variogram $(Z_i(s)-Z_{i+t}(s+h))^2$ is averaged over all time 
       |                                                       ^
checkRd: (-1) variogramST.Rd:50: Lost braces; missing escapes or markup?
    50 |   lagged observation sets $Z_i$ and $Z_{i+t}$ available (weighted by the number of pairs involved).
       |                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  krigeST.Rd: ST-class
  plot.gstatVariogram.Rd: xyplot
  variogramST.Rd: STFDF-class, STSDF-class, STIDF-class
  vgm.panel.Rd: lpoints
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) artset1987.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gte.Rd:98: Lost braces; missing escapes or markup?
    98 | \code{left} and {right} for illustrative purpose), one would need a third variable (\code{status}) taking the value 0 
       |                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gte.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.1Mb
File 'gtfstools/libs/x64/gtfstools.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Running 'testthat.R' [39s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > if (requireNamespace("testthat", quietly = TRUE)) {
  + 
  +   library(testthat)
  +   library(gtfstools)
  + 
  +   test_check("gtfstools")
  + 
  + }
  trying URL 'https://github.com/ipeaGIT/gtfstools/raw/master/inst/extdata/spo_gtfs.zip'
  Content type 'application/zip' length 191108 bytes (186 KB)
  ==================================================
  downloaded 186 KB
  
  [ FAIL 2 | WARN 8 | SKIP 2 | PASS 1243 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-download_validator.R:37:1', 'test-validate_gtfs.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-set_trip_speed.R:257:3'): results in identical gtfs if none of the specified trip_ids exist ──
  `same_speeds_gtfs <- set_trip_speed(gtfs, character(0), 1)` produced warnings.
  ── Failure ('test-set_trip_speed.R:263:3'): results in identical gtfs if none of the specified trip_ids exist ──
  `same_speeds_gtfs <- set_trip_speed(gtfs, character(0), numeric(0))` produced warnings.
  
  [ FAIL 2 | WARN 8 | SKIP 2 | PASS 1243 ]
  Error: Test failures
  Execution halted
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gstudy.Rd: lmer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.0Mb
    help   2.0Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) PLSSVD.Rd:24: Lost braces; missing escapes or markup?
    24 | The number of low-dimension (k < {N, M, L}, Default: .minDim(X, Y))
       |                                  ^
checkRd: (-1) guidedPLS.Rd:33: Lost braces; missing escapes or markup?
    33 | The number of low-dimension (k < {N, M, L, O}, Default: .minDim(X1, X2, Y1, Y2))
       |                                  ^
checkRd: (-1) sPLSDA.Rd:24: Lost braces; missing escapes or markup?
    24 | The number of low-dimension (k < {N, M, L}, Default: .minDim(X, Y))
       |                                  ^
checkRd: (-1) guild_merge.Rd:38: Lost braces; missing escapes or markup?
    38 |     \item{\code{summary_name}}{Name used for the run summary. Use '${run_id}' in the name to include the run ID.}
       |                                                                     ^
checkRd: (-1) guild_merge_cli.Rd:88: Lost braces; missing escapes or markup?
    88 | \item{summary_name}{Name used for the run summary. Use '${run_id}' in the name to include the run ID.}
       |                                                          ^
checkRd: (-1) gumbel.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:75: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  adonis3.Rd: vegdist, permustats
  dmanova.Rd: vegdist, nearPD
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GUTS-package.Rd: Rcpp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) esSim.Rd:81: Lost braces; missing escapes or markup?
    81 | \eqn{83} SNPs are in cluster {-}, \eqn{714} SNPs are in cluster \eqn{0},
       |                              ^
checkRd: (-1) esSimDiffPriors.Rd:91: Lost braces; missing escapes or markup?
    91 | \eqn{64} SNPs are in cluster {-}, \eqn{708} SNPs are in cluster \eqn{0},
       |                              ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following HTML validation problems:
GWASinlps.html:187:1 (GWASinlps.Rd:99): Warning: trimming empty <h4>
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_stream_network_interactively.Rd: elevatr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following HTML validation problems:
gedit.html:139:6 (gedit.Rd:72): Warning: trimming empty <p>
gedit.html:139:1 (gedit.Rd:72): Warning: trimming empty <li>
checkRd: (-1) gWidgets2tcltk-undocumented.Rd:285: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gWidgets2tcltk-undocumented.Rd:286-293: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gWidgets2tcltk-undocumented.Rd:378: Lost braces
   378 | \item{visible}{logical. If code{TRUE} window is drawn when
       |                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gWidgets2tcltk-undocumented.Rd: gbutton, gprogressbar
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 267.8Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    help    1.0Mb
    java  264.7Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  habCluster-package.Rd: raster, Rcpp, igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hac.Rd: nacopula
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    shiny   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    HaDeX   4.0Mb
    doc     4.0Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_kinetics.Rd: bind_rows
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  diversities_table.Rd: pander, pandoc.table
  individual_pathotypes.Rd: pander
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  format_long_hazards.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.ga.breed' '.ga.fitness' '.ga.init' '.ga.mutate' '.ga.step'
  '.ga.weight'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SaveAllLetterPlots.Rd: magick
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Parsimnet-class.Rd: network, networx
  as.DNAbin-methods.Rd: DNAbin
  as.dna-methods.Rd: DNAbin, phyDat
  as.network-methods.Rd: network
  as.networx-methods.Rd: networx, as.splits
  as.phyDat-methods.Rd: phyDat
  parsimnet-methods.Rd: network
  pielegend-methods.Rd: floating.pie, plot.network.default
  pieplot-methods.Rd: network.layout, floating.pie, network.vertex,
    plot.network.default
  plot-methods.Rd: plot.network.default
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.6Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File 'haven/libs/x64/haven.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  att.Rd: estimatr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R         2.6Mb
    extdata   1.3Mb
GNU make is a SystemRequirements.
checkRd: (-1) deff.sigma.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:35: Lost braces in \itemize; meant \describe ?
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dcbs.alg.Rd: foreach
  sbs.alg.Rd: foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) phenowheat.Rd:18: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) phenowheat.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) hdda.Rd:121-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdda.Rd:124-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdda.Rd:128-132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hddc.Rd:162-164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hddc.Rd:165-168: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cure_estimate.Rd: survfit
  nonzerocure_test.Rd: survfit
  sufficient_fu_test.Rd: survfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) lasso.proj.Rd:62: Lost braces; missing escapes or markup?
    62 |     indicated using an index vector with entries in {1,...,p} or a list thereof.}
       |                                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lasso.cv.Rd: cv.glmnet
  lasso.firstq.Rd: glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mediate_hdmm.Rd: mediate
  mediate_hima.Rd: hdi
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Malformed Title field: should not end in a period.
checkRd: (-1) colByValue.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.}
       |                       ^
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
checkRd: (-1) heatmaply.Rd:282: Lost braces
   282 | row and column dendrograms. The default uses stats{reorder.dendrogram}}
       |                                                   ^
checkRd: (-1) heatmapr.Rd:93: Lost braces
    93 | \item{reorderfun}{function(d, w) of dendrogram and weights for reordering the row and column dendrograms. The default uses stats{reorder.dendrogram}}
       |                                                                                                                                 ^
checkRd: (-1) is.plotly.Rd:16: Lost braces
    16 | Helpful for the plot_method in link{heatmaply}.
       |                                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RColorBrewer_colors.Rd: brewer.pal, viridis
  heatmaply.Rd: scale_color_gradient
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) category.Rd:117-118: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) category.Rd:119-120: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) category.Rd:121: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) category.Rd:122-123: Lost braces in \enumerate; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  category.Rd: y
  geom_flame.Rd: layer
  geom_lolli.Rd: layer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) marker_h2.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:96-97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:98-99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:41-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:46-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:49-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:52-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:55-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:61-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:66-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) phermite.Rd:38: Lost braces; missing escapes or markup?
    38 |   {b} and \code{m} to be lower (or greater) than \code{q}.
       |   ^
GNU make is a SystemRequirements.
checkRd: (-1) hero.Rd:67-68: Lost braces
    67 | then \code{\link[pbapply]{pblapply}} is used. If code{package ==
       |                                                      ^
checkRd: (-1) hero.Rd:69: Lost braces
    69 | code{package == "Rmpi"}, then \code{\link[Rmpi]{mpi.applyLB}} is used.}
       |     ^
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.4Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  create_IndivCtstmTrans.Rd: R6Class
  create_trans_dt.Rd: data.table
  input_mats.Rd: data.table, print.data.table
  partsurvfit.Rd: flexsurvreg, flexsurvspline
  plot_ceac.Rd: ggplot2
  plot_ceaf.Rd: ggplot2
  plot_ceplane.Rd: ggplot2
  plot_evpi.Rd: ggplot2
  summary.eval_rng.Rd: data.table
  summary.params.Rd: data.table
  summary.tparams_transprobs.Rd: data.table
  summary.tpmatrix.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) mleHetGP.Rd:57: Lost braces; missing escapes or markup?
    57 | Level \code{2} gives more details. Level {3} additionaly displays all details about initialization of hyperparameters.
       |                                          ^
checkRd: (-1) mleHetTP.Rd:61: Lost braces; missing escapes or markup?
    61 | Level \code{2} gives more details. Level {3} additionaly displays all details about initialization of hyperparameters.
       |                                          ^
checkRd: (-1) mleHomTP.Rd:76: Lost braces; missing escapes or markup?
    76 | \item \code{nit_opt}, \code{msg}: \code{counts} and {msg} returned by \code{\link[stats]{optim}}
       |                                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fh_hetop.Rd: jags
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'heumilkr/libs/x64/heumilkr.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) predictPair.Rd:20: Lost braces; missing escapes or markup?
    20 | A number in the set {-1, 0, 1}, where 1 means row1 is predicted to
       |                     ^
checkRd: (-1) predictPairInternal.Rd:18: Lost braces; missing escapes or markup?
    18 | A number in the set {-1, 0, 1}, where 1 means row1 is predicted to
       |                     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.hglasso.Rd: layout.kamada.kawai, plot.igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
get_breaks.html:78:1 (get_breaks.Rd:37): Warning: trimming empty <dt>
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addGroups2WFUN.Rd: W_powerlaw, W_np
  fitC.Rd: hhh4, update.hhh4
  noroBE.Rd: sts-class, nbOrder, poly2adjmat
  plotHHH4_fitted_groups.Rd: hhh4, plotHHH4_fitted
  plotHHH4_maps_groups.Rd: plotHHH4_maps
  plotHHH4_season_groups.Rd: plotHHH4_season, epochInYear
  stsplothook.Rd: stsplot_time1
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ResizeEtc.likertPlot.Rd: barchart
  ToBW.likert.Rd: panel.bwplot
  ancovaplot.Rd: panel.superpose, panel.xyplot
  latticeresids.Rd: xyplot
  likertWeighted.Rd: xyplot, panel.bwplot
  lmatPairwise.Rd: mcp
  residual.plots.lattice.Rd: xyplot
  useOuterScales.Rd: trellis.par.get, xyplot, panel.axis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DACrossVal.Rd: lda, predict.lda
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^
checkRd: (-1) hierNet.Rd:28: Lost braces; missing escapes or markup?
    28 |     terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |               ^
checkRd: (-1) hierNet.logistic.Rd:30: Lost braces; missing escapes or markup?
    30 |     terms, th_{jj}X_j^2, in the model.  Default TRUE.}  
       |               ^
checkRd: (-1) hierNet.logistic.Rd:63: Lost braces
    63 | \seealso{\link{predict.hierNet.logistic},link{hierNet.logistic.path}}
       |                                              ^
checkRd: (-1) hierNet.logistic.path.Rd:39: Lost braces; missing escapes or markup?
    39 |   terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |             ^
checkRd: (-1) hierNet.path.Rd:38: Lost braces; missing escapes or markup?
    38 |   terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |             ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'colorfulVennPlot'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File 'hilbert/libs/x64/hilbert.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
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 Rd file(s) with Rd \link{} targets missing package
anchors:
  dblassoHIMA.Rd: hdi
  hima.Rd: ncvreg
  qHIMA.Rd: conquer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
File 'hipread/libs/x64/hipread.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'HadoopStreaming'
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hlm_resid.lmerMod.Rd: ranef
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) hlt.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:77-78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hlt.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hlt.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hlt.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hlt.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.3Mb
html_describe_con: multiple local function definitions for 'g' with
  different formal arguments
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  popower.Rd: ggplot2
  transcan.Rd: multinom
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) nafracCalc.Rd:45: Lost braces
    45 |   as if code{y} were not of class \code{"multipleHmmDataSets"}.
       |             ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
checkRd: (-1) sampleMcmc.Rd:93: Lost braces; missing escapes or markup?
    93 |   disable some of them, by adding a \code{$UPDATER_NAME=FALSE} pair to the {updater} argument. Another usage of
       |                                                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotBeta.Rd: image.plot
  plotGamma.Rd: image.plot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hms.Rd: vec_cast
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hnp.Rd: glm.nb, multinom
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hoard.Rd: rappdirs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) HOasso.Rd:43: Lost braces; missing escapes or markup?
    43 | Arguments \code{x} and {y} are \code{character} objects and can assume values   \code{"sout"}, \code{"dout"}, \code{"lout"}, \code{"sin"}, \code{"din"}, \code{"lin"} representing the out-strength, out-degree, out-log-strength, in-strength, in-degree, and in-log-strength respectively.
       |                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  holland-package.Rd: MplusAutomation
  sim_score_data.Rd: rmvnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    app   1.7Mb
    doc   3.3Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hommel-class.Rd: select
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PaillierKeyPair.Rd: R6Class
  PaillierPrivateKey.Rd: R6Class
  PaillierPublicKey.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  poly2form.Rd: legendre.polynomials
  psiandrew.Rd: rlm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  HospiNet.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) hd.ord.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Lchs.Rd: plot.Lc, Lc
  plot.hotspots.Rd: densityplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) HPLB.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  scale_x_percent.Rd: guides
  theme_ipsum.Rd: ggplot2
  theme_ipsum_es.Rd: ggplot2
  theme_ipsum_gs.Rd: ggplot2
  theme_ipsum_inter.Rd: ggplot2
  theme_ipsum_ps.Rd: ggplot2
  theme_ipsum_pub.Rd: ggplot2
  theme_ipsum_rc.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  critical.value.Rd: davies
  size.Rd: davies
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  HSDiC_ADMM.Rd: solve.QP
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  causalForest.Rd: rpart.control, rpart.object, summary.rpart,
    rpart.plot
  causalTree.Rd: rpart.control, rpart.object, summary.rpart, rpart.plot
  causalTree.control.Rd: rpart.control
  honest.causalTree.Rd: rpart.control, rpart.object, summary.rpart,
    rpart.plot
  honest.est.causalTree.Rd: rpart.object
  honest.rparttree.Rd: rpart.control
  model.frame.causalTree.Rd: rpart, rpart.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File 'htmltools/libs/x64/htmltools.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) BD_shift.Rd:67-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BD_shift.Rd:74-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BD_shift.Rd:78-82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BD_shift.Rd:83-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data-physeq_rep3.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) heavy_SIP.Rd:69-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) heavy_SIP.Rd:72-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) heavy_SIP.Rd:76-79: Lost braces in \itemize; meant \describe ?
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.3Mb
    help   1.1Mb
Specified C++14: please drop specification unless essential
File 'httpgd/libs/x64/httpgd.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CalcROC.Rd:47: Lost braces
    47 | The accuracy of the classifier is the mean value of dQuote{(optSn, optSp)} for two-class problem and the mean value of \dQuote{(optSn, optSp,optS3)} for three-class problem.
       |                                                           ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
checkRd: (-1) simgl.Rd:50: Lost braces; missing escapes or markup?
    50 | Uses the {updog} R package for simulating read counts and generating
       |          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hwep-package.Rd: future
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ws_download.Rd:31: Lost braces; missing escapes or markup?
