checkRd: (-1) app_server.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{input, output, session}{Internal parameters for {shiny}.
       |                                                       ^
checkRd: (-1) plot.ehh.Rd:27: Lost braces
    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}} and \code{\link[graphics]{matplot}}). 
       |                                ^
checkRd: (-1) plot.ehhs.Rd:27: Lost braces
    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}}.
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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    26 | {Pd = sqrt(sum(p_j*(x_j-mean(x_p))/4.5)^2)}
       | ^
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    37 | The set of divisors is formed by the odd numbers, that is {1,3,..,2n+1}.
       |                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plconfint.Rd:30: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) plconfint.Rd:33: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) plot.inference.Rd:68-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.inference.Rd:71: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) termtable.Rd:49: Lost braces; missing escapes or markup?
    49 |   --- {F}{or t for objects of class \code{lm, lmrob} and \code{glm}
       |       ^
checkRd: (-1) termtable.Rd:49-50: Lost braces
    49 |   --- {F}{or t for objects of class \code{lm, lmrob} and \code{glm}
       |          ^
checkRd: (-1) termtable.Rd:51: Lost braces; missing escapes or markup?
    51 |   --- {Chi-squared}{for other \code{glm}s and \code{survreg}}\cr
       |       ^
checkRd: (-1) termtable.Rd:51: Lost braces
    51 |   --- {Chi-squared}{for other \code{glm}s and \code{survreg}}\cr
       |                    ^
checkRd: (-1) rem.dyad.Rd:121: Lost braces; missing escapes or markup?
   121 | \item Single or multiple covariates, time varying: For \code{CovSnd}, \code{CovRec}, or \code{CovInt}, an \code{m} by \code{p} by {n} array whose respective dimensions index time (i.e., event number), covariate, and actor.  For \code{CovEvent}, a \code{m} by \code{p} by \code{n} by \code{n} array, whose dimensions are analogous to the previous case.
       |                                                                                                                                   ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) LS.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LS.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) RE2C.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ena.plot.group.Rd:44: Escaped LaTeX specials: \$
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checkRd: (-1) REndo.Rd:19: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) rentrez.Rd:17-21: Lost braces
    17 | /enumerated{
       |            ^
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) twosidedPValuestobins.Rd:84: Lost braces; missing escapes or markup?
    84 | A matrix with \code{n.bins + 1} rows and {ncol(zmat)} columns, representing for each study the discretization chosed. Values are the between bin breaks. First and last values are the edges of the outmost bins.
       |                                          ^
checkRd: (-1) ztobins.Rd:90: Lost braces; missing escapes or markup?
    90 | A matrix with \code{n.bins + 1} rows and {ncol(zmat)} columns, representing for each study the discretization chosed. Values are the between bin breaks. First and last values are the edges of the outmost bins.
       |                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) method.A.Rd:200-205: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.A.Rd:206-211: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) method.B.Rd:238-243: Lost braces in \itemize; \value handles \item{}{} directly
Found the following files/directories:
  ‘PackageCites.bib’
'LazyData' is specified without a 'data' directory
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No news entries found.
checkRd: (-1) repo_build.Rd:44-47: Lost braces
    44 | ## chunk "item 1" {
       |                   ^
checkRd: (-1) repo_dependencies.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repo_dependencies.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repo_dependencies.Rd:51-53: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'REPPlab-package.Rd':
  ‘R/EPP-lab-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) NCBirths2004.Rd:16: Lost braces
    16 |     \item{\code{Smoker}}{Mother a smoker? code{No}, \code{Yes}}
       |                                               ^
checkRd: (-1) ExpandProbs.Rd:35: Lost braces; missing escapes or markup?
    35 |      {z_probs2 sqrt((n-1)/n) = t_probs,n-1}
       |      ^
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'gaussian_process_cv.Rd':
  ‘ncomp’

Documented arguments not in \usage in Rd file 'get_samples_from_strata.Rd':
  ‘starta’

Documented arguments not in \usage in Rd file 'ith_subsets_ortho_diss.Rd':
  ‘remove’

Documented arguments not in \usage in Rd file 'pca_nipals.Rd':
  ‘Y’

Documented arguments not in \usage in Rd file 'predict_gaussian_process.Rd':
  ‘b’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
checkRd: (-1) cast.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) cast.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-df-v7.rd:3: Escaped LaTeX specials: \_
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checkRd: (-1) resistance.Rd:52: Lost braces
    52 |     \item B. Bollob\'{a}s, 1998.  \emph{Modern Graph Theory}.  Springer.
       |                      ^
checkRd: (-1) calc_MO2.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_MO2.Rd:31: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'get.V.Rd':
  ‘ct.lst’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Re-building vignettes had CPU time 2.6 times elapsed time
checkRd: (-1) harmonize_values.Rd:44: Lost braces; missing escapes or markup?
    44 | \item{perl}{Use perl-like regex? Defaults to {FALSE}.}
       |                                              ^
checkRd: (-1) getPartialGamelog.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getPartialGamelog.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
Rd files without \alias:
  ‘retry-package.Rd’
'LazyData' is specified without a 'data' directory
checkRd: (-1) elink.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elink.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elink.Rd:74-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reutils-package.Rd:114: Lost braces
   114 |      code{reutils.test.remote} to \code{TRUE} to run the full suite of tests.
       |          ^
checkRd: (-1) cpUpper.Rd:39: Lost braces
    39 | \code{"fastfloyd"}{ (default) uses an iterative variant of the Floyd-Warshall algorithm, in which the check of consistency of the current observation with a given cluster is done in a single step of the Floyd-Warshall algorithm. Much faster than \code{"floyd"}.}
       |                   ^
checkRd: (-1) cpUpper.Rd:41: Lost braces
    41 | \code{"floyd"}{ uses the algorithm described in Crawford and Pendakur (2013): at each step the complete Floyd-Warshall algorithm is run to check whether each cluster can accomodate the current observation.}
       |               ^
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) saveRev.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{use_wd}{logical - If TRUE, the history will be prepended by setwd({'users current working directory'}). This function will set the script's working directory to
       |                                                                         ^
'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) fs_search.Rd:76: Lost braces
    76 | \\code{\link{fs_auth}} \code{\link{fs_browse}}
       |       ^
checkRd: (-1) GenericDataFile.Rd:87-88: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) GenericDataFile.Rd:92: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'compareChecksum.GenericDataFile.Rd':
  ‘verbose’

Documented arguments not in \usage in Rd file 'dim.GenericTabularFile.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'dsApplyInPairs.GenericDataFileSet.Rd':
  ‘ds’

Documented arguments not in \usage in Rd file 'fromFile.GenericDataFile.Rd':
  ‘unknown’

Documented arguments not in \usage in Rd file 'gzip.GenericDataFile.Rd':
  ‘verbose’

Documented arguments not in \usage in Rd file 'readChecksum.ChecksumFile.Rd':
  ‘verbose’

Documented arguments not in \usage in Rd file 'writeChecksum.GenericDataFile.Rd':
  ‘verbose’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) disp.Rd:20: Lost braces; missing escapes or markup?
    20 | sum_{i=1}^n a(R(e_i)) * e_i where 
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
checkRd: (-1) logLoss.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{y}{vector of observed binomial values {0,1}}
       |                                             ^
checkRd: (-1) logLoss.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{p}{vector of predicted probabilities {0-1}}
       |                                            ^
checkRd: (-1) logLoss.Rd:35: Lost braces; missing escapes or markup?
    35 |       in {0,1} and estimated probability yp that yt = 1, the log loss is derived as: 
       |          ^
checkRd: (-1) rf.modelSel.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rf.modelSel.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rf.modelSel.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rf.modelSel.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rf.modelSel.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rf.modelSel.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rf.modelSel.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataset_search.Rd:64: Lost braces; missing escapes or markup?
    64 | \code{facetMincount={#}} to exclude facets with a count less than {#}}
       |                                                                   ^
checkRd: (-1) name_lookup.Rd:114: Lost braces; missing escapes or markup?
   114 | facetMincount={#} to exclude facets with a count less than {#}, e.g.
       |               ^
checkRd: (-1) name_lookup.Rd:114: Lost braces; missing escapes or markup?
   114 | facetMincount={#} to exclude facets with a count less than {#}, e.g.
       |                                                            ^
checkRd: (-1) tk.browse.Rd:29: Lost braces
    29 |     Single logical value, whether to wait for the interface window to be closed before unfreezing the R console. The \code{FALSE} default let you use R and the interface in parallel (see the 'Typing R commands while browsing' section below), the code{TRUE} value is used essentially in the stand alone version.
       |                                                                                                                                                                                                                                                           ^
checkRd: (-1) tk.convert.Rd:17: Lost braces
    17 |     Single logical value, whether to wait for the interface window to be closed before unfreezing the R console. The \code{FALSE} default let you use R and the interface in parallel, the code{TRUE} is used essentially in the stand alone version.
       |                                                                                                                                                                                                ^
checkRd: (-1) tk.tracks.Rd:8: Lost braces
     8 |   This function allows to load and edit the \code{\linkS4class{drawable.list}} object that is to be passed to \code{\link{tk.browse}} and code{\link{browsePlot}}, using a Tcl-tk interface
       |                                                                                                                                               ^
Running examples in ‘RGCCA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: print.rgcca
> ### Title: Print a fitted object from the RGCCA package
> ### Aliases: print.rgcca print.rgcca_cv print.rgcca_permutation
> ###   print.rgcca_bootstrap print.rgcca_stability
> 
> ### ** Examples
> 
> ## Printing of an rgcca object
> data(Russett)
> blocks <- list(
+   agriculture = Russett[, seq(3)],
+   industry = Russett[, 4:5],
+   politic = Russett[, 6:8]
+ )
> C <- matrix(c(0, 0, 1, 0, 0, 1, 1, 1, 0), 3, 3)
> res <- rgcca(blocks,
+   connection = C, ncomp = rep(2, 3), tau = c(1, 1, 1),
+   scheme = "factorial", scale = TRUE, verbose = FALSE
+ )
> print(res)
Fitted RGCCA model. 
The algorithm converged to a stationnary point:
	- After 2 iterations for component 1.
	- After 6 iterations for component 2.
> 
> ## Printing of an rgcca_cv object
> res <- rgcca_cv(blocks,
+   response = 3, method = "rgcca", par_type = "tau",
+   par_value = c(0, 0.2, 0.3), n_run = 1, n_cores = 1,
+   verbose = TRUE
+ )
> print(res)
RGCCA cross-validation object obtained with 10 sets of parameters using 5 folds.
Regression was performed using lm model.
> 
> ## Printing of an rgcca_permutation object
> perm.out <- rgcca_permutation(blocks,
+   par_type = "tau",
+   n_perms = 5, n_cores = 1,
+   verbose = TRUE
+ )
Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘RGCCA.Rmd’ using rmarkdown