    31 | (while using the {hwsdr} package for HWSD v2.0).
       |                  ^
Package suggested but not available for checking: 'microViz'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hybridModel.Rd: GillespieSSA
  simHM.Rd: GillespieSSA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) extractPeriod.Rd:57: Lost braces
    57 | NOTE: all the dates in the datalist should follow the format in ?as.Date{base}.
       |                                                                         ^
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hyper.fit.Rd: LaplaceApproximation, LaplacesDemon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  buhring.Rd: residue
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  map-sel-poly.Rd: levelplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CompareFiles.Rd: full_join
  PlotMapOutput.Rd: geom_sf, geom_sf_text, ggsave
  PlotMapPoints.Rd: geom_sf, geom_sf_text, ggsave
  PlotPerformanceByAttribute.Rd: left_join, scale_color_manual,
    geom_smooth, geom_density, geom_boxplot, scale_x_log10,
    scale_y_log10, pseudo_log_trans, scale_x_continuous,
    scale_y_continuous, xlab, ylab, ggarrange, ggsave
  ReadBasinOutput.Rd: data.table
  ReadGeoData.Rd: data.table
  ReadMapOutput.Rd: data.table
  ReadObs.Rd: data.table
  ReadTimeOutput.Rd: data.table
  ReadXobs.Rd: data.table
  WriteHarmonizedData.Rd: getDTthreads
  WriteHarmonizedSpatialDescription.Rd: getDTthreads
  distinctColorPalette.Rd: darken
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hypoRF.Rd: ranger
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calc_areas.Rd: area, values
  generateHypsoTables.Rd: crop, mask, classify
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) IATData.Rd:24: Lost braces; missing escapes or markup?
    24 | Dan Martin {dpmartin42@gmail.com}
       |            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Tgraph.Rd: qgraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  IBDsim.Rd: linkdat
  oneLocusIBD.Rd: linkdat
  oneLocusJacquard.Rd: jacquard, linkdat
  twoLocusIBD.Rd: linkdat
  twoLocusJacquard.Rd: linkdat, jacquard
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SparkR'
checkRd: (-1) setServerLogLevel.Rd:20: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:23: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) betaS1lr.Rd:28: Lost braces; missing escapes or markup?
    28 |  \item{Rm1U}{matrix R^{-1}U (see reference).}
       |                       ^
checkRd: (-1) lrsmoother.Rd:32: Lost braces; missing escapes or markup?
    32 |   R^{-1}U (see reference) and \link{smoothCon} for the definition of smoothobject}
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  forward.Rd: gam
  ibr.Rd: gam, smoothCon
  ibr.fit.Rd: gam, smoothCon
  lrsmoother.Rd: smoothCon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AnnotateDBSVCF.Rd: BSgenome
  AnnotateSBSVCF.Rd: BSgenome
  GeneExpressionData.Rd: data.table
  ICAMS.Rd: BSgenome
  MutectVCFFilesToCatalog.Rd: BSgenome
  MutectVCFFilesToCatalogAndPlotToPdf.Rd: BSgenome
  MutectVCFFilesToZipFile.Rd: BSgenome
  NormalizeGenomeArg.Rd: BSgenome
  PlotTransBiasGeneExp.Rd: data.table
  PlotTransBiasGeneExpToPdf.Rd: data.table
  StrelkaSBSVCFFilesToCatalog.Rd: BSgenome
  StrelkaSBSVCFFilesToCatalogAndPlotToPdf.Rd: BSgenome
  StrelkaSBSVCFFilesToZipFile.Rd: BSgenome
  VCFsToCatalogs.Rd: BSgenome
  VCFsToCatalogsAndPlotToPdf.Rd: BSgenome
  VCFsToDBSCatalogs.Rd: BSgenome
  VCFsToSBSCatalogs.Rd: BSgenome
  VCFsToZipFile.Rd: BSgenome
  revc.Rd: reverseComplement
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  crt.minimax.control.Rd: nl.opts
  sens.control.Rd: nl.opts
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'icd'
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  run.umap.Rd: umap_transform
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Bpa.Rd:39-40: Lost braces
    39 | stocks. \doi{10.17895/ices.pub.3036}{\emph{ICES Advice
       |                                     ^
checkRd: (-1) Fpa.Rd:42-43: Lost braces
    42 | stocks. \doi{10.17895/ices.pub.3036}{\emph{ICES Advice
       |                                     ^
checkRd: (-1) icesRound.Rd:64-65: Lost braces
    64 | \doi{10.17895/ices.pub.3038}{\emph{ICES Advice Technical
       |                             ^
checkRd: (-1) mohn.Rd:71-72: Lost braces
    71 | \doi{10.17895/ices.pub.5997}{\emph{ICES Scientific Reports
       |                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  taf.colors.Rd: TAF-package
  taf.skeleton.sa.org.Rd: TAF-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  INCAnumclu.Rd: pam, diana, fanny
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'ichimoku/libs/x64/ichimoku.dll':
  Found non-API call to R: 'R_shallow_duplicate_attr'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Specified C++11: please drop specification unless essential
checkRd: (-1) ic.ranks.Rd:46: Lost braces; missing escapes or markup?
    46 | \item{n_adjust}{an integer-valued entry for advanced control over the lower- or upper-bound algorithms. When the "adjustL" parameter is TRUE, the new value of n_adjust is chosen automatically as the best adjustment on the lower affine bound of the chi-square quantiles according to the data. If adjustU is TRUE, then n_adjust contains the point at which the upper affine bound is tangent on the chi-square quantiles. Possible values {1,...,n-1}. If both adjustL and adjustU variables are left FALSE, then the default choice is that the lower affine bound passes between the chi-square quantiles at 1 and n-1 degrees of freedom, and the upper affine bound is tangent on n-1.}
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ICSClust.Rd: ICS-S3
  component_plot.Rd: ICS-S3
  normal_crit.Rd: jarque.test, anscombe.test, bonett.test,
    agostino.test
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ics.distances.Rd: ics2
  icsOut-class.Rd: plot.ics
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ICSShiny.Rd: ICSOutlier, dist.simu.test, comp.simu.test
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) data.Rd:7: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data.Rd:9: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  covSIR.Rd: ics
  ggplot.ictest.Rd: ggpairs
  ggplot.ladle.Rd: ggpairs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  filter_log_style.Rd: crayon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rggobi'
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gev.d.fit.Rd: gev.fit
  gev.d.params.Rd: gev.fit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  isurvdiff.Rd: Surv
  isurvdiff.smax.Rd: Surv
  isurvfit.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  madstat.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'IFCdata'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  metrics_heatmap.Rd: pheatmap
  plot_lasagna.Rd: scale_fill_gradient2
  plot_lasagna_1subject.Rd: scale_fill_gradient2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.2Mb
    help   2.0Mb
    libs   5.6Mb
File 'igraph/libs/x64/igraph.dll':
  Found non-API calls to R: 'PRENV', 'R_PromiseExpr', 'SETLENGTH',
    'SET_GROWABLE_BIT', 'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) simHawkes1a.Rd:35: Lost braces; missing escapes or markup?
    35 | distribution; 'd${dis}' gives the density function \eqn{g(\cdot)}.}
       |                  ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) lab.qcs.Rd:24: Lost braces
    24 | It develops an object of \code{lab.qcs}-code{link{class}} to perform statistical quality control.
       |                                             ^
checkRd: (-1) lab.qcs.Rd:24: Lost braces
    24 | It develops an object of \code{lab.qcs}-code{link{class}} to perform statistical quality control.
       |                                                  ^
checkRd: (-1) define_target_function.Rd:41: Lost braces; missing escapes or markup?
    41 | be done either as a single vector of values (e.g. `function(x) { ... }`), or individual inputs for each parameter
       |                                                                ^
checkRd: (-1) define_target_function.Rd:42: Lost braces; missing escapes or markup?
    42 | (e.g. `function(x1, x2) { ... }`). If a single vector is used, all parameters will be passed to the target function as
       |                         ^
checkRd: (-1) image_contour_detector.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_contour_detector.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_contour_detector.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitSpline.Rd:109: Lost braces
   109 |        \code{response} and it will have the same order of code{x} as \code{data}. 
       |                                                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  anomPlot.Rd: ggplot
  corrPlot.Rd: ggplot
  imagetimesPlot.Rd: ggplot
  longiPlot.Rd: ggplot, labeller
  probeDF.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         1.4Mb
checkRd: (-1) image_fhog.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) image_line_segment_detector.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_line_segment_detector.Rd:66-72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_line_segment_detector.Rd:73-76: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.7Mb
    extdata   1.0Mb
    include   3.3Mb
    libs     11.5Mb
checkRd: (-1) imagesToKerasInput.Rd:23: Lost braces
    23 | \item{grayscale}{logical. Defines color channels of images: 1 if code{TRUE}, 3 if \code{FALSE}.}
       |                                                                      ^
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs   10.5Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) oversample.Rd:23-24: Lost braces
    23 | minority examples and majority ones, that is, the quotient {size of
       |                                                            ^
checkRd: (-1) oversample.Rd:24: Lost braces; missing escapes or markup?
    24 | minority class}/{size of majority class}. There are methods, such as
       |                 ^
File 'imbibe/libs/x64/imbibe.dll':
  Found non-API call to R: 'SET_TYPEOF'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  imgur_login.Rd: oauth2.0_token
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coding.Rd: data.table, copy_to
  dbAnnotate.Rd: data.table, copy_to
  geneUsage.Rd: data.table, copy_to
  getKmers.Rd: data.table, copy_to
  immunr_hclust.Rd: fviz_nbclust, hcut, dbscan
  immunr_pca.Rd: isoMDS, Rtsne
  inc_overlap.Rd: data.table, copy_to
  pubRep.Rd: data.table, copy_to
  repAlignLineage.Rd: data.table
  repClonality.Rd: data.table, copy_to
  repDiversity.Rd: data.table, copy_to
  repExplore.Rd: data.table, copy_to
  repGermline.Rd: data.table
  repOverlap.Rd: data.table, copy_to
  repSample.Rd: data.table, copy_to
  select_barcodes.Rd: data.table, copy_to
  seqCluster.Rd: data.table
  seqDist.Rd: data.table
  spectratype.Rd: data.table, copy_to
  top.Rd: data.table, copy_to
  trackClonotypes.Rd: data.table, copy_to
  vis.immunr_gene_usage.Rd: chordDiagram
  vis.immunr_hclust.Rd: fviz_dend
  vis.immunr_kmeans.Rd: fviz_cluster
  vis.immunr_ov_matrix.Rd: chordDiagram
  vis.immunr_public_statistics.Rd: upset
  vis_box.Rd: melt
  vis_circos.Rd: chordDiagram
  vis_hist.Rd: melt
  vis_textlogo.Rd: geom_logo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) stringCSSRule.Rd:22: Lost braces
    22 | using the {{placeholder}} convention.
       |           ^
checkRd: (-1) stringTemplate.Rd:23: Lost braces
    23 | placeholders are marked using the {{placeholder}} convention.
       |                                   ^
checkRd: (-1) stringTemplate.Rd:12: Lost braces
    12 | {{placeholder}} format.}
       | ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  flexPage.Rd: htmlDependency, tagList, shinyUI
  flexPanel.Rd: HTML, htmlDependency, tagList
  gridPage.Rd: htmlDependency, tagList, shinyUI
  gridPanel.Rd: HTML, htmlDependency, tagList
  stringCSSRule.Rd: htmlTemplate
  stringTemplate.Rd: htmlTemplate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'accdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  excel_export.Rd: read_excel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) imptree_params.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imptree_params.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imptree_params.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.imptree.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  in2extRemes-package.Rd: extRemes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) kmpp.Rd:27: Lost braces
    27 |   \item{call}{a string containing the matched function call that generates this sQuote{inaparc} object.}
       |                                                                                       ^
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  if_case.Rd: magrittr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calculate.orbit.counts.Rd: count5
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  add.blocks.Rd: igraph
  curveball.Rd: igraph
  incidence.from.adjacency.Rd: igraph
  incidence.from.distribution.Rd: igraph
  incidence.from.probability.Rd: igraph
  incidence.from.vector.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) make_likelihood_matrix.Rd:16: Lost braces; missing escapes or markup?
    16 | This function creates a matrix such that P[t, s] = P(C = t | I = s) = theta_{t-s} for s <= t and 0 otherwise.
       |                                                                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  incRplot.Rd: ggplot2
  incRt.Rd: getSunlightTimes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) IndexComp.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly
File 'indexthis/libs/x64/indexthis.dll':
  Found non-API call to R: 'STRING_PTR'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cooks.distance.Rd: ols, lad, ridge
  leverages.Rd: ols, ridge
  logLik.displacement.Rd: ols, lad, ridge
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  indicators.Rd: how
  multipatt.Rd: how
  signassoc.Rd: how
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  InDisc.Rd: psych
  indisc-package.Rd: psych
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) process_stats.Rd:11: Lost braces; missing escapes or markup?
    11 | the {janitor} package}
       |     ^
checkRd: (-1) theme_industRial.Rd:40: Lost braces; missing escapes or markup?
    40 | adapted from the package {cowplot} by Claus O.Wilke and reflects the principles
       |                          ^
checkRd: (-1) theme_industRial.Rd:45: Lost braces; missing escapes or markup?
    45 | It basically combines the half open theme with a grid background from {cowplot}
       |                                                                       ^
checkRd: (-1) vaccinesim.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vaccinesim.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vaccinesim.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vaccinesim.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vaccinesim.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vaccinesim.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:18: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  score_calc.Rd: grad
  score_matrix.Rd: grad
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Deltachi.Rd: lavaan, sem
  Likedist.Rd: lavaan, sem
  fitinfluence.Rd: lavaan, sem
  genCookDist.Rd: lavaan, sem
  parinfluence.Rd: lavaan, sem
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
Package which this enhances but not available for checking: 'gurobi'
checkRd: (-1) write_workflow.Rd:8: Lost braces
     8 | code{write_workflow} writes a workflow script for inference. Beyond possibly saving some typing, this suggests what may be a reasonably good starting workflow. One should not expect to control all options of the workflow through the \code{write_workflow} arguments.
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  infer_logLs.Rd: HLfit
  infer_surface.Rd: corrHLfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  worldMap.Rd: sf, terra
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AgnosticWrapper.Rd: torch_tensor
  ConnectionWeights.Rd: torch_tensor, torch_float, torch_double
  Converter.Rd: nn_sequential
  DeepLift.Rd: torch_tensor, torch_float, torch_double
  DeepSHAP.Rd: torch_tensor, torch_float, torch_double
  ExpectedGradient.Rd: torch_tensor, torch_float, torch_double
  Gradient.Rd: torch_tensor, torch_float, torch_double
  GradientBased.Rd: torch_tensor, torch_float, torch_double
  IntegratedGradient.Rd: torch_tensor, torch_float, torch_double
  InterpretingMethod.Rd: torch_float, torch_double, torch_tensor
  LIME.Rd: torch_tensor
  LRP.Rd: torch_tensor, torch_float, torch_double
  SHAP.Rd: torch_tensor
  SmoothGrad.Rd: torch_tensor, torch_float, torch_double
  innsight_ggplot2-class.Rd: ggplot2
  innsight_ggplot2-plus.Rd: ggplot2
  innsight_sugar.Rd: nn_sequential, torch_tensor
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  InPosition-package.Rd: ExPosition
  boot.compute.fj.Rd: ExPosition, epPCA, epMCA, supplementaryCols
  contingency.data.break.Rd: epCA
  epCA.inference.battery.Rd: epGraphs, epCA, coreCA, epMCA
  epGPCA.inference.battery.Rd: expo.scale, epGraphs, epGPCA, corePCA,
    epPCA
  epMCA.inference.battery.Rd: epGraphs, epMCA, coreCA, epCA
  epPCA.inference.battery.Rd: expo.scale, epGraphs, epPCA, corePCA,
    epGPCA
  inGraphs.Rd: prettyGraphs, createColorVectorsByDesign, prettyPlot,
    epGraphs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  manipulate.Rd: ape
  purge.Rd: kmer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  csmf.diag.Rd: heidel.diag, gelman.diag
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
checkRd: (-1) ask.user.yn.question.Rd:44: Lost braces; missing escapes or markup?