Quitting from lines 786-792 [unnamed-chunk-12] (RGCCA.Rmd)
Error: processing vignette 'RGCCA.Rmd' failed with diagnostics:
wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
--- failed re-building ‘RGCCA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) gd_region.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{x}{either a WKT string (character), a {terra} SpatRaster(Collection)/SpatVector(Collection)/SpatExtent, an {sf} object, an {sp} Spatial* object or a {raster} RasterLayer/RasterStack.}
       |                                             ^
checkRd: (-1) gd_region.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{x}{either a WKT string (character), a {terra} SpatRaster(Collection)/SpatVector(Collection)/SpatExtent, an {sf} object, an {sp} Spatial* object or a {raster} RasterLayer/RasterStack.}
       |                                                                                                                  ^
checkRd: (-1) gd_region.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{x}{either a WKT string (character), a {terra} SpatRaster(Collection)/SpatVector(Collection)/SpatExtent, an {sf} object, an {sp} Spatial* object or a {raster} RasterLayer/RasterStack.}
       |                                                                                                                                  ^
checkRd: (-1) gd_region.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{x}{either a WKT string (character), a {terra} SpatRaster(Collection)/SpatVector(Collection)/SpatExtent, an {sf} object, an {sp} Spatial* object or a {raster} RasterLayer/RasterStack.}
       |                                                                                                                                                            ^
checkRd: (-1) GenDataPopulation.Rd:21: Lost braces
    21 | {data}{Population of data}
       |       ^
checkRd: (-1) GenDataSample.Rd:23: Lost braces
    23 | {data}{Sample of data}
       |       ^
'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) genoud.Rd:165-170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) genoud.Rd:171-176: Lost braces in \itemize; meant \describe ?
checkRd: (-1) genoud.Rd:177-186: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) RiemannianMetric.Rd:450-453: Lost braces
   450 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
checkRd: (-1) RiemannianMetric.Rd:484-487: Lost braces
   484 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
checkRd: (-1) RiemannianMetric.Rd:588-591: Lost braces
   588 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
Package suggested but not available for checking: ‘rgdal’
checkRd: (-1) Ghana_2021_school_attendance.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Ghana_2021_school_attendance_geometry.Rd:75: Lost braces in \itemize; meant \describe ?
Found the following significant warnings:
  Rglpk_read_file.c:215:26: warning: format ‘%c’ expects argument of type ‘int’, but argument 2 has type ‘char *’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rglpk.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
'LazyData' is specified without a 'data' directory
checkRd: (-1) regCVCF.Rd:52: Lost braces; missing escapes or markup?
    52 | a decision tree with {C4.5} on each one. Using each classifier, a prediction of the whole dataset is obtained.
       |                      ^
checkRd: (-1) summary.rfdata.Rd:17: Lost braces; missing escapes or markup?
    17 | A list including information related to the noise filtering process contained in the object \code{object} of class {rfdata} with the following elements:
       |                                                                                                                    ^
'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) code_sawtooth_design.Rd:53: Lost braces
    53 | /url{http://www.sawtoothsoftware.com/help/lighthouse-studio/manual/index.html?hid_web_cbc_exporting.html}
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) rhandsontable-package.Rd:8: Lost braces
     8 | R interface for creating tables using Handsontable, url{https://handsontable.com/}
       |                                                        ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘mydata.rda’ ‘thedata.rda’
checkRd: (-1) GenerateClusterData.Rd:34: Lost braces; missing escapes or markup?
    34 | origin, v_1, -v_1, v_2, -v_2, v_3, -v_3,..., v_{(numberOfClusters-1)/2},
       |                                                ^
checkRd: (-1) GenerateClusterData.Rd:35: Lost braces; missing escapes or markup?
    35 | -v_{(numberOfClusters-1)/2} (if \code{numberOfClusters} is odd)
       |    ^
checkRd: (-1) GenerateClusterData.Rd:36: Lost braces; missing escapes or markup?
    36 | origin, v_1, -v_1, v_2, -v_2, v_3, -v_3,..., v_{(numberOfClusters-1)/2}
       |                                                ^
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:21-22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:23-24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:25-26: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:27-28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:29-30: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:31-32: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:33-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:35-36: Lost braces
    35 |    \item{pam_cluster_64_7_5715},{N=64, seven clusters with 5715 vectors per
       |                                 ^
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:37-38: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:39-40: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:21-22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:23-24: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'dimnames.AbstractFileArray.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'length.AbstractFileArray.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'readContiguousValues.AbstractFileArray.Rd':
  ‘length’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Specified C++11: please drop specification unless essential
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) iex.chart.Rd:23: Lost braces; missing escapes or markup?
    23 | r takes only of of the values accepted IN API request. {"5y", "2y", "1y", "ytd", "6m", "3m", "1m", "1d"}
       |                                                        ^
checkRd: (-1) descrip.Rd:122: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:123: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:124-125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:126-128: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:129-133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:134-135: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:136-138: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:139-140: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:141-144: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:145-146: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:147: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:148: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:149: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) correct_sign.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct_sign.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ipc_get_analyses.Rd:46: Lost braces; missing escapes or markup?
    46 | available on the \strong{analyses/{id}/{period}} advanced API endpoint,
       |                                   ^
checkRd: (-1) ipc_get_analyses.Rd:46: Lost braces; missing escapes or markup?
    46 | available on the \strong{analyses/{id}/{period}} advanced API endpoint,
       |                                        ^
checkRd: (-1) ipc_get_areas.Rd:50: Lost braces; missing escapes or markup?
    50 | and period, available on the \strong{areas/{id}/{period}} advanced API endpoint,
       |                                            ^
checkRd: (-1) ipc_get_areas.Rd:50: Lost braces; missing escapes or markup?
    50 | and period, available on the \strong{areas/{id}/{period}} advanced API endpoint,
       |                                                 ^
checkRd: (-1) ipc_get_icons.Rd:49: Lost braces; missing escapes or markup?
    49 | and period, available on the \strong{types/{id}/{period}} advanced API endpoint,
       |                                            ^
checkRd: (-1) ipc_get_icons.Rd:49: Lost braces; missing escapes or markup?
    49 | and period, available on the \strong{types/{id}/{period}} advanced API endpoint,
       |                                                 ^
checkRd: (-1) ipc_get_points.Rd:47: Lost braces; missing escapes or markup?
    47 | and period, available on the \strong{types/{id}/{period}} advanced API endpoint,
       |                                            ^
checkRd: (-1) ipc_get_points.Rd:47: Lost braces; missing escapes or markup?
    47 | and period, available on the \strong{types/{id}/{period}} advanced API endpoint,
       |                                                 ^
checkRd: (-1) ipc_get_population.Rd:49: Lost braces; missing escapes or markup?
    49 | analysis, available on the \strong{types/{id}} advanced API endpoint,
       |                                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) pkg_ref.Rd:74-93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkg_ref.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkg_ref.Rd:78-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkg_ref.Rd:81-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkg_ref.Rd:84-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkg_ref.Rd:86-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkg_ref.Rd:88-89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:168: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:169: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskPredict.Rd:38: Lost braces
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       | ^
checkRd: (-1) riskPredict.Rd:38: Lost braces
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       |     ^
checkRd: (-1) riskPredict.Rd:38: Lost braces; missing escapes or markup?
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       |             ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       | ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |     ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces; missing escapes or markup?
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |             ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |                      ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces; missing escapes or markup?
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |                              ^
checkRd: (-1) iidCox.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iidCox.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iidCox.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iidCox.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iidCox.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iidCox.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iidCox.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iidCox.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotCalibration.Rd:53-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotCalibration.Rd:57-61: Lost braces
    57 | \item{\code{"nne"}}: {The observed proportion at predicted risk value 'p' is obtained based
       |                      ^
checkRd: (-1) plotCalibration.Rd:65-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotCalibration.Rd:68-71: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
checkRd: (-1) CovsAlignedToADesign-class.Rd:22: Lost braces; missing escapes or markup?
    22 | specified stratum weight to the product of h_b (the harmonic mean of n_{tb} and
       |                                                                        ^
checkRd: (-1) CovsAlignedToADesign-class.Rd:23: Lost braces; missing escapes or markup?
    23 | n_{cb}, the counts of treatment and control clusters in stratum b) with bar-w_b,
       |   ^
checkRd: (-1) DesignWeights.Rd:39: Lost braces; missing escapes or markup?
    39 | mean of n_{tb} and n_{cb}, the number of treatment and control
       |           ^
checkRd: (-1) DesignWeights.Rd:39: Lost braces; missing escapes or markup?
    39 | mean of n_{tb} and n_{cb}, the number of treatment and control
       |                      ^
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'inner_t_index_calculation.Rd':
  ‘param_’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) RivivcA.Rd:7: Lost braces
     7 | This is the major function to be called where numerical convolution ad/or deconvolution might be used for a linear in vitro in vivo correlation level A. It performes either numerical convolution via /code{NumConv()} or deconvolution via /code{NumDeconv()} and correlates their results with the known.data object via linear regression \code{lm()}. If you just want raw results of convolution/deconvolution then call explicitely \code{\link{NumConv}} or \code{link{NumDeconv}}
       |                                                                                                                                                                                                             ^
checkRd: (-1) RivivcA.Rd:7: Lost braces
     7 | This is the major function to be called where numerical convolution ad/or deconvolution might be used for a linear in vitro in vivo correlation level A. It performes either numerical convolution via /code{NumConv()} or deconvolution via /code{NumDeconv()} and correlates their results with the known.data object via linear regression \code{lm()}. If you just want raw results of convolution/deconvolution then call explicitely \code{\link{NumConv}} or \code{link{NumDeconv}}
       |                                                                                                                                                                                                                                                   ^
Non-standard file/directory found at top level:
  ‘jri’
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
Documented arguments not in \usage in Rd file 'rJava-internal.Rd':
  ‘r.convertor’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
License stub is invalid DCF.
'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
Invalid package aliases in Rd file 'rkt-package.Rd':
  ‘tkt-package’
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) basic_GS.Rd:42: Lost braces; missing escapes or markup?
    42 | \eqn{L} and {U} are strictly lower/upper triangular matrix respectively.
       |             ^
checkRd: (-1) basic_SOR.Rd:45: Lost braces; missing escapes or markup?
    45 | \eqn{L} and {U} are strictly lower/upper triangular matrix respectively.
       |             ^
checkRd: (-1) basic_SSOR.Rd:45: Lost braces; missing escapes or markup?
    45 | \eqn{L} and {U} are strictly lower/upper triangular matrix respectively.
       |             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ms_simplify.Rd:36: Lost braces
    36 | \url{https://github.com/mbloch/mapshaper/wiki/Simplification-Tips}{link}
       |                                                                   ^
Specified C++11: please drop specification unless essential
checkRd: (-1) ioslides_presentation.Rd:239: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ioslides_presentation.Rd:240: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ioslides_presentation.Rd:241: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ioslides_presentation.Rd:242: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ioslides_presentation.Rd:243: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setOption.Matlab.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setOption.Matlab.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ComprehensiveTemperatureGenerator.Rd:68: Lost braces; missing escapes or markup?
    68 | \item{exogen_all}{data frame containing exogenous variable formatted like \code{Tx_all} and {Tn_all}. Default is \code{NULL}. 
       |                                                                                             ^
checkRd: (-1) qqplot_RMAWGEN_Tx.Rd:70: Lost braces; missing escapes or markup?
    70 | \code{Tx_gen},{Tn_gen} and \code{main} must have an even number of elements.
       |               ^
GNU make is a SystemRequirements.
checkRd: (-1) RMBC.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:31-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:52-53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:60-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:62-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robustINIT.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robustINIT.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robustINIT.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robustINIT.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weightedSestimator.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weightedSestimator.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weightedSestimator.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) plot.mcfs.Rd:24: Lost braces; missing escapes or markup?
    24 |     \item\code{ri} {plots top features set with their RIs as well as max RI obtained from permutation experiments. Red color denotes important features.}
       |                    ^
checkRd: (-1) rmdcev.Rd:11: Lost braces
    11 | Lloyd-Smith, P. (2020). Kuhn-Tucker and Multiple Discrete-Continuous Extreme Value (MDCEV) Model Estimation and Simulation in R: The rmdcev Package. R Journal. 12(2): 251-265. \doi{doi.org/10.32614/RJ-2021-015}{(link)}
       |                                                                                                                                                                                                                   ^
checkRd: (-1) rmdcev.Rd:12: Lost braces
    12 | Bhat, CR (2008). The multiple discrete-continuous extreme value (MDCEV) model: Role of utility function parameters, identification considerations, and model extensions. Transportation Research Part B: Methodological, 42(3): 274-303.\doi{10.1016/j.trb.2007.06.002}{(link)}
       |                                                                                                                                                                                                                                                                        ^
checkRd: (-1) rmdcev.Rd:13: Lost braces
    13 | Lloyd-Smith, P (2018). A new approach to calculating welfare measures in Kuhn-Tucker demand models. Journal of Choice Modeling 26:19–27. \doi{10.1016/j.jocm.2017.12.002}{(link)}
       |                                                                                                                                                                          ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfft-class.Rd:65: Lost braces
    65 | code{dfft(object, index=0)} on an object created from a forecast with 
       |     ^
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) mgraph.Rd:62: Lost braces
    62 |   \item{TC}{target class (for multi-class classification class) within {1,...,\emph{Nc}}, where \emph{Nc} is the number of classes. If multi-class and TC==-1 then TC is set to 
       |                                                                        ^
checkRd: (-1) mmetric.Rd:112: Lost braces
   112 |   \item{TC}{target class index or vector of indexes (for multi-class classification class) within {1,...,\emph{Nc}}, where \emph{Nc} is the number of classes:<cr>
       |                                                                                                   ^
checkRd: (-1) mparheuristic.Rd:27: Lost braces
    27 | except for SVM several \code{rbfdot} kernel based models (\code{"ksvm"},\code{"rsvm"},\code{"lssvm"}, which can assume \code{2^}{search-range}; please check the result of this function to confirm if the search is linear or \code{2^}{search-range}). 
       |                                                                                                                                 ^
checkRd: (-1) mparheuristic.Rd:27: Lost braces
    27 | except for SVM several \code{rbfdot} kernel based models (\code{"ksvm"},\code{"rsvm"},\code{"lssvm"}, which can assume \code{2^}{search-range}; please check the result of this function to confirm if the search is linear or \code{2^}{search-range}). 
       |                                                                                                                                                                                                                                         ^
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) histMisclassif.Rd:22: Lost braces
    22 | err_i = 1 - max_{k={1,\ldots,K}} P(Z_i=k|x_i)
       |                 ^
checkRd: (-1) histMisclassif.Rd:22: Lost braces
    22 | err_i = 1 - max_{k={1,\ldots,K}} P(Z_i=k|x_i)
       |                    ^
Documented arguments not in \usage in Rd file 'bind.Rd':
  ‘.single_on_bind’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) nsgaControl.Rd:20-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nsgaControl.Rd:28-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nsgaControl.Rd:36-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nsgaControl.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:56: Lost braces in \itemize; meant \describe ?
Found the following calls to attach():
File ‘Rmosek/R/builder.R’:
  attach(builderenv, pos, name, warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
Found the following significant warnings:
  npmpois.c:408:36: warning: too many arguments for format [-Wformat-extra-args]
  rmg.c:471:43: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘int’ [-Wformat=]
  rmg.c:507:36: warning: too many arguments for format [-Wformat-extra-args]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rmp.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
'LazyData' is specified without a 'data' directory
checkRd: (-1) DO.unit.convert.Rd:24: Lost braces; missing escapes or markup?
    24 |     Units of dissolved oxygen concentration desired, i.e. to be converted to. Must be \code{"mg/L"}, \code{"PP"}, or {"pct"}.
       |                                                                                                                      ^
checkRd: (-1) MR.loops.Rd:80: Lost braces; missing escapes or markup?
    80 | Returns a list of 2. \code{$MR.summary} is of class {data.frame} with 3 columns: \code{$MR} (metabolic rate in user specified units, this is the same as the slope in each linear model), \code{$sd.slope} (standard deviation of slopes calculation), \code{$r.square} (adjusted r square value from each model). This second object is a list of \code{biglm} objects, each one representing a metabolic loop (see McDonnell and Chapman 2016). 
       |                                                     ^
checkRd: (-1) get.pcrit.Rd:27: Lost braces; missing escapes or markup?
    27 | Metabolic rate variable name, formatted as character. Default = \code{NULL}. If this argument takes a value, Pcrit will be calculated by regressing \code{MR.var.name} on \code{DO.var.name}. \code{time.var} and {time.interval} should, in this case, take no value. If \code{MR.var.name} is left as\code{NULL}, then instantaneous metabolic rates (MR) at specified time intervals (see \code{time.interval}) from \code{DO.var.name} and \code{time.var}.
       |                                                                                                                                                                                                                   ^
checkRd: (-1) tot.rss.Rd:35: Lost braces
    35 | code{\link{sumsq}}
       |     ^
checkRd: (-1) tot.rss.Rd:36: Lost braces
    36 | code{\link{get.pcrit}}
       |     ^
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
checkRd: (-1) myTarGetClientList.Rd:33: Lost braces
    33 | {MyTarget API Documenation}{https://target.my.com/doc/api/detailed/#resource_agency_clients}
       |                            ^
checkRd: (-1) validateFromString.Rd:6: Lost braces
     6 | e.g. the string "{ mzQC : {}}"}
       |                  ^
checkRd: (-1) GLMnetwork.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GLMnetwork.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imputeHD.Rd:26-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imputeHD.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imputeHD.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imputedGLMnetwork.Rd:27-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) imputedGLMnetwork.Rd:30-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stabilitySelection.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stabilitySelection.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stabilitySelection.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stabilitySelection.Rd:26-27: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘rnaturalearthhires’
Malformed Title field: should not end in a period.
checkRd: (-1) NCEP.track2kml.Rd:36: Lost braces
    36 |   There are several options for specifying \code{col.scheme}.  A single color may be specified for all points (using e.g. \code{'red'}, \code{2}, or \code{"#FF0000"}), specific colors may be given for each point (e.g. \code{c('red','blue','green', etc.)} or code{c('#FF0000','#0000FF','#00FF00', etc.)}), or the function can automatically assign colors, according to the values in \code{clo.variable}, if \code{col.scheme} is any color palette in \code{\link[RColorBrewer]{display.brewer.all}} or one of the recognizezd R color palettes (i.e. \code{'rainbow'}, \code{'heat.colors'}, \code{'terrain.colors'}, \code{'topo.colors'}, \code{'cm.colors'}, or \code{'bpy.colors'}).  An alpha value (0-255) may be supplied to \code{point.alpha} to adjust transparencies.
       |                                                                                                                                                                                                                                                                       ^
checkRd: (-1) rncl.Rd:53-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:59-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:65-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:73-78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:80-84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:86-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:92-93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:98-99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:101-102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:107-110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:112-115: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:117-119: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:121-124: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
checkRd: (-1) term_day_dist.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) term_day_dist.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) term_day_dist.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) term_day_dist.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) term_day_dist.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) term_day_dist.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nexml_get.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:35: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgdal’
checkRd: (-1) PlotWindProfile.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PlotWindProfile.Rd:83: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'SanitizeURL.Rd':
  ‘bad.str’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) projectRoads.Rd:116-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) projectRoads.Rd:118-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) projectRoads.Rd:121-125: Lost braces in \itemize; meant \describe ?
checkRd: (-1) projectRoads.Rd:126-128: Lost braces in \itemize; meant \describe ?
checkRd: (-1) projectRoads.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) projectRoads.Rd:99-100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) projectRoads.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) projectRoads.Rd:102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) projectRoads.Rd:103-106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) outliergram.Rd:45-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:55-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:59-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:63-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:66-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) outliergram.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) outliergram.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) internal_plots.Rd:193-203: Lost braces
   193 | \code{.cexscale}{rescales the point sizes of the points to be plotted;
       |                 ^
checkRd: (-1) internal_plots.Rd:204: Lost braces
   204 | \code{.getDimsTD}{returns the number of different coordinates to be plotted.}
       |                  ^
checkRd: (-1) internal_plots.Rd:205-207: Lost braces
   205 | \code{.producePanelFirstS}{for each graphical panel inserts
       |                           ^
checkRd: (-1) internal_plots.Rd:208-209: Lost braces
   208 | \code{.getX.vec}{produces the x-grid (on original scale) for each of the panels
       |                 ^
checkRd: (-1) internal_plots.Rd:211-212: Lost braces
   211 | \code{.getXlimYlim}{produces panel-wise \code{xlim} and \code{ylim} arguments
       |                    ^
checkRd: (-1) internal_plots.Rd:213: Lost braces
   213 | \code{.prepareTitles}{produces the titles for the panels}
       |                      ^
checkRd: (-1) internal_plots.Rd:214: Lost braces
   214 | \code{.getToDraw}{computes which panels are to be drawn}
       |                  ^
checkRd: (-1) internal_plots.Rd:215-216: Lost braces
   215 | \code{.preparePanelFirstLast}{prepares the \code{panel.first} and \code{panel.last}
       |                              ^
Documented arguments not in \usage in Rd file 'internal_plots.Rd':
  ‘panelFirst’