    44 | menu in the {utils} package, yesno in the {devtools} package.
       |             ^
checkRd: (-1) ask.user.yn.question.Rd:44: Lost braces; missing escapes or markup?
    44 | menu in the {utils} package, yesno in the {devtools} package.
       |                                           ^
checkRd: (-1) install.FFmpeg.Rd:25: Lost braces; missing escapes or markup?
    25 | This function is useful for saveVideo() in the {animation} package.
       |                                                ^
checkRd: (-1) install.SWFTools.Rd:27: Lost braces; missing escapes or markup?
    27 | This function is useful for saveSWF() in the {animation} package.
       |                                              ^
checkRd: (-1) os.shutdown.Rd:25: Lost braces; missing escapes or markup?
    25 | This function is a modified version of Yihui's shutdown function from the {fun} package.
       |                                                                           ^
Malformed Title field: should not end in a period.
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) remit.Rd:32: Lost braces
    32 | A data set to replicate the findings of Escrib\`{a}-Folch,
       |                                                 ^
checkRd: (-1) remit.Rd:38: Lost braces
    38 | Escrib\`{a}-Folch, A., Meseguer, C. and Wright, J. (2018), Remittances and Protest in Dictatorships. American Journal of Political Science, 62: 889-904. \doi{10.1111/ajps.12382}
       |         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) interval-internal.Rd:40: Lost braces
    40 | \item{dqfunc}{function, density of the results of the quantile function, e.g., function(x){dnorm(qnorm(x))} (used for 'general' scores, 
       |                                                                                           ^
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc   9.7Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  inTextSummaryTable-stats.Rd: roundHalfUpTextFormat
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) decompose_volume.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decompose_volume.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decompose_volume.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decompose_volume.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fit_volume.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fit_volume.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fit_volume.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fit_volume.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_plots.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_plots.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_plots.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) intRvals-package.Rd:60: Lost braces
    60 | B\'{e}dard, J. & Gauthier, G. 1986. Assessment of faecal output in geese. Journal of Applied Ecology, 23, 77-90.
       |    ^
checkRd: (-1) partition.Rd:64: Lost braces
    64 | Bates, D., M\"{a}chler, M., Bolker, B.M. & Walker, S.C. (2015). Fitting linear mixed-effects models using lme4. Journal of Statistical Software, 67, 1-48.
       |               ^
Specified C++11: please drop specification unless essential
checkRd: (-1) cox_cure_net.Rd:132: Lost braces
   132 | \code{surv_lambda} (or code{cure_lambda}) that produces all-zero
       |                            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Inventorymodel-package.Rd:34: Lost braces
    34 | M.G. Fiestras-Janeiro, I. García-Jurado, A. Meca, M.A. Mosquera (2015). Cooperation on capacitated inventory situations with fixed holding costs. emph{European Journal of Operational Research}, \bold{241}(3), 719--726.
       |                                                                                                                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NormalizedLaplacian.Rd: Matrix-class
  PerturbedLaplacian.Rd: Matrix-class
  RegularizedLaplacian.Rd: Matrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  iNZightSummary.Rd: survey
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'surveyspec'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  survey_IQR.Rd: srvyr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) f.influence.Rd:25: Lost braces; missing escapes or markup?
    25 | where F is the field of influence, k is order of influence, l_{ij} is the ith row and jth column element of the Leontief Inverse and -s indicates the sth element has been removed.
       |                                                               ^
Specified C++11: please drop specification unless essential
checkRd: (-1) IOHproblem.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:46-48: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) aiPux.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dls2007.Rd:19: Lost braces
    19 | impact. emph{Journal of Applied Psychology}, 92(5), 1380.
       |             ^
checkRd: (-1) paretoXX.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXX.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXX.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXY.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXY.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXY.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_iota.Rd: ggplot2
  plot_iota2_alluvial.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'NAMED', 'R_GetConnection',
    'R_ReadConnection', 'R_WriteConnection', 'SETLENGTH', 'SET_NAMED'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(IPDFileCheck)
  > 
  > test_check("IPDFileCheck")
  The following errors were returned during `::()`, `gtsummary()`, and `modify_header()`:
  x For variable `age` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `marker` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `response` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-IPDFilecheck.R:948:3'): testing getting summary from gtsummary ──
  summary_tempdata$N (`actual`) not equal to 4 (`expected`).
  
  `actual` is NULL
  `expected` is a double vector (4)
  ── Error ('test-IPDFilecheck.R:951:3'): testing getting summary from gtsummary ──
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(dplyr::tibble(variable = names(fns)), summary_type = map_chr(.data$variable, 
      ~x$inputs$type[[.x]]), row_type = map_chr(.data$variable, 
      ~location[[.x]]), label = map2(.data$variable, .data$row_type, 
      ~dplyr::filter(x$table_body, .data$variable == .x, .data$row_type == 
          .y)$label))`: i In argument: `summary_type = map_chr(.data$variable, ~x$inputs$type[[.x]])`.
  Caused by error in `.data$variable`:
  ! Column `variable` not found in `.data`.
  
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  Error: Test failures
  Execution halted
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  curvIPEC.Rd: hessian, jacobian, rms.curv
  skewIPEC.Rd: ginv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) check_convergence.Rd:47: Lost braces
    47 | \code{conv_plot}: code{ipm} invisibly.
       |                       ^
checkRd: (-1) init_ipm.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:63-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:70-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make_ipm.Rd:276: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) make_ipm.Rd:277-281: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) make_ipm.Rd:282-286: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) make_ipm.Rd:287-291: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) make_ipm.Rd:292-293: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ipsecr-internal.Rd: detectfn, addCovariates, sim.popn, sim.capthist,
    popn, capthist
  ipsecr-package.Rd: sim.popn, sim.capthist, usage, makeStart, Parallel
  ipsecr.fit.Rd: mask, detectfn, verify, setNumThreads
  ipsecrdemo.Rd: capthist, read.capthist, secrdemo
  plot.ipsecr.Rd: Detection functions, detectfnplot
  plotProxy.Rd: detectfn
  predict.ipsecr.Rd: predictDsurface
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DNAbin2index.Rd: DNAbin
  EmptyCells.Rd: DNAbin
  code.simple.gaps.Rd: DNAbin
  collapseUnsupportedEdges.Rd: phylo
  combMyTree.Rd: phylo
  del.miss.Rd: DNAbin
  deleteGaps.Rd: DNAbin
  fixNodes.Rd: phylo, read.nexus
  forceEqualTipHeights.Rd: is.ultrametric, chronos
  index2DNAbin.Rd: DNAbin
  ips-package.Rd: ladderize, rotate
  ips.16S.Rd: DNAbin
  ips.28S.Rd: DNAbin
  ips.cox1.Rd: DNAbin
  mafft.Rd: phylo
  mafft.merge.Rd: DNAbin, AAbin, phylo
  mrbayes.Rd: DNAbin
  multistate.Rd: ace
  neighboringPairs.Rd: mst
  ntip.Rd: phylo
  pathd8.Rd: phylo
  phylo2mafft.Rd: phylo
  phylo2mst.Rd: phylo
  pis.Rd: DNAbin
  raxml.Rd: DNAbin, phylo
  raxml.partitions.Rd: DNAbin, cbind.DNAbin
  rbeauti.Rd: DNAbin
  read.Rd: cbind.DNAbin
  sister.Rd: phylo
  splitIntoClades.Rd: phylo
  terminalSisters.Rd: phylo
  tipHeights.Rd: phylo, branching.times
  traitRate.Rd: phylo, DNAbin, read.tree
  write.fas.Rd: DNAbin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ipwpoint.Rd: multinom, polr
  ipwtm.Rd: coxph, multinom, polr, geeglm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  parallel_coord.Rd: plotly
  parameters_summarise.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) createBssUrl.Rd:28: Lost braces
    28 |     \code{constraint}{ a character string containing value constraints }
       |                      ^
checkRd: (-1) createBssUrl.Rd:29: Lost braces
    29 |     \code{url}{ optional url of the BSS measurements service }
       |               ^
checkRd: (-1) getGeneralValueMetrics.Rd:28: Lost braces
    28 |       \code{constraint}{ a character string containing value constraints }
       |                        ^
checkRd: (-1) getGeneralValueMetrics.Rd:29: Lost braces
    29 |       \code{url}{ optional url of the MUSTANG measurements service} 
       |                 ^
checkRd: (-1) getMustangMetrics.Rd:28: Lost braces
    28 |      \code{constraint}{ a character string containing value constraints }
       |                       ^
checkRd: (-1) getMustangMetrics.Rd:29: Lost braces
    29 |      \code{url}{ optional url of the MUSTANG measurements service }
       |                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  upDownTimesMetric.Rd: getUpDownTimes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) getTimeseries.Rd:30: Lost braces
    30 |      \code{processing}{optional character string with processing commands }
       |                       ^
checkRd: (-1) mergeTraces.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mergeTraces.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) psdStatistics.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psdStatistics.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) partial_eigen.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) partial_eigen.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:41-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:47-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DataGeneration.Rd: rBeta.4P
  plot.IRTest.Rd: stat_function, geom_line
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) est_mg.Rd:284: Lost braces
   284 | item parameter estimates across the groups in the code{\link{est_mg}} function.
       |                                                       ^
checkRd: (-1) llike_score.Rd:22: Lost braces
    22 | function. See \code{\link{est_irt}}, \code{\link{irtfit}}, \\code{\link{info}},
       |                                                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) analyseISE.Rd:66: Lost braces; missing escapes or markup?
    66 |         False positive rate used for detection threshold (not output) to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                                                     ^
checkRd: (-1) analyseISE.Rd:69: Lost braces; missing escapes or markup?
    69 |         False negative rate used to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                ^
checkRd: (-1) describeISE.Rd:71: Lost braces; missing escapes or markup?
    71 |         False positive rate used for detection threshold (not output) to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                                                     ^
checkRd: (-1) describeISE.Rd:74: Lost braces; missing escapes or markup?
    74 |         False negative rate used to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  islasso.Rd: cv.glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File 'isoband/libs/x64/isoband.dll':
  Found non-API call to R: 'SETLENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) CLM.Rd:30: Lost braces
    30 | item{tau0}{the mean circular Kendall Tau of the initial order with the data.}
       |     ^
checkRd: (-1) CLM.Rd:30: Lost braces
    30 | item{tau0}{the mean circular Kendall Tau of the initial order with the data.}
       |           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mrl.Rd: rho.circular
  plot.isocir.Rd: eqscplot, plot.circular
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plots.Rd: terra
  serialize.Rd: terra
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++14: please drop specification unless essential
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.3Mb
    libs   3.1Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
checkRd: (-1) is_israd_database.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) secretin.Rd:17: Lost braces
    17 |       {\code{a}: 1st sample};
       |       ^
checkRd: (-1) secretin.Rd:18: Lost braces
    18 |       {\code{b}: 2nd sample}.}
       |       ^
checkRd: (-1) secretin.Rd:20: Lost braces
    20 |       {\code{20+}: 20 minutes or longer since injection};
       |       ^
checkRd: (-1) secretin.Rd:21: Lost braces
    21 |       {\code{pre}: before injection.}}
       |       ^
checkRd: (-1) secretin.Rd:23: Lost braces
    23 |       {\code{20}:  20 minutes since injection};
       |       ^
checkRd: (-1) secretin.Rd:24: Lost braces
    24 |       {\code{30+}: 30 minutes or longer since injection};
       |       ^
checkRd: (-1) secretin.Rd:25: Lost braces
    25 |       {\code{pre}: before injection.  }}
       |       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  createFastIhtPrior.Rd: fitCyclopsModel
  createIhtPrior.Rd: fitCyclopsModel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fvisgam.Rd: gradientLegend
  plot_diff2.Rd: gradientLegend
  plot_parametric.Rd: dotplot_error
  plot_pca_surface.Rd: gradientLegend
  plot_topo.Rd: gradientLegend
  pvisgam.Rd: gradientLegend
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cmcc_bioclim.Rd: sf, sfc
  detect_envi_change.Rd: st_as_stars, read_stars, explain, geom_smooth
  dim_reduce.Rd: sf, sfc
  future_cmcc_bioclim.Rd: sf, sfc
  future_worldclim2.Rd: sf, sfc
  independent_response.Rd: st_as_stars, read_stars
  isotree_po.Rd: isolation.forest, sf
  mainland_africa.Rd: sf, sfc
  marginal_response.Rd: st_as_stars, read_stars
  plot.EnvironmentalOutlier.Rd: geom_sf
  plot.ShapDependence.Rd: geom_smooth
  shap_dependence.Rd: st_as_stars, read_stars, explain
  shap_spatial_response.Rd: st_as_stars, read_stars, explain
  spatial_response.Rd: st_as_stars, read_stars, explain
  suspicious_env_outliers.Rd: outlier.tree, crs, sf
  variable_analysis.Rd: st_as_stars, read_stars, explain
  variable_contrib.Rd: explain
  worldclim2.Rd: sf, sfc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'gurobi'
Package suggested but not available for checking: 'locClass'
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
checkRd: (-1) sTsls.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{pi}{the matrix E[XZ']E[ZZ']^{-1}}
       |                                   ^
checkRd: (-1) sTslsSplines.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{pi}{matrix, corresponds to E[XZ']E[ZZ']^{-1}, the first stage
       |                                               ^
Specified C++11: please drop specification unless essential
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) jaccard.test.Rd:41: Lost braces; missing escapes or markup?
    41 | The {bootstrap} method uses resampling with replacement binary vectors to compute a p-value (see optional arguments).
       |     ^
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          11.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
File 'JavaGD/libs/x64/JavaGD.dll':
  Found non-API call to R: 'Rf_gsetVar'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   4.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
Specified C++11: please drop specification unless essential
File 'jinjar/libs/x64/jinjar.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) data_timeinv.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{X5}{categorical covariate taking values from {1, 2, 3, 4, 5}; time-invariant}
       |                                                    ^
checkRd: (-1) data_timeinv.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{g}{true latent class identifier {1, 2, 3, 4}, which is determined by 
       |                                       ^
checkRd: (-1) data_timevar.Rd:15: Lost braces; missing escapes or markup?
    15 | \item{X5}{categorical covariate taking values from {1, 2, 3, 4, 5}; time-varying}
       |                                                    ^
checkRd: (-1) data_timevar.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{g}{true latent class identifier {1, 2, 3, 4}, which is determined by 
       |                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  jlctree.Rd: rpart.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) jointLPM.Rd:298: Lost braces; missing escapes or markup?
   298 | following transformation b_1 + b_2*I_1(Y(t)) + ... + b_{n+2}*I_{n+1}(Y(t)),
       |                                                        ^
checkRd: (-1) jointLPM.Rd:298: Lost braces; missing escapes or markup?
   298 | following transformation b_1 + b_2*I_1(Y(t)) + ... + b_{n+2}*I_{n+1}(Y(t)),
       |                                                                ^
checkRd: (-1) jointLPM.Rd:299: Lost braces; missing escapes or markup?
   299 | where I_1,...,I_{n+1} is the basis of quadratic I-splines. To constraint the
       |                 ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) jmdem.control.Rd:42: Lost braces; missing escapes or markup?
    42 |     The control argument of \code{jmdem} is by default passed to the control argument of {jmdem.fit}, which uses its elements as arguments to {jmdem.control}: the latter provides defaults and sanity checking.
       |                                                                                          ^
checkRd: (-1) jmdem.control.Rd:42: Lost braces; missing escapes or markup?