Documented arguments not in \usage in Rd file 'internals.Rd':
  ‘L2fam’
Objects in \usage without \alias in Rd file 'internals.Rd':
  ‘.evalListRec’ ‘.filterEargsWEargList’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘RobAStBase-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RobAStBase-package
> ### Title: Robust Asymptotic Statistics
> ### Aliases: RobAStBase-package RobAStBase
> ### Keywords: package
> 
> ### ** Examples
> 
> library(RobAStBase)
> ## some L2 differentiable parametric family from package distrMod, e.g.
> B <- BinomFamily(size = 25, prob = 0.25) 
Warning in .local(.Object, ...) : you have to specify slot r at least
Error: unable to find an inherited method for function ‘r’ for signature ‘object = "numeric"’
Execution halted
Invalid package aliases in Rd file '0RobRDA-package.Rd':
  ‘RobRDA-package’
'LazyData' is specified without a 'data' directory
checkRd: (-1) cubinf.summaries.Rd:46: Lost braces
    46 | The class "lm" functions \code{effects}, \code{alias}, \code{add1}, \code{drop1}, code{kappa},
       |                                                                                       ^
Specified C++11: please drop specification unless essential
checkRd: (-1) GEV-class.Rd:27: Lost braces
    27 | point (if eqn{s > 0}).
       |              ^
Documented arguments not in \usage in Rd file 'internal-interpolate.Rd':
  ‘upRad.s’
Objects in \usage without \alias in Rd file 'internal-interpolate.Rd':
  ‘.getPsi.wL’ ‘.getPsi.P’

Objects in \usage without \alias in Rd file 'rescaleFunction-methods.Rd':
  ‘rescaleFunction’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'createITPSplineResult.Rd':
  ‘measure’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) weighted_median_line.Rd:34: Lost braces; missing escapes or markup?
    34 |                     {m([y - m(y, w)][x - m(x, w)], w) / m([x - m(x, w)]^2, w).}
       |                     ^
checkRd: (-1) predict.robu.Rd:36-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.robu.Rd:43-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.robu.Rd:50-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rcalibration_MS-class.Rd:21: Lost braces; missing escapes or markup?
    21 |     \item{\code{input}:}{Object of class \code{list}. Each element is a \code{matrix} of the design of experiments in each source with dimension n_i x p_{x,i}, for i=1,...,num_sources.}
       |                                                                                                                                                          ^
checkRd: (-1) separable_kernel.Rd:26: Lost braces
    26 | A vector specifying the type of kernels of each coordinate of the input. \code{matern_3_2} and \code{matern_5_2} are \code{Matern correlation} with roughness parameter 3/2 and 5/2 respectively. \code{pow_exp} is power exponential correlation with roughness parameter alpha. If \code{pow_exp} is to be used, one needs to specify its roughness parameter alpha. The default choice is \code{matern_5_2}. The \code{periodic_gauss} means the Gaussian kernel with periodic folding method with be used. The code{periodic_exp} means the exponential kernel with periodic folding method will be used.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        ^
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'Sample.rgasp.Rd':
  ‘interval_data’