    42 |     The control argument of \code{jmdem} is by default passed to the control argument of {jmdem.fit}, which uses its elements as arguments to {jmdem.control}: the latter provides defaults and sanity checking.
       |                                                                                                                                               ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R      3.8Mb
    i18n   6.7Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  jnt_cat.Rd: corStruct, corClasses
  jnt_cont.Rd: corStruct, corClasses
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.ranef.mjoint.Rd: ranef
  vcov.mjoint.Rd: getVarCov
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package which this enhances but not available for checking: 'remMap'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SpATS.nogeno.Rd: SAP, PSANOVA, SpATS, controlSpATS
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  queryBuilderInput.Rd: shiny
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  manip.Rd: add
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PlotSickleJrUMAP.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) jrt.Rd:45-46: Lost braces
    45 | \item{Difference models (more or less constrained versions of the
       |      ^
checkRd: (-1) jrt.Rd:54-55: Lost braces
    54 |  \item{Divide-by-total models (more or less constrained versions of the
       |       ^
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
checkRd: (-1) jSDM_binomial_probit_long_format.Rd:45: Lost braces
    45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr 
       |                                             ^
checkRd: (-1) jSDM_binomial_probit_long_format.Rd:45: Lost braces; missing escapes or markup?
    45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr 
       |                                                ^
checkRd: (-1) jSDM_binomial_probit_long_format.Rd:45: Lost braces
    45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr 
       |                                                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  standardize_variable.Rd: dplyr_tidy_select
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  jmodelMult.Rd: lme, coxph, Surv
  jmodelTM.Rd: lme, coxph, Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File 'jsonify/libs/x64/jsonify.dll':
  Found non-API call to R: 'SET_TYPEOF'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  js_validate_script.Rd: V8
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) export_summs.Rd:26: Lost braces; missing escapes or markup?
    26 | Default: "({std.error})"}
       |            ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  includeAudio.Rd: knitr
  includeText.Rd: knitr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gglikert.Rd: geom_point
  scoring.Rd: omega
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kanjistat.data'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kanjivec.Rd: dendextend
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) get.fit.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:57-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.sim.trajectories.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.sim.trajectories.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.kdecopula.Rd: wireframe
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  parametric_starts.Rd: univariateML
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  contour.kdevinecop.Rd: contour.kdecopula
  kdevinecop.Rd: kdecopula
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fit_model.Rd: Dirichlet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) kdist.Rd:14: Lost braces; missing escapes or markup?
    14 | The {kdist} functions dk, pk, qk and rk, calculates the K-distribution
       |     ^
'LazyData' is specified without a 'data' directory
prepare_Rd: NEWS.Rd:58: Dropping empty section 'kelvin INITIAL VERSION 1.0-0 (2012-05-30)'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Beir.Rd: BesselJ, BesselK
  Keir.Rd: BesselK
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MannKendall.Rd: tsboot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   8.2Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  KerasCallback.Rd: R6Class
  KerasConstraint.Rd: R6Class
  KerasLayer.Rd: R6Class
  KerasWrapper.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  simulate.covAll.Rd: mvrnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) kernelFactory.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{method}{Can be one of the following: POLynomial kernel function (\code{pol}), LINear kernel function (\code{lin}), Radial Basis kernel Function \code{rbf}), random choice (random={pol, lin, rbf}) (\code{random}), burn- in choice of best function (burn={pol, lin, rbf }) (\code{burn}). Use \code{random} or \code{burn} if you don't know in advance which kernel function is best.}
       |                                                                                                                                                                                          ^
checkRd: (-1) kernelFactory.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{method}{Can be one of the following: POLynomial kernel function (\code{pol}), LINear kernel function (\code{lin}), Radial Basis kernel Function \code{rbf}), random choice (random={pol, lin, rbf}) (\code{random}), burn- in choice of best function (burn={pol, lin, rbf }) (\code{burn}). Use \code{random} or \code{burn} if you don't know in advance which kernel function is best.}
       |                                                                                                                                                                                                                                                                   ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute_all_tests.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) subjOCCDIF.Rd:23: Lost braces
    23 | the scale on which to evaluate each subject. \code{stype = "ObsScore"} uses the subject's total score. \code{stype = "Theta"} uses the subject's rank on the \code{thetadist} scale. \code{stype = "ThetaML"} uses the maximum likelihood estimate for the subject on the \code{thetadist} scale. code{stype = "ScoreML"} uses the maximum likelihood estimate for the subject on the overall test score scale.
       |                                                                                                                                                                                                                                                                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  read_keywords.Rd: dictionary
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  keyed-df-one-tbl.Rd: dplyr
  keyed-df-two-tbl.Rd: dplyr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) useKeys.Rd:13: Lost braces; missing escapes or markup?
    13 | This function adds the {keys} dependencies to your application
       |                        ^
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor Changes
checkRd: (-1) kfda.Rd:26: Lost braces
    26 |  \item{kpca.train}{An object of class "kpca". It has results of \code{kpca} function. (see{\code{\link[kernlab]{kpca}}} (in package \pkg{kernlab}))}
       |                                                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) kfino_plot.Rd:52: Lost braces; missing escapes or markup?
    52 |        plus the OK values. Prediction corresponds to E[X_{t} | Y_{1...t}] 
       |                                                          ^
checkRd: (-1) kfino_plot.Rd:52: Lost braces; missing escapes or markup?
    52 |        plus the OK values. Prediction corresponds to E[X_{t} | Y_{1...t}] 
       |                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Kernel.Rd: R6Class
  MLP.Rd: R6Class
  RBF.Rd: R6Class
  Warp.Rd: R6Class
  ode.Rd: R6Class
  rkg3.Rd: R6Class
  rkhs.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kibior.Rd: R6Class, count
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) mount_appdata.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{x}{An object of class \code{KinPairData} or {KinPairSimulation}}
       |                                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  convertIBD.Rd: pedtools
  logL.UKX.Rd: logL.UK
  logLX.Rd: logL
  mixMLX.Rd: mixML
  pedigreeIBD.Rd: pedtools
  wlr.Rd: map.genotypes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ibdMatrix.Rd: Matrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  delete_fmri_data.Rd: delete_kirby21_data
  download_fmri_data.Rd: download_kirby21_data
  get_fmri_filenames.Rd: get_image_filenames
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  delete_t1_data.Rd: delete_kirby21_data
  download_t1_data.Rd: download_kirby21_data
  get_t1_filenames.Rd: get_image_filenames
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cross_spectrum.Rd: pspectrum
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'kit/libs/x64/kit.dll':
  Found non-API call to R: 'STRING_PTR'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  specClust.Rd: arpack
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package which this enhances but not available for checking: 'rkward'
checkRd: (-1) klausuR.answ-class.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:18-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:110-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:114-116: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:117-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:119-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:121-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:124-126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:152-155: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RGeostats'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kmBlockORPC.Rd: genRandomPar
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) plotkmc.Rd:21: Lost braces; missing escapes or markup?
    21 |     list of two functions,flist=list( f1=function( x ) { x } ,f2=function( x ) { x^2 } )  
       |                                                        ^
checkRd: (-1) plotkmc.Rd:21: Lost braces; missing escapes or markup?
    21 |     list of two functions,flist=list( f1=function( x ) { x } ,f2=function( x ) { x^2 } )  
       |                                                                                ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ClusterLongData3d-class.Rd: Partition-class, plotCriterion,
    LongData3d-class, ListPartition-class
  clusterLongData3d.Rd: ClusterLongData-class
  generateArtificialLongData3d.Rd: ClusterLongData-class,
    generateArtificialLongData
  kml3d-package.Rd: Partition-class, choice, saveTrianglesAsASY
  kml3d.Rd: Partition-class, plot,ClusterLongData, ParKml-class,
    ordered,ListPartition, choice
  parKml3d.Rd: ParKml-class, imputation, restoreRealData, kml
  plot.Rd: Partition-class, ParLongData-class, plotTraj, plotCriterion
  plot3d.Rd: Partition-class, ParLongData-class
  plot3dPdf.Rd: Partition-class, ClusterLongData-class,
    saveTrianglesAsASY, makeLatexFile
  plotMean3d.Rd: Partition-class, ParLongData-class
  plotTraj3d.Rd: Partition-class, ParLongData-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ClusterLongData-class.Rd: Partition-class, plotCriterion,
    LongData-class, ListPartition-class
  ParKml-class.Rd: restoreRealData
  choice.Rd: Partition-class
  getBestPostProba.Rd: Partition-class
  kml-package.Rd: Partition-class
  kml.Rd: Partition-class, ordered,ListPartition
  parKml.Rd: imputation, restoreRealData
  plot.Rd: Partition-class, ParLongData-class, plotCriterion
  plotMeans.Rd: Partition-class, ParLongData-class, ParWindows-class,
    plotCriterion
  plotTraj.Rd: Partition-class, ParLongData-class, ParWindows-class,
    plotCriterion
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  knit_bootstrap_md.Rd: knit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) knockoff.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knockoff.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MapPolygon.Rd:20: Lost braces
    20 |   \item{shape}{If the estimators in the function link[KnowBR]{KnowBPolygon} were calculated using an external shape file, it is necessary to indicate the file in this argument. It is not necessary to select any polygon within the file, just to load the whole shape file.}
       |                                                              ^
checkRd: (-1) SurveyQ.Rd:26: Lost braces
    26 |   \item{shape}{If the estimators in the function link[KnowBR]{KnowBPolygon} were calculated using an external shape file, it is necessary to indicate the file in this argument. It is not necessary to select any polygon within the file, just to load the whole shape file.}
       |                                                              ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) hsic.perm.Rd:36: Lost braces; missing escapes or markup?
    36 | Let x and y be two samples of length n. Gram matrices K and L are defined as: \eqn{K_{i,j} = \exp\frac{(x_i-x_j)^2}{\sigma^2}}{K_{i,j} =exp((x_i-x_j)^2/sig^2)} and \eqn{L_{i,j} = \exp\frac{(y_i-y_j)^2}{\sigma^2}}{L_{i,j} =exp((y_i-y_j)^2/sig^2)}. \eqn{H_{i,j} = \delta_{i,j} - \frac{1}{n}}{H_{i,j} = \delta_{i,j} - 1/n}. Let \eqn{A=HKH} and \eqn{B=HLH}, then \eqn{HSIC(x,y)=\frac{1}{n^2}Tr(AB)}{HSIC(x,y)=Tr(AB)/n^2}. Permutation test permutes y p times to get \eqn{y_{(p)}} and calculates HSIC(x,y_{(p)}). \eqn{pval = \frac{1(HSIC(x,y)>HSIC(x,y_{(p)}))}{p}}{(HSIC(x,y)>HSIC(x,y_{(p)}))/p}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dcov.gamma.Rd: dcov.test
  frml.additive.smooth.Rd: gam
  frml.full.smooth.Rd: gam
  kernelCItest.Rd: skeleton, pc
  kpc.Rd: pc, dcov.test, udag2pdag, pcAlgo
  regrVonPS.Rd: gam
  regrXonS.Rd: gam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) kpmt.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) compose.Rd:13: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) compose.Rd:14: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) EGIparallel.Rd:60: Lost braces; missing escapes or markup?
    60 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion.
       |                                    ^
checkRd: (-1) max_sur_parallel.Rd:29: Lost braces; missing escapes or markup?
    29 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion. 
       |                                    ^
checkRd: (-1) max_timse_parallel.Rd:30: Lost braces; missing escapes or markup?
    30 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion. 
       |                                    ^
checkRd: (-1) max_vorob_parallel.Rd:30: Lost braces; missing escapes or markup?
    30 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion.
       |                                    ^
checkRd: (-1) print_uncertainty_nd.Rd:72: Lost braces
    72 | Optional argument. When set to code{NULL} (default) the function performs the projections on plans spanned by each pair (i,j) of dimension. Otherwise, the argument is an array of size 2 corresponding to the dimensions spanning the (only) plan on which the projection is performed.
       |                                    ^
checkRd: (-1) Predict_kernel_Ridge_MM.Rd:45: Lost braces; missing escapes or markup?
    45 |   and alpha_train is the BLUP of alpha for the model, i.e. alpha_train=Cov(alpha,Y_train)*Var(Y_train)^{-1}*(Y_train - E[Y_train]) }
       |                                                                                                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) ks_test_stat.Rd:14: Lost braces
    14 | are valid. See /code{LcKS} for accepted functions.}
       |                     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_imputations.Rd: imputeTS, forecast
  kssa.Rd: imputeTS, forecast
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GenSyntheticLogistic.Rd:46: Lost braces; missing escapes or markup?
    46 | 3) Every coordinate yi of the outcome vector y exists in {-1, 1}^n is sampled 
       |                                                          ^
checkRd: (-1) L0Learn-package.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:25: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) CreateDataSet.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateDataSet.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateDataSet.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindElement.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindElement.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindNbrClusters.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindNbrClusters.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindStructure.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindStructure.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) l1_spectralclustering.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) l1_spectralclustering.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) l1_spectralclustering.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) l1_spectralclustering.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) reconcile.Rd:26: Lost braces
    26 | refer to as the sQuote{comm} data.frame.  The other data.frame contains all the
       |                       ^
checkRd: (-1) ln_quantile_value.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_stopwords.Rd: stopwords, data_stopwords_misc
  identify_language.Rd: cld2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lacm.Rd: gauss.quad
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  contagdiscstate.Rd: Hest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bounding_box.Rd: data.table
  voxelize.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) laf_open.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{model}{a {data model}, such as one returned by \link{read_dm} or
       |                ^
checkRd: (-1) conn.Rd:300: Lost braces
   300 | Soranno et al. (2017) \doi{10.1093/gigascience/gix101}{Gigascience 6:12}
       |                                                       ^
checkRd: (-1) lakes_limno.Rd:36: Lost braces
    36 | Soranno et al. (2017) \doi{10.1093/gigascience/gix101}{Gigascience 6:12}
       |                                                       ^
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  load.all.data.Rd: load.ts
  load.meta.Rd: load.ts
  metab.bayesian.Rd: ts.meta.depths
  metab.bookkeep.Rd: ts.meta.depths
  metab.kalman.Rd: ts.meta.depths
  metab.mle.Rd: ts.meta.depths
  metab.ols.Rd: ts.meta.depths
  o2.at.sat.Rd: water.density
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) lambda.r-package.Rd:71-74: Lost braces
    71 | x \%g\% y \%:=\% {
       |                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bootstrap.Rd: boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
checkRd: (-1) GenerateData.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:41-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) landmix.estimator.Rd:59-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) landmix.estimator.Rd:67-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DOS.Rd:34: Lost braces; missing escapes or markup?
    34 |         Band-specific sensor $G_{rescale}$ (gain). Require either gain and offset or Grescale and Brescale to convert DN to radiance.
       |                                 ^
checkRd: (-1) DOS.Rd:37: Lost braces; missing escapes or markup?
    37 |         Band-specific sensor $B_{rescale}$ (bias). Require either gain and offset or Grescale and Brescale to convert DN to radiance.
       |                                 ^
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  xylowess.fnc.Rd: xyplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) LML.Rd:43: Lost braces
    43 |     is specified only with the \code{GD}, code{HME}, or \code{NSIS}
       |                                               ^
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
checkRd: (-1) MISS.Rd:106: Lost braces
   106 |   code{Fit$Imp}. In the presence of numerous missing values, say more
       |       ^
checkRd: (-1) Matrices.Rd:316: Lost braces
   316 |   Gauss-Hermite quadrature rules. A grid of order eqn{K} provides an
       |                                                      ^
checkRd: (-1) PMC.Rd:214: Lost braces
   214 |   item{nu}{This is the degrees of freedom parameter \eqn{\nu}{nu} for
       |       ^
checkRd: (-1) PMC.Rd:214-215: Lost braces
   214 |   item{nu}{This is the degrees of freedom parameter \eqn{\nu}{nu} for
       |           ^
checkRd: (-1) caterpillar.plot.Rd:15: Lost braces
    15 |     code{demonoid.hpc}, \code{iterquad}, \code{laplace}, \code{pmc},
       |         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tree_var.Rd: rpart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  draw.lar.Rd: treemap
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  latentcor.Rd: nearPD
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ESEM.Rd: lavaan
  add_population_error.Rd: bifactor
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Intercept-ergmTerm-49126971.Rd: edges-ergmTerm, ergm, ergmTerm
  bilinear-ergmTerm-3e739bd7.Rd: ergm, ergmTerm
  ergmm.Rd: ergmTerm, ergm-package, network
  ergmm.prior.Rd: ergmTerm
  euclidean-ergmTerm-6ab46c25.Rd: ergm, ergmTerm
  euclidean2-ergmTerm-939e9c32.Rd: ergm, ergmTerm
  latentcov-ergmTerm-fba43306.Rd: ergm, ergmTerm
  latentnet-package.Rd: ergmTerm
  loopcov-ergmTerm-bbc2e00a.Rd: ergm, ergmTerm
  loopfactor-ergmTerm-19d02eff.Rd: ergm, ergmTerm
  loops-ergmTerm-968722e8.Rd: ergm, ergmTerm
  receivercov-ergmTerm-ea158ece.Rd: nodeicov-ergmTerm,
    nodeifactor-ergmTerm, nodecov-ergmTerm, nodefactor-ergmTerm, ergm,
    ergmTerm
  rreceiver-ergmTerm-abdcadad.Rd: ergm, ergmTerm
  rsender-ergmTerm-b342610b.Rd: ergm, ergmTerm
  rsociality-ergmTerm-7ae668b9.Rd: ergm, ergmTerm
  sendercov-ergmTerm-a7b5c66c.Rd: nodeocov-ergmTerm,
    nodeofactor-ergmTerm, nodecov-ergmTerm, nodefactor-ergmTerm, ergm,
    ergmTerm
  socialitycov-ergmTerm-339101cf.Rd: nodecov-ergmTerm,
    nodefactor-ergmTerm, ergm, ergmTerm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  latrend.Rd: Verbose
  latrendBatch.Rd: Verbose
  latrendBoot.Rd: Verbose
  latrendCV.Rd: Verbose
  latrendRep.Rd: Verbose
  update.lcModel.Rd: Verbose
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  latte-optim.Rd: mp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.layer.Rd: panel.axis
  c.trellis.Rd: xyplot, print.trellis, update.trellis, trellis.object
  combineLimits.Rd: Lattice, xyplot
  custom.theme.Rd: simpleTheme, trellis.par.get, trellis.device
  dendrogramGrob.Rd: levelplot
  doubleYScale.Rd: simpleKey
  ecdfplot.Rd: panel.qqmath, panel.xyplot, qqmath
  ggplot2like.theme.Rd: simpleTheme, axis.default, trellis.par.set,
    lattice.options
  horizonplot.Rd: xyplot.ts, levelplot, xyplot, update.trellis,
    print.trellis, Lattice
  layer.Rd: trellis.currentLayout, trellis.par.set, panel.superpose,
    update.trellis
  mapplot.Rd: xyplot, Lattice
  marginal.plot.Rd: xyplot, panel.densityplot, panel.dotplot
  panel.2dsmoother.Rd: levelplot, panel.levelplot
  panel.3dmisc.Rd: cloud, panel.cloud
  panel.ellipse.Rd: panel.xyplot
  panel.key.Rd: simpleKey, draw.key, xyplot
  panel.lmlineq.Rd: panel.abline, panel.lmline, panel.text
  panel.qqmath.tails.Rd: qqmath, panel.qqmath, panel.xyplot
  panel.scaleArrow.Rd: panel.arrows, panel.text, panel.abline
  panel.segplot.Rd: levelplot, panel.segments, panel.arrows
  panel.smoother.Rd: panel.loess
  panel.tskernel.Rd: panel.lines, xyplot.ts
  panel.voronoi.Rd: levelplot, panel.levelplot, panel.xyplot
  panel.xblocks.Rd: xyplot.ts, panel.rect
  panel.xyarea.Rd: panel.polygon, panel.superpose, panel.qqmath,
    panel.xyplot
  panel.xyimage.Rd: xyplot, panel.xyplot, panel.abline
  resizePanels.Rd: Lattice, xyplot
  rootogram.Rd: xyplot
  scale.components.Rd: xscale.components.default
  segplot.Rd: levelplot, update.trellis, print.trellis, Lattice, xyplot
  theEconomist.theme.Rd: simpleTheme, panel.xyplot, xyplot
  tileplot.Rd: levelplot, xyplot
  useOuterStrips.Rd: xyplot, Lattice
  xyplot.stl.Rd: xyplot.ts, update.trellis, print.trellis, xyplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
checkRd: (-1) VignetteExamples.Rd:25: Lost braces; missing escapes or markup?
    25 |  See Section 4 in the {LatticeKrig Vignette} for the use of these data.
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LKDist.Rd: spind2spam, spind2full
  LKrigSAR.Rd: spind2full
  LatticeKrig.Rd: spind2spam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'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
File 'lazyeval/libs/x64/lazyeval.dll':
  Found non-API calls to R: 'PRENV', 'R_PromiseExpr'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
File 'lazy/libs/x64/lazy.dll':
  Found non-API call to R: 'STRING_PTR'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SFSQL.Rd: dbConnect
  SFSQLConnection-class.Rd: DBIConnection-class
  SFSQLDriver-class.Rd: dbConnect, DBIDriver-class, dbUnloadDriver
  SFSQLResult-class.Rd: dbSendQuery, dbSendStatement, DBIResult-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) univ.Rd:35: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:36: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:37: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:38: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:40: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:41: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:42: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:43: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:44: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:45: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:46: Lost braces in \enumerate; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lazy.footnote.Rd: latexTranslate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fitLCA.Rd: poLCA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  anova.lcc.Rd: anova.lme, nlme
  coef.lcc.Rd: nlme
  getVarCov.lcc.Rd: nlme
  lcc.Rd: nlme
  logLik.lcc.Rd: nlme
  print.anova.lcc.Rd: anova.lme, nlme
  ranef.lcc.Rd: nlme
  residuals.lcc.Rd: nlme
  vcov.lcc.Rd: nlme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gw.zi.Rd: zeroinfl
  gw.zi.bw.Rd: zeroinfl
  gw.zi.cv.Rd: zeroinfl
  gw.zi.light.Rd: zeroinfl
  gw.zi.mc.test.Rd: zeroinfl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Plot_Biplot.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.Treee.Rd: visNetwork
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) TS_diagnostics_plot.Rd:19: Lost braces
    19 | \item{interactive}{\code{logical} input, should be code{TRUE} unless
       |                                                        ^
checkRd: (-1) plot.TS_fit.Rd:29: Lost braces
    29 | \item{interactive}{\code{logical} input, should be code{TRUE} unless
       |                                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FindTopicsNumber.Rd: LDAcontrol-class
  Griffiths2004.Rd: LDAcontrol-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  layer.Rd: R6Class
  leabRa.Rd: R6Class
  network.Rd: R6Class
  unit.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addFeatures.Rd: addCircleMarkers, addPolylines, addPolygons
  addRasterRGB.Rd: plotRGB, addRasterImage
  addStarsImage.Rd: addRasterImage
  garnishMap.Rd: addLayersControl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) dynamicMapLayerOptions.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{layerDefs}{A string representing a query to run against the service before the image is rendered. This can be a string like "3:STATE_NAME="Kansas"" or an object mapping different queries to specific layers {3:"STATE_NAME="Kansas"", 2:"POP2007>25000"}.}
       |                                                                                                                                                                                                                     ^
checkRd: (-1) featureLayerOptions.Rd:35: Lost braces; missing escapes or markup?
    35 | Can be an object like {start:"startTime", end:"endTime"} or a string like "created".}
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addEsriFeatureLayer.Rd: addTiles, labelOptions, popupOptions
  addEsriHeatmapFeatureLayer.Rd: addTiles
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addTangram.Rd: clearGroup, addLayersControl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  heatmap.Rd: clearGroup, addLayersControl, colorNumeric
  omnivore.Rd: addTiles, labelOptions, popupOptions
  webglheatmap.Rd: clearGroup, addLayersControl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addRasterImage.Rd: projectRaster
  gadmCHE.Rd: getData
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lp_book_info.Rd: GET
  lp_coupons.Rd: GET
  lp_download.Rd: GET
  lp_get_wrapper.Rd: GET
  lp_job_status.Rd: GET
  lp_links.Rd: GET
  lp_preview.Rd: GET
  lp_publish.Rd: GET
  lp_sales.Rd: GET
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) clusterDistance.Rd:28-29: Lost braces
    28 | \code{approach} indicates the algorithm used to get the value. \code{distance} indicates the distance used to get the value. Possible values: {\code{'MAX'},
       |                                                                                                                                               ^
checkRd: (-1) clusterDistance.details.Rd:28-29: Lost braces
    28 | \code{approach} indicates the algorithm used to get the value. \code{distance} indicates the distance used to get the value. Possible values: {\code{'MAX'},
       |                                                                                                                                               ^
checkRd: (-1) clusterDistanceByApproach.Rd:24-25: Lost braces
    24 | \code{approach} indicates the algorithm used to get the value. Possible values: {\code{'MAX'},
       |                                                                                 ^
checkRd: (-1) clusterDistanceByApproach.details.Rd:24-25: Lost braces
    24 | \code{approach} indicates the algorithm used to get the value. Possible values: {\code{'MAX'},
       |                                                                                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) S2mu.Rd:18: Lost braces; missing escapes or markup?
    18 | \code{S2mu} computes a estimation of the variance, given a sample {x} with known population mean (denoted by \code{mu}).
       |                                                                   ^
checkRd: (-1) sample.quantile.Rd:20: Lost braces; missing escapes or markup?
    20 | \code{sample.quantile} computes a estimation of different quantiles, given a sample {x}, using order statistics.
       |                                                                                     ^
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.4Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lemna.Rd: deSolve
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  brackets.Rd: theme
  coord_capped.Rd: coord_cartesian, coord_flip
  coord_flex.Rd: absoluteGrob
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following HTML validation problems:
annotate_axis.html:91:1 (annotate_axis.Rd:54): Warning: trimming empty <h3>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   4.0Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lessSEM.Rd: Stat
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lets.presab.Rd: terra, sf
  lets.presab.grid.Rd: terra, sf
  lets.shFilter.Rd: terra, sf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) hash_sentiment_slangsd.Rd:28-37: Lost braces
    28 | article{DBLP:journals/corr/Wu-etal16,
       |        ^
checkRd: (-1) hash_sentiment_slangsd.Rd:29: Lost braces; missing escapes or markup?
    29 |   author    = {Liang Wu and Fred Morstatter and Huan Liu},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:30-31: Lost braces
    30 |   title     = {SlangSD: Building and Using a Sentiment Dictionary of Slang 
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:32: Lost braces; missing escapes or markup?
    32 |   journal   = {CoRR},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:33: Lost braces; missing escapes or markup?
    33 |   volume    = {abs/1608.05129},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:34: Lost braces; missing escapes or markup?
    34 |   year      = {2016},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:35: Lost braces; missing escapes or markup?
    35 |   url       = {http://arxiv.org/abs/1608.05129},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:36: Lost braces; missing escapes or markup?
    36 |   timestamp = {Wed, 17 Aug 2016 23:32:57 GMT}
       |               ^
checkRd: (-1) sw_python.Rd:32: Lost braces; missing escapes or markup?
    32 | * Neither the name of the {organization} nor the names of its
       |                           ^
File 'lfe/libs/x64/lfe.dll':
  Found non-API calls to R: 'NAMED', 'SET_NAMED'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Package suggested but not available for checking: 'doMC'
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
checkRd: (-1) flowunit.Rd:30: Lost braces; missing escapes or markup?
    30 | Usually flow units are of dimension $L^3 T^{-1}$. Currently a length $l$ can be on of \code{c("metre", "cm", "centimetre" "litre")}, whereas time $T$ can be one in \code{c("days", "hours", "mins", "secs")}, possibly abbreviated. The numerator of the fraction (everything before the literal \code{"/"}) is interpreted as the length (superscripts like \code{"^3"} are discarded), the denominator as time. E.g. valid units would be \code{"cm^3/s"}, \code{"m^3/day"} or \code{"litre/sec"}.
       |                                            ^
checkRd: (-1) seasindex.Rd:30: Lost braces
    30 | Laaha, G. and Bl{\"o}schl, G. (2006), Seasonality indices for regionalizing
       |                 ^
checkRd: (-1) seasindex.Rd:34: Lost braces
    34 | Mitteilungen, Inst. f{\"u}r Wasserbau u. Ingenieurhydrologie,
       |                      ^
checkRd: (-1) seasratio.Rd:31: Lost braces
    31 | Laaha, G. and Bl{\"o}schl, G. (2006), Seasonality indices for regionalizing low flows. Hydrol. Process., 20
       |                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  apply.seasonal.Rd: apply.daily, apply.monthly, apply.yearly
  as.xts.lfobj.Rd: as.xts
  cdf_ev.Rd: lmom
  fill_na.Rd: na.approx
  plot.deficit.Rd: plot.xts, dygraph
  rfa.Rd: regfit, lmom-package
  rfaplot.Rd: lmrd, lmom-package
  sbplot.Rd: barchart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coef.lgarch.Rd: zoo
  coef.mlgarch.Rd: zoo
  lgarch-package.Rd: zoo
  lgarchSim.Rd: zoo
  mlgarchSim.Rd: zoo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  density.stppp.Rd: density.ppp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
checkRd: (-1) prior_to_num.Rd:13: Lost braces; missing escapes or markup?
    13 |   {'uniform', 'normal', 'student-t', 'gamma', 'inv-gamma', 'log-normal'}
       |   ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rsyslog'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AppenderDbi.Rd: LogEvent, AppenderBuffer
  AppenderDigest.Rd: Layout, LogEvent, LayoutFormat, LayoutGlue
  AppenderDt.Rd: AppenderBuffer, LogEvent
  AppenderElasticSearch.Rd: AppenderBuffer
  AppenderGmail.Rd: AppenderBuffer, LayoutFormat, LayoutGlue
  AppenderPushbullet.Rd: AppenderBuffer, LayoutFormat, LayoutGlue
  AppenderSendmail.Rd: AppenderBuffer, LayoutFormat, LayoutGlue
  AppenderSyslog.Rd: log_levels, LayoutFormat, LayoutJson
  LayoutDbi.Rd: as.data.table.LogEvent
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) dij.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{i}{A positive integer, which stands for the i^{th} row of \code{X}.}
       |                                                     ^
checkRd: (-1) dij.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{j}{A positive integer, which stands for the j^{th} row of \code{X}. Both \code{i} and \code{j} should be in [1,nrow(X)] and they should not be equal to each other.}
       |                                                     ^
checkRd: (-1) exchange.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{j}{A positive integer, which stands for the j^{th} column (or row) of \code{X}, and it should be within [1,ncol(X)] (or [1,nrow(X)]).}
       |                                                     ^
checkRd: (-1) isingdata.Rd:14: Lost braces; missing escapes or markup?