Objects in \usage without \alias in Rd file 'neg_log_marginal_post_approx_ref_ppgasp.Rd':
  ‘neg_log_marginal_post_approx_ref’

Objects in \usage without \alias in Rd file 'separable_multi_kernel.Rd':
  ‘separable_kernel’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) coefPlot.Rd:64: Lost braces
    64 | for the degrees of freedom.  For code{"sparseLTS"} objects, possible values
       |                                      ^
checkRd: (-1) coefPlot.Rd:65: Lost braces
    65 | are code{"lambda"} for the value of the penalty parameter (the default), or
       |         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'choose.test.Rd':
  ‘Xpaired’ ‘Ypaired’ ‘Xextra’ ‘Yextra’ ‘mc.rep’
Argument items with no description in Rd file 'multinom.test.Rd':
  ‘X’ ‘Y’ ‘alternative’ ‘correct’ ‘perm’ ‘mc.rep’ ‘method’ ‘verbose’
  ‘mode’ ‘useC’
Argument items with no description in Rd file 'mw.mw.2.perm.Rd':
  ‘X’ ‘Y’ ‘Xprime’ ‘Yprime’ ‘.corr’ ‘mc.rep’ ‘alternative’ ‘verbose’
Argument items with no description in Rd file 'pm.wilcox.test.Rd':
  ‘Xpaired’ ‘Ypaired’ ‘Xextra’ ‘Yextra’ ‘alternative’ ‘verbose’
Argument items with no description in Rd file 'sim.partially.matched.Rd':
  ‘meanRatio’ ‘sdRatio’ ‘within.sd’ ‘type’ ‘hyp’
Argument items with no description in Rd file 'wmw.paired.replicates.test.Rd':
  ‘X’ ‘Y’ ‘alternative’ ‘correct’ ‘perm’ ‘mc.rep’ ‘method’ ‘verbose’
  ‘mode’ ‘useC’
checkRd: (-1) hyper_names.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hyper_names.Rd:39-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hyper_names.Rd:42-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hyper_names.Rd:45-47: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
Objects in \usage without \alias in Rd file 'gettptnfpfn-defunct.Rd':
  ‘gettptnfpfn’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) descriptiveTable.Rd:18: Lost braces
    18 | other object type that does not fail in code{model.frame(object)}.}
       |                                             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) prereg_initialize.Rd:20: Lost braces; missing escapes or markup?
    20 | the (pre)registration form specification (in {preregr} format), see the
       |                                              ^
checkRd: (-1) prereg_initialize.Rd:23: Lost braces; missing escapes or markup?
    23 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
checkRd: (-1) prereg_initialize.Rd:26: Lost braces; missing escapes or markup?
    26 | For an introduction to working with {preregr} (pre)registrations,
       |                                     ^
checkRd: (-1) rmd_templates.Rd:70: Lost braces; missing escapes or markup?
    70 | This function creates an R Markdown template from a {preregr}
       |                                                     ^
checkRd: (-1) rmd_templates.Rd:72: Lost braces; missing escapes or markup?
    72 | Sheet holding the (pre)registration form specification (in {preregr}
       |                                                            ^
checkRd: (-1) rmd_templates.Rd:76: Lost braces; missing escapes or markup?
    76 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) funs.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funs.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funs.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pars.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pars.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pars.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pros.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pros.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pros.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pros.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stoi.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stoi.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stoi.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vars.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vars.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vars.Rd:12: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ROI_plugin_build_equality_constraints.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_equality_constraints.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:29: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_solve.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'add_matches_columns.Rd':
  ‘Matches’

Documented arguments not in \usage in Rd file 'run_checks_two.Rd':
  ‘lookback’ ‘standard_deviaion’ ‘match_on’ ‘model_type’