    14 |     \item{X}{a 5000-by-100 matrix, each entry is in {-1,1}.}
       |                                                     ^
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  raster2Cimg.Rd: as.cimg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    doc       1.0Mb
    extdata   1.1Mb
    libs      1.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  InsuranceContract.ParameterDefaults.Rd: mortalityTable
  makeContractGridDimname.Rd: mortalityTable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Person.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hmd.DA.Rd: MclustDA, Mclust
  hmd.DA.mx.Rd: MclustDA, Mclust
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) lx_list_lights.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:27: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Lightning.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) likelihood_calculation.Rd:24: Lost braces
    24 | For eqn{i = 1\dots N} independent observations in a vector \var{X}, with individual observations \eqn{x_i}{xi}, and a set of parameter values \eqn{\theta}:
       |        ^
checkRd: (-1) simulated_annealing_algorithm.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:27: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.likert.Rd: theme
  plot.likert.gap.Rd: theme
  print.xlikert.Rd: print.xtable
  xtable.likert.Rd: xtable, print.xtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  morphs.Rd: tourr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  map.feature.Rd: bandwidth.nrd, colorNumeric
  polygon.points_kde.Rd: bandwidth.nrd
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gvec2sf.Rd: sf
  manuallyBuild.Rd: roxygenize
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getLinkCommunities.Rd: igraph
  getOCG.clusters.Rd: igraph
  linkcomm-package.Rd: igraph, RColorBrewer
  meta.communities.Rd: igraph
  newLinkCommsAt.Rd: igraph
  plotLinkCommGraph.Rd: igraph, igraph.plotting
  plotOCGraph.Rd: igraph, igraph.plotting
  read.OCG.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fxInteractive.Rd: gam, lme
  fxInteractive.glm.Rd: gam, print.xtable, xtable
  fxInteractive.lm.Rd: print.xtable, xtable
  fxInteractive.lme.Rd: lme, predict.lme, print.xtable, xtable
  wrapRpSlider.Rd: rp.slider
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  VARselect.Rd: lm.ridge
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ld_build_html_site.Rd:41: Lost braces
    41 | directory specified by `rmd_dir`. Note that this is an {{rmarkdown}}
       |                                                        ^
checkRd: (-1) ld_create_doc.Rd:29: Lost braces
    29 | directory specified by `rmd_dir`. Note that this is an {{rmarkdown}}
       |                                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'literanger/libs/x64/literanger.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) lit.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lit.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lit.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lit_plink.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lit_plink.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lit_plink.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gamut_plink.Rd: genio
  lit_plink.Rd: genio
  marginal_plink.Rd: genio
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) is_natural_number.Rd:17: Lost braces; missing escapes or markup?
    17 | Test for natural numbers according to ISO 80000-2, that is the set  {0, 1, 2, ...}
       |                                                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  list_duplicates.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) vcov.liu.Rd:20: Lost braces
    20 | A list of matrix of estimated covariances in the linear Liu regression model for scalar or vector biasing parameter \code{d}{d} is produced. Each list element has row and column names corresponding to the parameter names given by the \code{coef(mod)}. List items are named correspond to values of biasing parameter \eqn{d}{d}.}
       |                                                                                                                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kNN.Rd: knn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  xtable.lm.beta.Rd: xtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lm.br_internal.Rd: C++Object-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs       1.3Mb
    testdata   1.3Mb
File 'lme4/libs/x64/lme4.dll':
  Found non-API call to R: 'SET_TYPEOF'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) relLik.Rd:16: Lost braces
    16 | \item{AIC(x), BIC(x) }{The \code{AIC} or ]code{BIC} value of the first model object.}
       |                                               ^
checkRd: (-1) relLik.Rd:17: Lost braces
    17 | \item{AIC(y), BIC(y) }{The \code{AIC} or ]code{BIC} value of the second model object.}
       |                                               ^
checkRd: (-1) bootstrap_pvals.Rd:78: Lost braces; missing escapes or markup?
    78 | $(n_{extreme} + 1) / (B + 1)$.
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  approx.Z.Rd: nlme
  smSplineEx1.Rd: lme
  smspline.Rd: predict.lme, nlme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fithd.Rd: nlme, lme, gls, gnls
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R              1.4Mb
    doc-overview   2.2Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cauchypoly.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) normpoly.Rd:38: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) normpoly.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) lmomPi-Package.Rd:9: Lost braces
     9 | {\code{\link{cdf}}}{: generic distribution function;  }  
       |                    ^
checkRd: (-1) lmomPi-Package.Rd:10: Lost braces
    10 | {\code{\link{qua}}}{: generic quantile function;  } 
       |                    ^
checkRd: (-1) lmomPi-Package.Rd:11: Lost braces
    11 | {\code{\link{pel}}}{: fitting of probability distribution function through L-moments. }
       |                    ^
checkRd: (-1) lmomPi-Package.Rd:27: Lost braces; missing escapes or markup?
    27 | The function  \code{\link{spi.cdf}()} is compared against \code{SPEI::spi()} in SPEI package (\url{https://cran.r-project.org/package=SPEI}). The differences in SPI extimation have order of magnitude averagely about 10^{-8},  due to  the different fitting methods implemented in the two packages. 
       |                                                                                                                                                                                                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cdf.Rd: cdfexp, cdfgam, cdfgev, cdfglo, cdfgpa, cdfgno, cdfgum,
    cdfkap, cdfln3, cdfnor, cdfpe3, cdfwak, cdfwei
  pel.Rd: pel..., samlmu, pelexp, pelgam, pelgev, pelglo, pelgpa,
    pelgno, pelgum, pelkap, pelln3, pelnor, pelpe3, pelwak, pelwei
  qua.Rd: quaexp, quagam, quagev, quaglo, quagpa, quagno, quagum,
    quakap, qualn3, quanor, quape3, quawak, quawei
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) vcov.Rd:20: Lost braces
    20 | A list of matrix of estimated covariances in the linear ridge regression model for scalar or vector biasing parameter \code{K}{K} is produced. Each list element has row and column names corresponding to the parameter names given by the \code{coef(mod)}. List items are named correspond to values of biasing parameter \eqn{K}{K}.}
       |                                                                                                                               ^
Specified C++11: please drop specification unless essential
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Author
    Maintainer
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  1.1.loaPlot.Rd: lattice, levelplot, xyplot
  1.2.loaMapPlot.Rd: RColorBrewer, xyplot, GetMap, openmap,
    coordinates, proj4string, spTransform, lattice, panel.xyplot,
    panel.levelplot
  1.3.trianglePlot.Rd: xyplot, lattice
  1.4.stackPlot.Rd: xyplot, panel.polygon, lattice
  1.5.loaBarPlot.Rd: barchart, lattice
  2.1.specialist.panels.Rd: lattice, levelplot, xyplot, vis.gam,
    panel.contourplot, lrect
  2.2.specialist.panels.Rd: xyplot, lattice
  2.3.specialist.panels.Rd: xyplot, lattice
  2.4.specialist.panels.Rd: xyplot, lattice
  4.1.panel.pal.Rd: lattice, xyplot
  4.2.plot.structure.handlers.Rd: lattice, levelplot
  4.3.lims.and.scales.handlers.Rd: xyplot, lattice
  4.4.cond.handers.Rd: lattice, xyplot, panel.xyplot, panel.levelplot
  4.5.plot.argument.handlers.Rd: lattice, levelplot, RColorBrewer,
    xyplot
  4.6.key.handlers.Rd: lattice, xyplot
  4.7.other.panel.functions.Rd: lattice, xyplot
  4.8.list.handlers.Rd: lattice, xyplot
  4.9.loa.shapes.Rd: lrect, lattice
  5.1.plot.interactives.Rd: trellis.focus, lpoints, XY2LatLon, lattice
  loa-package.Rd: lattice
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
File 'lobstr/libs/x64/lobstr.dll':
  Found non-API calls to R: 'FRAME', 'HASHTAB', 'NAMED', 'PRCODE',
    'PRENV', 'PRVALUE', 'Rf_findVarInFrame3', 'SETLENGTH',
    'SET_GROWABLE_BIT', 'SET_TRUELENGTH', 'TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Specified C++11: please drop specification unless essential
Found the following HTML validation problems:
UPSLTDdist.html:54:1 (UPSLTDdist.Rd:17): Warning: trimming empty <dt>
plot.LocalControlCR.html:63:1 (plot.LocalControlCR.Rd:29): Warning: trimming empty <dt>
plot.LocalControlCS.html:59:1 (plot.LocalControlCS.Rd:24): Warning: trimming empty <dt>
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) mte_tilde_at.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mte_tilde_at.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mte_tilde_at.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mte_tilde_at.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mte_tilde_at.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) Rvarlacf.Rd:104: Lost braces
   104 |         eqn{(2s+1)^{-2}} (this was the default in versions prior to
       |            ^
checkRd: (-1) Rvarlacf.Rd:104: Lost braces; missing escapes or markup?
   104 |         eqn{(2s+1)^{-2}} (this was the default in versions prior to
       |                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EstBetaCov.Rd: PsiJ
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) FootballBrain.Rd:15: Lost braces; missing escapes or markup?
    15 |     { } \tab {or \code{FBConcuss}=football player with concussion history} \cr
       |     ^
checkRd: (-1) HappyPlanetIndex.Rd:14: Lost braces; missing escapes or markup?
    14 |     { } \tab {\code{5}=South Asia, \code{6}=East Asia, \code{7}=former Communist countries}\cr
       |     ^
checkRd: (-1) RockandRoll2012.Rd:17: Lost braces; missing escapes or markup?
    17 |     { } \tab {\code{Lifetime Achievement}, \code{Sideman}} \cr
       |     ^
checkRd: (-1) RockandRoll2015.Rd:17: Lost braces; missing escapes or markup?
    17 |     { } \tab {\code{Lifetime Achievement}, \code{Sideman}} \cr
       |     ^
checkRd: (-1) StudentSurvey.Rd:12: Lost braces; missing escapes or markup?
    12 |     \item{\code{Sex}}{code {F}=female or \code{M}=male}
       |                            ^
checkRd: (-1) SynchronizedMovement.Rd:16: Lost braces; missing escapes or markup?
    16 |     { } \tab {for High/Low Synchronization + High/Low Exertion}\cr
       |     ^
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PRDenEstC.Rd: bkde, dpik
  locpol.Rd: locpoly
  locpolSmoothers.Rd: locpoly
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'rsyslog'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  logbin-package.Rd: glm2-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'rsyslog'
checkRd: (-1) analysis.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) analysis.Rd:63-64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) analysis.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) analysis.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) analysis.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  logistf-package.Rd: mice
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) logdensity.Rd:33: Lost braces; missing escapes or markup?
    33 | The function \code{logdensity} computes kernel density estimates (KDE) of strictly positive distributions by performing the KDE in the log domain and then transforming the result back again. The syntax and function structure is largely borrowed from the function \code{density} in package {stats}.
       |                                                                                                                                                                                                                                                                                                  ^
checkRd: (-1) logdensity_fft.Rd:33: Lost braces; missing escapes or markup?
    33 | The function \code{logdensity_fft} computes kernel density estimates (KDE) of strictly positive distributions by performing the KDE via fast fourier transform utilizing the \code{fft} function. The syntax and function structure is largely borrowed from the function \code{density} in package {stats}.
       |                                                                                                                                                                                                                                                                                                     ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  HMSkew-nonlin.Rd: gnm
  RCTrans-nonlin.Rd: gnm
  YRCSkew-nonlin.Rd: gnm
  anoas.Rd: gnm
  assoc.Rd: gnm
  hmskew.Rd: gnm
  hmskewL.Rd: gnm
  rc.Rd: gnm
  rcL.Rd: gnm
  rcL.trans.Rd: gnm
  svyassocmod.Rd: gnm
  unidiff.Rd: gnm, checkEstimable, qvcalc
  yrcskew.Rd: gnm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  inlineLologPlugin.Rd: cppFunction, sourceCpp
  plot.Rcpp_DirectedNet.Rd: plot.network
  plot.Rcpp_UndirectedNet.Rd: plot.network
  plot.lologGmm.Rd: geom_histogram
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'lolog/libs/x64/lolog.dll':
  Found non-API call to R: 'SET_TYPEOF'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  partition.X.Rd: partitions
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SAheart.Rd:96: Lost braces
    96 |   J.E. Rossouw, J.P.D. Plessis, A.J.S. Benad\'{e}, P.C.J. Jordaan, 
       |                                               ^
checkRd: (-1) SAheart.Rd:97: Lost braces
    97 |   J.P. Kotz\'{e}, P.L. Jooste, and J.J. Ferreira (1983)
       |              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  g_getLocations.Rd: l_getLocations
  g_getPlots.Rd: l_getPlots
  geom_imageGlyph-deprecated.Rd: geom_image_glyph, geom_polygon_glyph
  geom_pointrangeGlyph-deprecated.Rd: geom_pointrange
  geom_serialAxesGlyph-deprecated.Rd: geom_serialaxes_glyph
  geom_textGlyph-deprecated.Rd: geom_text
  ggSerialAxes-deprecated.Rd: coord_serialaxes
  interactivity.Rd: l_info_states
  l_ggplot.Rd: ggplot
  linking.Rd: l_getLinkedStates, l_setLinkedStates, l_configure
  scaleBox.Rd: l_scale3D
  selection.Rd: l_userOptions
  zoom.Rd: l_scaleto_plot, l_scaleto_layer, l_scaleto_world,
    l_scaleto_active, l_scaleto_selected
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) l_binCut.Rd:30: Lost braces
    30 | when 'code{labels = FALSE}, the default \code{active} is  \code{-1}; and when \code{labels} is a vector of length equal
       |           ^
checkRd: (-1) loon.shiny.Rd:93-102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loon.shiny.Rd:95-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loon.shiny.Rd:97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loon.shiny.Rd:98-100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loon.shiny.Rd:103-108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loon.shiny.Rd:105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loon.shiny.Rd:106: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  loon.shiny.Rd: ggplot2loon, grid.arrange, shinyApp, runApp
  shiny.loon-deprecated.Rd: ggplot2loon, grid.arrange, shinyApp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  l_tour.Rd: grand_tour, dependence_tour, frozen_tour, guided_tour,
    planned_tour
  tour_pairs.Rd: l_pairs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  extract.Rd: mirt
  lordif.Rd: mirt, lrm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'scio'
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) qut.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{q}{A number between \code{0} and \code{1}. The quantile of the distribution of $lambda_{QUT}$ to take.}
       |                                                                                              ^
checkRd: (-1) qut.Rd:25: Lost braces; missing escapes or markup?
    25 | the value of $lambda_{QUT}$ to use in LoRI.
       |                      ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lpacf.Epan.Rd: plot.lacf
  lpacf.Rd: plot.lacf
  summary.lpacf.Rd: print.lacf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.lpcde.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lpdensity.plot.Rd: ggplot2
  plot.lpdensity.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) lp_nl.Rd:70: Lost braces; missing escapes or markup?
    70 | Regime 1 = (1-\eqn{F(z_{t-1})})*y_{(t-p)}, \cr
       |                                   ^
checkRd: (-1) lp_nl.Rd:71: Lost braces; missing escapes or markup?
    71 | Regime 2 = \eqn{F(z_{t-1})}*y_{(t-p)}.}
       |                               ^
checkRd: (-1) lp_nl.Rd:128: Lost braces; missing escapes or markup?
   128 | \item{fz}{A vector containing the values of the transition function F(z_{t-1}).}
       |                                                                         ^
checkRd: (-1) lp_nl_iv.Rd:84: Lost braces; missing escapes or markup?
    84 | Regime 1 = (1-\eqn{F(z_{t-1})})*y_{(t-p)}, \cr
       |                                   ^
checkRd: (-1) lp_nl_iv.Rd:85: Lost braces; missing escapes or markup?
    85 | Regime 2 = \eqn{F(z_{t-1})}*y_{(t-p)}.}
       |                               ^
checkRd: (-1) lp_nl_iv.Rd:129: Lost braces; missing escapes or markup?
   129 | \item{fz}{A vector, containing the values of the transition function F(z_{t-1}).}
       |                                                                          ^
checkRd: (-1) lp_nl_panel.Rd:103: Lost braces; missing escapes or markup?
   103 | Regime 1 = (1-\eqn{F(z_{t-1})})*y_{(t-p)}, \cr
       |                                   ^
checkRd: (-1) lp_nl_panel.Rd:104: Lost braces; missing escapes or markup?
   104 | Regime 2 = \eqn{F(z_{t-1})}*y_{(t-p)}.
       |                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ag_data.Rd: tibble
  interest_rules_var_data.Rd: tibble
  monetary_var_data.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lplb.Rd: coxph
  lple.Rd: coxph
  predict.lple.Rd: predict.coxph
  survfit.lple.Rd: survfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  surv.colors.Rd: Surv
  surv.scale.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AvBasis.wst2D.Rd: wst2D, wst2D.object
  imwr.imwd.rd: imwd.object, filter.select, imwr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'kerdiest'
checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) plot.int.lsbclust.Rd:112: Lost braces
   112 | \code{"rows"} and code{"columns"}.}
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cfsim.Rd: cl_agreement
  cfsim.T3Clusf.Rd: cl_agreement
  cfsim.akmeans.Rd: cl_agreement
  cfsim.lsbclust.Rd: cl_agreement
  int.lsbclust.Rd: cl_agreement
  lsbclust.Rd: cl_agreement
  plot.T3Clusf.Rd: theme
  plot.bicomp.Rd: grid.arrange, scale_fill_gradient2, theme
  plot.col.kmeans.Rd: theme
  plot.int.lsbclust.Rd: grid.arrange, geom_segment, theme
  plot.lsbclust.Rd: theme
  plot.ovl.kmeans.Rd: theme
  plot.row.kmeans.Rd: theme
  plot.step.lsbclust.Rd: grid.arrange, theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  read.doe.lsd.Rd: select.colnames.lsd, select.colattrs.lsd
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ref.grid-class.Rd: emmGrid-class
  ref.grid.Rd: ref_grid, recover_data, emm_basis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lsprobust.plot.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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 Rd file(s) with Rd \link{} targets missing package
anchors:
  mosaic_cull_for_do.Rd: do
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) spectral.density.Rd:55: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  diagnosys.Rd: corpus
  smooth_lss.Rd: locfit, lp
  textstat_context.Rd: textstat_keyness, tokens_select
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) k.Rd:27: Lost braces
    27 |  code{\link{ACSPlan-class}}, 
       |      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pbcsample.Rd: pbcseq, survival
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'LTRCforests/libs/x64/LTRCforests.dll':
  Found non-API call to R: 'STRING_PTR'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LTRCART.Rd: rpart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) DLSimulate.Rd:38: Lost braces
    38 | code{\link{arima.sim}} 
       |     ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  luca.Rd: coxph, clogit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Upload_to_db.Rd:43: Lost braces
    43 | lucas]{Connect_to_db}
       |       ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calc_MinDose.Rd: mle2, profile.mle2
  combine_De_Dr.Rd: mclust-package
  plot_NRt.Rd: rollmean
  read_XSYG2R.Rd: xml
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   1.0Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  evaluate.Rd: nn_module
  fit.luz_module_generator.Rd: nn_module
  luz_load_model_weights.Rd: torch_load
  predict.luz_module_fitted.Rd: nn_module
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) LVGP_fit.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_predict.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_predict.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) math_example.Rd:21: Lost braces
    21 | Data are sampled from the modified math function based on the first example in the paper listed in code{references}.
       |                                                                                                        ^
Specified C++11: please drop specification unless essential
checkRd: (-1) StEM_pcirt.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{response}{N by J matrix containing {0,1,...,M-1} responses, where N is the number of respondents and J is the number of items.}
       |                                          ^
Package suggested but not available for checking: 'depth'
checkRd: (-1) geom_lv.Rd:101: Lost braces; missing escapes or markup?
   101 | determines whether the width of the box for letter value LV(i) should be proportional to i (linear), proportional to $2^{-i}$ (height), or  whether
       |                                                                                                                         ^
checkRd: (-1) geom_lv.Rd:102: Lost braces; missing escapes or markup?
   102 | the area of the box should be proportional to $2^{-i}$ (area).}
       |                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_lv.Rd: stat_quantile
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gamtable1.Rd: gamObject
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is 30.6Mb
  sub-directories of 1Mb or more:
    gdal   3.0Mb
    libs  19.0Mb
    proj   8.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) xytb-class.Rd:26: Lost braces; missing escapes or markup?
    26 | v: \tab speed (m.s^{-1})\cr
       |                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  xytb-class.Rd: distVincentyEllipsoid
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  factor_poly.Rd: mp
  gb.Rd: mp, mpolyList
  ideal.Rd: mp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) examinee-class.Rd:61: Lost braces; missing escapes or markup?
    61 | \item{\code{routing_based_on}}{a vector containing the routing was based on \code{estimated_theta_by_phase} or {estimated_theta_by_test} at each module position.}
       |                                                                                                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  createModule.Rd: loadConstraints, loadItemPool, loadItemAttrib,
    loadStAttrib
  examinee-class.Rd: item_pool-class
  excludeAdministeredItems.Rd: constraints-class
  maat.Rd: config_Shadow-class
  module-class.Rd: constraints-class
  output_maat-class.Rd: config_Shadow-class
  simTheta.Rd: mvrnorm
  updateAssessmentLevelTheta.Rd: config_Shadow-class
  updateGrade.Rd: item_pool-class
  updateItemData.Rd: output_Shadow_all-class, item_pool-class
  updateThetaUsingCombined.Rd: config_Shadow-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) mable.dr.Rd:23: Lost braces
    23 | \item{x, y}{original two sample raw data, code{x}:"Control", \code{y}: "Case".}
       |                                               ^
checkRd: (-1) mable.dr.group.Rd:26: Lost braces
    26 | specified by \code{t}. code{n0}:"Control", \code{n1}: "Case".}
       |                            ^
checkRd: (-1) mable.reg.Rd:50: Lost braces
    50 | Wrapping all code{mable} fit of regression models in one function.
       |                  ^
checkRd: (-1) maple.dr.Rd:23: Lost braces
    23 | \item{x, y}{original two sample raw data, code{x}:"Control", \code{y}: "Case".}
       |                                               ^
checkRd: (-1) maple.dr.group.Rd:27: Lost braces
    27 | specified by \code{t}. code{n0}:"Control", \code{n1}: "Case".}
       |                            ^
Package suggested but not available for checking: 'rnaturalearthhires'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mediate_iv.Rd: el.test, BBoptim, spg
  mediate_zi.Rd: survreg, Surv, mgcv, s, summary.mediate, plot.mediate
  mediate_zi_vcoef.Rd: summary.mediate, plot.mediate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) mada-data.Rd:45: Lost braces
    45 | Kriston, L., H{\"o}elzel, L., Weiser, A., Berner, M., & Haerter, M. (2008).\dQuote{ Meta-analysis: Are 3
       |               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SummaryPts.Rd: rmvnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
checkRd: (-1) toolAggregate.Rd:49: Lost braces; missing escapes or markup?
    49 | If {rel} is missing \code{to} refers to the aggregation target dimension name.}
       |    ^
checkRd: (-1) toolGetMapping.Rd:18: Lost braces
    18 | and rda (which needs to have the data stored with the object name "data"!). Use code{\link{toolConvertMapping}}
       |                                                                                     ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'quitte'
Package suggested but not available for checking: 'doMC'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  magerr.Rd: draw.ellipse
  magproj.Rd: mapproject, deg2hms, deg2dms
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 65.6Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs  58.9Mb
'LazyData' is specified without a 'data' directory
File 'magrittr/libs/x64/magrittr.dll':
  Found non-API calls to R: 'Rf_findVarInFrame3', 'SET_ENCLOS',
    'SET_PRCODE', 'SET_PRENV', 'SET_PRVALUE'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  reportCovariates.Rd: wtd.var
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   1.3Mb
checkRd: (-1) RepLOptim.Rd:21: Lost braces; missing escapes or markup?
    21 |         \item{gr}{A function to return the gradient for the \dQuote{nlminb}, \dQuote{BFGS}, \dQuote{CG} and {L-BFGS-B} methods.  If it is \sQuote{NULL}, a finite-difference approximation will be used. For the \dQuote{SANN} method it specifies a function to generate a new candidate point.  If it is \sQuote{NULL} a default Gaussian Markov kernel is used.}
       |                                                                                                             ^
checkRd: (-1) Robda-methods.Rd:69: Lost braces
    69 | \seealso{\code{\link{lda}}, \code{\link{qda}}, \code{\link{snda}}, \code{\linkS4class{IData}}, \code{\linkS4class{RobEstControl}},code{\link{ConfMat}} }
       |                                                                                                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RobEstControl-class.Rd: CovControlMcd-class, CovControl-class
  fasttle-methods.Rd: rrcov.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) makeProject.Rd:34: Lost braces
    34 | email{noahsilverman@ucla.edu}
       |      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as_tbl_graph.malan_pedigreelist.Rd: tbl_graph
  get_nodes_edges.Rd: as_tbl_graph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MALDIrppa-package.Rd: MALDIquant
  addMetadata.Rd: AbstractMassObject-class
  alignPeaks.Rd: MassPeaks, MALDIquant, referencePeaks, binPeaks,
    warpMassPeaks
  countPeaks.Rd: MassPeaks
  detectOutliers.Rd: MassSpectrum, covMcd
  importSpectra.Rd: MassSpectrum
  peakPatterns.Rd: intensityMatrix, MassPeaks
  rawToPeaks.Rd: MassPeaks
  rawToSpectra.Rd: MassSpectrum
  redResolution.Rd: MassSpectrum-class
  screenSpectra.Rd: MassSpectrum, Qn
  snrPeaks.Rd: MassPeaks, detectPeaks
  spectra.Rd: MassSpectrum
  summaryPeaks.Rd: MassPeaks
  summarySpectra.Rd: MassSpectrum
  transfIntensity.Rd: MassSpectrum-class, transformIntensity
  wavSmoothing.Rd: MassSpectrum
  writeIntensity.Rd: intensityMatrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) create_terminal_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                              ^
checkRd: (-1) create_terminal_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                                                   ^
checkRd: (-1) full_repo_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                              ^
checkRd: (-1) full_repo_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                                                   ^
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
checkRd: (-1) manet.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MangroveTree.Rd:37: Lost braces
    37 |       An object of class \\code{\link[Mangrove]{MangrovePed}}
       |                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  manhattanly.Rd: plotly
  volcanoly.Rd: plotly
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mp_interpolate.Rd: na.approx
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) manipulateWidget.Rd:113-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manipulateWidget.Rd:118-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manipulateWidget.Rd:121-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manipulateWidget.Rd:124-127: Lost braces in \itemize; meant \describe ?
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.5Mb
checkRd: (-1) EEGwide.Rd:30-33: Lost braces
    30 |   if(requireNamespace("ggplot2")){ 
       |                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  check_path.Rd: lavaan
  index_of_mome.Rd: lavaan-class
  plot.cond_indirect_effects.Rd: ggplot2
  plot_effect_vs_w.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) shortestpath.Rd:19: Lost braces; missing escapes or markup?
    19 | \eqn{0} means there exists no path for node \eqn{i} and {j}.
       |                                                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GetGeneList.Rd: rentrez
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
Specified C++14: please drop specification unless essential
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   3.5Mb
    libs          3.0Mb
File 'mapdeck/libs/x64/mapdeck.dll':
  Found non-API call to R: 'SET_TYPEOF'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Bug Fixes
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  selectFeatures.Rd: geos_binary_pred
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  modgam.Rd: gam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DE.Rd: st_crs
  EU.Rd: st_crs
  FR.Rd: st_crs
  IT.Rd: st_crs
  UK.Rd: st_crs
  US.Rd: st_crs
  WR.Rd: st_crs
  loadCoordDE.Rd: st_crs
  loadCoordEU.Rd: st_crs
  loadCoordFR.Rd: st_crs
  loadCoordIT.Rd: st_crs
  loadCoordUK.Rd: st_crs
  loadCoordUS.Rd: st_crs
  loadCoordWR.Rd: st_crs
  mapping.options.Rd: tm_layout, tm_borders, tm_fill, tm_style
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mapStats.Rd: spplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clip.rpart.Rd: rpart, prune.rpart
  draw.clust.Rd: pltree
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mapView.Rd: levelplot, addControl, addLegend, addRasterImage,
    addCircles, addPolygons, addPolylines, addMapPane,
    highlightOptions, st_sf, brick, satellite, st_sfc, st_bbox,
    SpatialPixelsDataFrame, SpatialGridDataFrame,
    SpatialPointsDataFrame, SpatialPoints, SpatialPolygonsDataFrame,
    SpatialPolygons, SpatialLinesDataFrame, SpatialLines
  mapviewColors.Rd: level.colors
  mapviewOptions.Rd: addRasterImage, addLegend, addMapPane,
    rasterOptions
  mapviewOutput.Rd: shinyWidgetOutput
  viewExtent.Rd: popupTable, addControl, addRectangles
  viewRGB.Rd: plotRGB
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
checkRd: (-1) locate_shift.Rd:29: Lost braces
    29 | \code{\link{quickfit}}, code{\link{locator}}
       |                             ^
checkRd: (-1) marcher-package.Rd:14: Lost braces; missing escapes or markup?
    14 | 1. \code{\link{estimate_shift}} {Estimate a range shift process.}
       |                                 ^
checkRd: (-1) marcher-package.Rd:16: Lost braces; missing escapes or markup?
    16 | 2. \code{\link{simulate_shift}} {Simulate a range shift process.}
       |                                 ^
checkRd: (-1) marcher-package.Rd:18: Lost braces; missing escapes or markup?
    18 | 3. \code{\link{plot.shiftfit}} {Visualize a range shift process.}
       |                                ^
checkRd: (-1) marcher-package.Rd:20: Lost braces; missing escapes or markup?
    20 | 4. \code{\link{test_rangeshift}} {Test whether a range shift occurred.}
       |                                  ^
checkRd: (-1) marcher-package.Rd:22: Lost braces; missing escapes or markup?
    22 | 5. \code{\link{test_return}} {Test whether a migration was a return migration.}
       |                              ^
checkRd: (-1) marcher-package.Rd:24: Lost braces; missing escapes or markup?
    24 | 6. \code{\link{test_stopover}} {Test whether a stopover occurred during a migration.}
       |                                ^
checkRd: (-1) quickfit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickfit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MargCond.Rd: lmer, gee
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rsm.Rd: survreg.fit
  rsm.surv.Rd: survreg.fit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) marima.Rd:28: Lost braces; missing escapes or markup?
    28 | ( if(is.ts(DATA)) { DATA <- as.matrix(data.frame(DATA)) } and a message
       |                   ^
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) markdownInput.Rd:17: Lost braces
    17 | \item{inputId}{The code{input} slot that will be used to access the value.}
       |                        ^
checkRd: (-1) markdownInput.Rd:35: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) markdownInput.Rd:36: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) markdownInput.Rd:81-82: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) markdownInput.Rd:84-86: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) markdownInput.Rd:89-90: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) moduleMarkdownInput.Rd:64-65: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) moduleMarkdownInput.Rd:67-69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) moduleMarkdownInput.Rd:72-73: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs       1.3Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) markovchainFit.Rd:31: Lost braces; missing escapes or markup?
    31 | \item{stringchar}{It can be a {n x n} matrix or a character vector or a list}
       |                               ^
checkRd: (-1) markovchainFit.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{data}{It can be a character vector or a {n x n} matrix or a {n x n} data frame or a list}
       |                                               ^
checkRd: (-1) markovchainFit.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{data}{It can be a character vector or a {n x n} matrix or a {n x n} data frame or a list}
       |                                                                   ^
checkRd: (-1) markovchainFit.Rd:61: Lost braces; missing escapes or markup?
    61 | {k x k} where k is the number of states in the chain and the values
       | ^
GNU make is a SystemRequirements.
checkRd: (-1) Markovchart.Rd:154: Lost braces
   154 | If either \code{h} or \code{k} have length greater than 1, then the \code{G-value} (weighted average of average cost and cost standard deviation) is calculated for all given values without optimisation. The value of the function in this case is a data frame of class code{Markov_grid} with \code{length(h)*length(k)} number of rows and three columns for \code{h}, \code{k} and the \code{G-value}.
       |                                                                                                                                                                                                                                                                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  na_assignments.Rd: match_ext
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  autoplot.bathy.Rd: coord_map
  get.area.Rd: areaPolygon
  plotArea.Rd: areaPolygon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) marqLevAlg-package.Rd:14: Lost braces; missing escapes or markup?