Documented arguments not in \usage in Rd file 'trim_pool.Rd':
  ‘standard_deviaion’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Auto-generated content requiring editing in Rd file 'roloc-package.Rd':
  \references: ‘~~ Literature or other references for background information ~~’
  \seealso: ‘~~ Optional links to other man pages, e.g. ~~’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) update_tidy_omic.Rd:16-17: Lost braces
    16 | in \code{updated_tidy_data} (names) and the table {features, samples,
       |                                                   ^
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'DOLLAR.Class.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'DOLLARLT_-.Class.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'getMethods.Class.Rd':
  ‘unqiue’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) read_ascii.Rd:33: Lost braces
    33 | \item{respondent_pattern}{For use when the file does not contain a line for every card for every respondent (or contains extra lines that correspond to no respondent), a regular expression that matches the file's respondent identifier; e.g., if the respondent number is stored in the first four digits of each line, preceded by a space, "(?<=^\\s)\\d{4}".}
       |                                                                                                                                                                                                                                                                                                                                                               ^
Running examples in ‘ROptEstOld-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BinomFamily
> ### Title: Generating function for Binomial families
> ### Aliases: BinomFamily
> ### Keywords: models
> 
> ### ** Examples
> 
> (B1 <- BinomFamily(size = 25, prob = 0.25))
Warning in .local(.Object, ...) : you have to specify slot r at least
Error: unable to find an inherited method for function ‘r’ for signature ‘object = "numeric"’
Execution halted
checkRd: (-1) internal-interpolate.Rd:160: Lost braces
   160 |   \code{.saveGridToCSV}{\code{invisible(NULL)}. }
       |                        ^
checkRd: (-1) internal-interpolate.Rd:162-164: Lost braces
   162 |   \code{.readGridFromCSV}{ a list with the read-in items, i.e.,
       |                          ^
checkRd: (-1) internal-interpolate.Rd:166: Lost braces
   166 |   \code{.generateInterpGrid}{\code{invisible(NULL)}. }
       |                             ^
Documented arguments not in \usage in Rd file 'internal-interpolate.Rd':
  ‘upRad.s’ ‘withSmooth’
Assignments in \usage in Rd file 'internal-interpolate.Rd':
  .readGridFromCSV <- function(fromFileCSV) .generateInterpGrid(thGrid, 
      PFam, toFileCSV = "temp.csv", getFun = .getLMGrid, ..., modifyfct, 
      nameInSysdata, GridFileName, withPrint = TRUE, len = 13)

Objects in \usage without \alias in Rd file 'internalRobestHelpers.Rd':
  ‘.constructArg.list’ ‘.fix.in.defaults’ ‘.pretreat’ ‘.check.eps’
  ‘.isOKsteps’ ‘.isOKfsCor’

Documented arguments not in \usage in Rd file 'internal_Cniperplots.Rd':
  ‘origCl’