    14 | (GH^{-1}G).
       |     ^
File 'marquee/libs/x64/marquee.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT',
    'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'marssTMB'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MARSSFisherI.Rd: fdHess, nlme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) focalCompare.Rd:14: Lost braces
    14 | \item{fun}{The function fun should take multiple numbers, and return a single number. For example mean, modal, min or max. It should also accept a na.rm argument (or ignore it, e.g. as one of the 'dots' arguments. For example, length will fail, but function(x, ...){na.omit(length(x))} works. (Specifications from `raster::focal`)}
       |                                                                                                                                                                                                                                                                          ^
checkRd: (-1) hr_levels.Rd:9-12: Lost braces
     9 | kernelBiweight <- function(x, mean = 0, sd = 1) {
       |                                                 ^
checkRd: (-1) hr_levels.Rd:33-36: Lost braces
    33 | kernelCosine <- function(x, mean = 0, sd = 1) {
       |                                               ^
checkRd: (-1) hr_levels.Rd:41-44: Lost braces
    41 | kernelEpanechnikov <- function(x, mean = 0, sd = 1) {
       |                                                     ^
checkRd: (-1) hr_levels.Rd:58-61: Lost braces
    58 | kernelOptCosine <- function(x, mean = 0, sd = 1) {
       |                                                  ^
checkRd: (-1) hr_levels.Rd:65-68: Lost braces
    65 | kernelRectangular <- function(x, mean = 0, sd = 1) {
       |                                                    ^
checkRd: (-1) hr_levels.Rd:72-75: Lost braces
    72 | kernelSquaredCosine <- function(x, mean = 0, sd = 1) {
       |                                                      ^
checkRd: (-1) hr_levels.Rd:79-82: Lost braces
    79 | kernelTriangular <- function(x, mean = 0, sd = 1) {
       |                                                   ^
checkRd: (-1) hr_levels.Rd:86-89: Lost braces
    86 | kernelTricube <- function(x, mean = 0, sd = 1) {
       |                                                ^
checkRd: (-1) hr_levels.Rd:93-96: Lost braces
    93 | kernelTriweight <- function(x, mean = 0, sd = 1) {
       |                                                  ^
checkRd: (-1) hr_levels.Rd:100-103: Lost braces
   100 | kernelUniform <- function(x, mean = 0, sd = 1) {
       |                                                ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_geneSets_from_msigdbr.Rd: msigdbr
  plot.mGST.Rd: visOptions, visNetwork
  save_as_xls.Rd: WriteXLS
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) CF2004.Rd:8: Lost braces; missing escapes or markup?
     8 |   \item{X2}{an optional second variable with same length as \code{X}, should the equation be multiple (see Details) {in mm}}
       |                                                                                                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tabMWRacc.Rd: flextable
  tabMWRcom.Rd: flextable
  tabMWRfre.Rd: flextable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
checkRd: (-1) Rand.index.Rd:22: Lost braces; missing escapes or markup?
    22 | The two vectors \code{x} and \code{y} must have equal length. Given a set \eqn{S} and two partitions \eqn{X} and \eqn{Y} of \eqn{S}, the Rand index is the proportion of pairs of elements in \eqn{S} (out of all pairs) that are either concordant in both \eqn{X} and \eqn{Y} (i.e., they belong to the same member of \eqn{X} and to the same member of \eqn{Y}) or discordant (i.e., not concordant) in both \eqn{X} and {Y}.  
       |                                                                                                                                                                                                                                                                                                                                                                                                                              ^
checkRd: (-1) predict.matchFeat.Rd:21: Lost braces
    21 | The function \code{predict.matchFeat} finds the best matching for new feature vectors relative to an existing set of cluster/class centers. If code{object} results from a call to \code{\link{match.gaussmix}}, the same function is used for prediction (with fixed mean vectors and covariance matrices). In other cases, the function \code{\link{match.template}} is used for prediction. 
       |                                                                                                                                                    ^
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   1.7Mb
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
checkRd: (-1) Match.Rd:90: Lost braces; missing escapes or markup?
    90 | expression in braces. For example, the condition "{[ab]*}" is equivalent
       |                                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kNearNeighbors.Rd: knn.dist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) MatrixCorrelation.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RV.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RV.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RV.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RV.Rd:67-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:64-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) r1.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) r1.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) r1.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) r1.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) r1.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Matrix_eQTL_main.Rd:31: Lost braces; missing escapes or markup?
    31 |     {genepos} in the call of \code{Matrix_eQTL_main} function.
       |     ^
checkRd: (-1) Matrix_eQTL_main.Rd:35: Lost braces; missing escapes or markup?
    35 |     the data frames \code{snpspos} and {genepos}.
       |                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lm.fit.sparse.Rd: dsparseMatrix-class, sparse.model.matrix
  model.Matrix.Rd: sparse.model.matrix
  modelMatrix-class.Rd: dgCMatrix-class, Matrix-class, dgeMatrix-class,
    sparse.model.matrix
  predModule-class.Rd: Cholesky-class, CHMfactor-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  loop.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  predict.mave.Rd: mars
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) MaxentVariableSelection-package.Rd:46: Lost braces; missing escapes or markup?
    46 | \tab Tyberghein L, Verbruggen H, Pauly K, Troupin C, Mineur F and {De Clerck}, O (2012)\cr
       |                                                                   ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  carw.Rd: raster
  maxlike-package.Rd: raster
  maxlike.Rd: raster-package, raster
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  activePar.Rd: nObs
  nObs.Rd: nParam
  nParam.Rd: nObs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fitDR.Rd: mledist, mmedist, constrOptim.nl, gofstat, plotdist,
    cdfcomp, bootdist, qmedist, mgedist, denscomp, qqcomp, ppcomp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  upsilon.Rd: lavaan, boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mhglm.Rd: glmer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) findDescendingTrans.Rd:29: Lost braces
    29 |    Foster, S.D., Hosack, G.R., J. Monk, Lawrence, E., Barrett, N.S., Williams, A. and Przeslawski, P. (2020) Spatially-Balanced Designs for Transect-Based Surveys. Methods in Ecology and Evolution. emph{11}: 95--105
       |                                                                                                                                                                                                           ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mcaSmoother.Rd: lmrob
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Family.Rd: Surv
  confint.Rd: levelplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) SIGMAS.Rd:17: Lost braces; missing escapes or markup?
    17 | Sigmahat =  (Y^{T} Y)/n;
       |                ^
checkRd: (-1) SIGMAS.Rd:18: Lost braces; missing escapes or markup?
    18 | Sigmahat_fit = (Y^{T}  P_fx  Y)/n;
       |                   ^
checkRd: (-1) matpower.Rd:17: Lost braces; missing escapes or markup?
    17 | The function computes M^{power} for a symmetric matrix M. }
       |                         ^
Found the following HTML validation problems:
compile_sbtests.html:31:1 (compile_sbtests.Rd:29): Warning: trimming empty <li>
dorepart.html:93:1 (dorepart.Rd:47): Warning: trimming empty <li>
dosequa.html:94:1 (dosequa.Rd:49): Warning: trimming empty <li>
checkRd: (-1) satisfaction.Rd:28: Lost braces
    28 | Della Valle E (2010) Della Valle E 2010 Analisi Multidimensionale dei Dati: la Qualit\'{a} del Lavoro nelle Cooperative Sociali. 
       |                                                                                        ^
checkRd: (-1) satisfaction.Rd:29: Lost braces
    29 | Unpublished thesis, Seconda Universit\'{a}  degli Studi di Napoli, Capua Italy.
       |                                        ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AuditorFitter.Rd: data.table
  CVLearnerAuditorFitter.Rd: data.table
  LearnerAuditorFitter.Rd: data.table
  MCBoost.Rd: data.table
  SubgroupAuditorFitter.Rd: data.table
  SubpopAuditorFitter.Rd: data.table
  mlr_pipeops_mcboost.Rd: R6Class, data.table, PipeOp, Learner
  ppl_mcboost.Rd: Graph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   1.4Mb
checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) MCbound.precalc1.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MclustMEM.Rd: Mclust, densityMclust
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  method_plot.Rd: hdi
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  caterplot.Rd: denstrip
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'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) ess.Rd:14: Lost braces
    14 | \code{g} should take a vector input only. Ifcode{g} is \code{NULL}, \code{g} is set to be identity, which is estimation
       |                                                 ^
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  spearmanTest.Rd: boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) eigp.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:41: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial version.
checkRd: (-1) mcvis.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mcvis.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mcvis.Rd:34: 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) pBED.Rd:34: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CDF_3dPlot.Rd: lattice
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  linkage.Rd: agnes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) get_mdgc.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_mdgc.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_mdgc.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_mdgc.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^
Package suggested but not available for checking: 'RGtk2'
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mdmr.Rd: davies
  mixed.mdmr.Rd: lmer, lme4, davies
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ramachandran.Rd: hist2d
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) mdp_example_forest.Rd:36: Lost braces; missing escapes or markup?
    36 | Let {1, ... S} be the states of the forest. the Sth state being the oldest.
       |     ^
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.pcmap3d.Rd: rgl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  findOptimalSmacofSym.rd: data.Normalization, dist.GDM, smacofSym
  optSmacofSymInterval.rd: data.Normalization, interval_normalization,
    dist.Symbolic, smacofSym
  optSmacofSym_mMDS.rd: data.Normalization, dist.GDM, smacofSym
  optSmacofSym_nMDS.rd: data.Normalization, dist.GDM, smacofSym
  rotation2dAnimation.rd: ani.options, im.convert, saveGIF, saveHTML,
    saveLatex, saveSWF
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Elections.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) 
       |                          ^
checkRd: (-1) Elections.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) 
       |                                                        ^
checkRd: (-1) Elections.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) 
       |                                                                     ^
checkRd: (-1) Violations.Rd:39-45: Lost braces
    39 | {
       | ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MLB_teams.Rd: tbl_df
  macros.Rd: x
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'cmdstanr'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  crossRings.Rd: dplR, corr.rwl.seg, ccf.series.rwl, spag.plot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  betaturn.Rd: microtable, trans_beta
  taxaturn.Rd: microtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) bhm.mcmc.Rd:37: Lost braces; missing escapes or markup?
    37 |   where \eqn{N_{ij}} denotes the number of times that the error profile \eqn{i} is cited on a report from hospital {j} and \eqn{y_{ij}} is the corresponding number of times that profile \eqn{i} in hospital \eqn{j} was reported with harm.
       |                                                                                                                    ^
checkRd: (-1) strings-internal.Rd:14: Lost braces
    14 | code{stringPlaceExact}: find location of string, using exact match
       |     ^
checkRd: (-1) strings-internal.Rd:17: Lost braces
    17 | code{stringPlaceFuzzy}: find location of string, using partial match
       |     ^
checkRd: (-1) strings-internal.Rd:19: Lost braces
    19 | code{stringPlace}: find location of string, generic
       |     ^
checkRd: (-1) strings-internal.Rd:21: Lost braces
    21 | code{checkFuzzy}: check for "close" string matches
       |     ^
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  neLht-methods.Rd: coef.glht
  neLht.Rd: coef.glht
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mediate.Rd: survreg, Surv, mgcv, s
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  generate_comorbidity_df.Rd: ddply
  melt_icd9list.Rd: ddply
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) MED.Rd:25: Lost braces
    25 | The vector of treatment assignments of length \eqn{n}. Must be coded as \eqn{\{0,1} {{0,1}}.
       |                                                                                     ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Xtab.Rd: sparseMatrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Mega2gdsfmt.Rd: gdsfmt
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  melt_delim.Rd: tibble
  melt_delim_chunked.Rd: tibble
  melt_fwf.Rd: tibble
  melt_table.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'meltr/libs/x64/meltr.dll':
  Found non-API calls to R: 'Rf_findVarInFrame3', 'SETLENGTH',
    'SET_GROWABLE_BIT', 'SET_TRUELENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) mgLandscape.Rd:79: Lost braces
    79 | A code{$summary} table giving the results of the variation partitioning.  The following table
       |       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mgLandscape.Rd: raster
  mgMap.Rd: ade4
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'memo/libs/x64/memo.dll':
  Found non-API call to R: 'PRCODE'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  memmodel.Rd: boot.ci, boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Mercator-class.Rd: Rtsne, som, silhouette, umap
  coloring.Rd: remap, Thresher
  threshLGF.Rd: Thresher
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bread.glmerMod.Rd: glmerMod-class
  bread.lmerMod.Rd: lmerMod-class
  estfun.glmerMod.Rd: glmerMod-class
  estfun.lmerMod.Rd: lmerMod-class
  llcont.glmerMod.Rd: glmerMod-class
  llcont.lmerMod.Rd: lmerMod-class
  vcov.glmerMod.Rd: glmerMod-class
  vcov.lmerMod.Rd: lmerMod-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  VarCorr.merModList.Rd: merMod-class
  modelFixedEff.Rd: tidy
  plotFEsim.Rd: merMod
  plotREsim.Rd: merMod
  ranef.merModList.Rd: merMod-class
  thetaExtract.Rd: merMod
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  QIC.Rd: ginv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
checkRd: (-1) CVLasoelacox.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:70-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:74-76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:77-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:82-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FEmrt.Rd: rpart, rpart.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as_phyloseq.Rd: ape
  heat_tree.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.3Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  misc-options.Rd: dat.moura2021
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) datagenerator.Rd:17: Lost braces; missing escapes or markup?
    17 | Returns data frame with \code{n*K} rows (if \code{n} is a scalar), or \code{sum(n)} rows (if \code{n} is a \code{K}-element vector). The data frame contains columns "y", "x1", \dots, "x_{p-1}" and "group" if \code{family="gaussian"}, \code{"binomial"} or \code{"poisson"}; or contains columns "time", "status", "x1", \dots, "x_{p-1}" and "group" if \code{family="cox"}.
       |                                                                                                                                                                                           ^
checkRd: (-1) datagenerator.Rd:17: Lost braces; missing escapes or markup?
    17 | Returns data frame with \code{n*K} rows (if \code{n} is a scalar), or \code{sum(n)} rows (if \code{n} is a \code{K}-element vector). The data frame contains columns "y", "x1", \dots, "x_{p-1}" and "group" if \code{family="gaussian"}, \code{"binomial"} or \code{"poisson"}; or contains columns "time", "status", "x1", \dots, "x_{p-1}" and "group" if \code{family="cox"}.
       |                                                                                                                                                                                                                                                                                                                                        ^
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) asympVar_LinReg.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gamma_EB.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gamma_EB.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gamma_EB.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data       3.0Mb
    examples  10.3Mb
checkRd: (-1) rland.graph.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  metamedian-defunct.Rd: qe.fit, print.qe.fit
  qe.Rd: qe.fit
  qe.study.level.Rd: qe.fit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  select_features.Rd: glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ge_stats.Rd: polar
  path_coeff.Rd: dplyr_tidy_select
  utils_as.Rd: dplyr_tidy_select
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  forest.metarep.Rd: forest.meta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) param.Rd:29: Lost braces
    29 | T. Strub, S. Giuliano, T. Ye, et al. (2011) Essential role of microphthalmia transcription factor for DNA replication, mitosis and genomic stability in melanoma. emph{Oncogene} \bold{30}:2319-32.
       |                                                                                                                                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  doiplot.Rd: metabias, funnel.meta
  forest.orbbound.Rd: forest.meta
  funnel.limitmeta.Rd: funnel.meta
  lfkindex.Rd: metabias, funnel.meta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  KODAMA.chem.sim.Rd: KODAMA.matrix, KODAMA.visualization
  chemical.dissimilarity.Rd: fp.sim.matrix, get.fingerprint
  clusters.detection.Rd: KODAMA.matrix, KODAMA.visualization
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getRaster.Rd: Extent, extent, getZ
  meteo-package.Rd: raster, zoo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   1.2Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fit.lasso.Rd: glmnet, cv.glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) cardiac.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) plvol.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) sbp.Rd:16: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pairs.Rd: Lattice, xyplot, densityplot
  trace.MCmcmc.Rd: Lattice
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.