Objects in \usage without \alias in Rd file 'internals.Rd':
  ‘.isVirginW’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘ROptEst-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RMXEOMSEMBREOBRE
> ### Title: Optimally robust estimation: RMXE, OMSE, MBRE, and OBRE
> ### Aliases: RMXEstimator OMSEstimator OBREstimator MBREstimator
> ### Keywords: robust
> 
> ### ** Examples
> 
> #############################
> ## 1. Binomial data
> #############################
> ## generate a sample of contaminated data
> set.seed(123)
> ind <- rbinom(100, size=1, prob=0.05)
> x <- rbinom(100, size=25, prob=(1-ind)*0.25 + ind*0.9)
> 
> ## ML-estimate
> MLE.bin <- MLEstimator(x, BinomFamily(size = 25))
Warning in .local(.Object, ...) : you have to specify slot r at least
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'object' in selecting a method for function 'startPar': unable to find an inherited method for function ‘r’ for signature ‘object = "numeric"’
Calls: MLEstimator ... initialize -> initialize -> .local -> table -> r -> <Anonymous>
Execution halted
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
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                ^
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                       ^
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                                  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) FS.DAAR.heuristic.RST.Rd:20: Lost braces
    20 | code{decision.table}. It usually corresponds to \code{attr(decision.table, "desc.attrs")}.}
       |     ^
checkRd: (-1) RoughSetData.Rd:19: Lost braces; missing escapes or markup?
    19 | \item Diploma: it has the following values: {"MBA", "MSc", "MCE"}.
       |                                             ^
checkRd: (-1) RoughSetData.Rd:20: Lost braces; missing escapes or markup?
    20 | \item Exprience: it has the following values: {"High", "Low", "Medium"}.
       |                                               ^
checkRd: (-1) RoughSetData.Rd:21: Lost braces; missing escapes or markup?
    21 | \item French: it has the following values: {"Yes", "No"}.
       |                                            ^
checkRd: (-1) RoughSetData.Rd:22: Lost braces; missing escapes or markup?
    22 | \item Reference: it has the following values: {"Excellent", "Good", "Neutral"}.
       |                                               ^
checkRd: (-1) RoughSetData.Rd:23: Lost braces; missing escapes or markup?
    23 | \item Decision: it is a decision attribute that contains the following values: {"Accept", "Reject"}.
       |                                                                                ^
checkRd: (-1) RoughSetData.Rd:87: Lost braces; missing escapes or markup?
    87 | \item class: it is nominal decision attribute that has values: {1, 2, 3}.
       |                                                                ^
Invalid package aliases in Rd file 'A.Introduction-RoughSets.Rd':
  ‘A.Introduction-RoughSets-package’
Invalid package aliases in Rd file 'B.Introduction-FuzzyRoughSets.Rd':
  ‘B.Introduction-FuzzyRoughSets-package’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) getAvailablePlotTypes.Rd:30: Lost braces; missing escapes or markup?
    30 | Returns a list if \code{option} is either \code{capnum} or {numcap}
       |                                                            ^
checkRd: (-1) getRawData.Rd:39-41: Lost braces
    39 | if (event == TRUE) {\cr
       |                    ^
checkRd: (-1) getRawData.Rd:41-43: Lost braces
    41 | } else if (dropoutEvent == TRUE) {\cr
       |                                  ^
checkRd: (-1) getRawData.Rd:43-45: Lost braces
    43 | } else {\cr
       |        ^
checkRd: (-1) getSimulationSurvival.Rd:339-341: Lost braces
   339 | if (event == TRUE) {\cr
       |                    ^
checkRd: (-1) getSimulationSurvival.Rd:341-343: Lost braces
   341 | } else if (dropoutEvent == TRUE) {\cr
       |                                  ^
checkRd: (-1) getSimulationSurvival.Rd:343-345: Lost braces
   343 | } else {\cr
       |        ^
checkRd: (-1) readDataset.Rd:22: Lost braces
    22 | \item{...}{Further arguments to be passed to code{\link[utils]{read.table}}.}
       |                                                  ^
Package suggested but not available for checking: ‘RandomFields’
checkRd: (-1) Clyde.Rd:8: Lost braces
     8 | These data record the water quality, in terms of dissolved oxygen (\code{DO}) on a percentage scale, at a number of sampling stations (\code{Station}) on the River Clyde.  The date (\code{Day}, \\code{Month}, \code{Year}) is also available, along with the day of the year (\code{Doy} between 1 and 365) and an identified (\code{id}) of the survey on which each measurement was made.
       |                                                                                                                                                                                                         ^
checkRd: (-1) rp.pos.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:31-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prp.Rd:565: Lost braces
   565 |      The border is by default invisible, see code{split.border.col}.
       |                                                  ^
GNU make is a SystemRequirements.
Found the following significant warnings:
  phylopars_rcpp.cpp:125:26: warning: ‘void arma::set_cerr_stream(const std::ostream&)’ is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  phylopars_rcpp.cpp:144:26: warning: ‘void arma::set_cerr_stream(const std::ostream&)’ is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  phylopars_rcpp.cpp:179:26: warning: ‘void arma::set_cerr_stream(const std::ostream&)’ is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rphylopars.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) simtraits.Rd:7: Lost braces
     7 | Simulates traits for code{phylopars} estimation.
       |                          ^
Argument items with no description in Rd file 'anova.phylopars.lm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'logLik.phylopars.Rd':
  ‘\dots’
Argument items with no description in Rd file 'logLik.phylopars.lm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.SSC.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.phylopars.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.phylopars.lm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.phylopars.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.phylopars.lm.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
checkRd: (-1) rpivotTable.Rd:60: Lost braces; missing escapes or markup?
    60 | An example is: onRefresh=htmlwidgets::JS("function(config) { Shiny.onInputChange('myPivotData', config); }")
       |                                                            ^
checkRd: (-1) plotImage.blcTree.Rd:17: Lost braces
    17 |   \item{method}{Method to determine width of columns that represent classes: \dQuote{weight} (subject weight in class) or dQuote{binary} (depth in tree).}
       |                                                                                                                                 ^
checkRd: (-1) plotImage.glcTree.Rd:16: Lost braces
    16 |   \item{method}{Method to determine width of columns that represent classes: \dQuote{weight} (subject weight in class) or dQuote{binary} (depth in tree).}
       |                                                                                                                                 ^
checkRd: (-1) fauxmatching.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fauxmatching.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fauxmatching.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fauxmatching.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fauxmatching.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpm.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpm.Rd:114-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpm.Rd:116: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpm_MLPLE.Rd:110-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpm_MLPLE.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpm_MLPLE.Rd:114: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary_rpm.Rd:95-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary_rpm.Rd:97-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary_rpm.Rd:99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.poetry.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{output}{Can be any or a combination of the input terms {'author', 'title', 'lines', 'linecount'}. If NULL, all
       |                                                              ^
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  RS-pgsql-copy.c:305:44: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RPostgreSQL.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) rpql.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.tg.Rd:18: Lost braces; missing escapes or markup?
    18 | Renames the \code{class(tg)["name"]} attribute and sets {class(tg)["type"] <- "TextGrid"} (if it is not already set)
       |                                                         ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) psel.Rd:83: Lost braces; missing escapes or markup?
    83 | For example, a \code{top=1} preference selection on the tuples {(a=1, b=1), (a=1, b=2)}
       |                                                                ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) RprobitB_normalization.Rd:85: Lost braces; missing escapes or markup?
    85 | \item For level normalization, {RprobitB} takes utility differences with
       |                                ^
checkRd: (-1) RprobitB_normalization.Rd:87: Lost braces; missing escapes or markup?
    87 | For the ordered model where only one utility is modeled, {RprobitB}
       |                                                          ^
checkRd: (-1) as_cov_names.Rd:22: Lost braces; missing escapes or markup?
    22 | In {RprobitB}, alternative specific covariates must be named in the format
       |    ^
checkRd: (-1) update_s.Rd:30: Lost braces; missing escapes or markup?
    30 | Note that in {RprobitB}, \eqn{\delta_1=\dots=\delta_C}. This restriction is necessary because the class number \eqn{C} can change.
       |              ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) check_node.Rd:11: Lost braces
    11 | \item{x}{\\code{list}, the node to check}
       |                ^
checkRd: (-1) rptBinary.Rd:89: Lost braces
    89 |      Note that the distribution might not be symmetrical, in which case the emph{se} is less informative.}
       |                                                                                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ex.Rd:20: Lost braces
    20 | Execute a ops-dag using `code{wrap()}` data as values.
       |                              ^
checkRd: (-1) sql_node.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{expand_braces}{logical if TRUE use {col} notation to ensure {col} is a column name.}
       |                                          ^
checkRd: (-1) sql_node.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{expand_braces}{logical if TRUE use {col} notation to ensure {col} is a column name.}
       |                                                                   ^
checkRd: (-1) R2_lik.Rd:37: Lost braces; missing escapes or markup?
    37 | \code{R2_lik()} is also computed for LMMs and GLMMs in the {MuMIn} package.
       |                                                            ^
checkRd: (-1) R2_pred.Rd:32: Lost braces; missing escapes or markup?
    32 | Note that the version of \code{binaryPGLMM()} in the package ape is replaced by a version contained within {rr2} that outputs all of the required information for the calculation of R2_resid.
       |                                                                                                            ^
checkRd: (-1) R2_resid.Rd:69: Lost braces; missing escapes or markup?
    69 | Note that the version of \code{binaryPGLMM()} in the package ape is replaced by a version contained within {rr2} that outputs all of the required information for the calculation of \code{R2_resid()}
       |                                                                                                            ^
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
checkRd: (-1) Boost.Rd:40: Lost braces; missing escapes or markup?
    40 | \item{niter}{number of boosting iterations (for RRBoost: T_{1,max} + T_{2,max}) (numeric)}
       |                                                            ^
checkRd: (-1) Boost.Rd:40: Lost braces; missing escapes or markup?
    40 | \item{niter}{number of boosting iterations (for RRBoost: T_{1,max} + T_{2,max}) (numeric)}
       |                                                                        ^
checkRd: (-1) Boost.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{niter}{number of iterations for the boosting algorithm (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                                             ^
checkRd: (-1) Boost.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{niter}{number of iterations for the boosting algorithm (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                                                         ^
checkRd: (-1) Boost.control.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{n_init}{number of iterations for the SBoost step of RRBoost ($T_{1,max}$) (int)}
       |                                                                       ^
checkRd: (-1) Boost.validation.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{niter}{number of iterations (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                  ^
checkRd: (-1) Boost.validation.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{niter}{number of iterations (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                              ^
checkRd: (-1) impseq.Rd:29: Lost braces
    29 |     \emph{Computational Biology and Chemistry}, bold{31},  320--327.
       |                                                     ^
checkRd: (-1) impseqrob.Rd:39: Lost braces
    39 |     \emph{Computational Biology and Chemistry}, bold{31},  320--327.
       |                                                     ^
Documented arguments not in \usage in Rd file 'rrcov-utils.Rd':
  ‘tol’ ‘sv’ ‘n’ ‘p’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) rrecsys.Rd:72: Lost braces; missing escapes or markup?
    72 |  The average deviation rating $dev_{ij}$ between co-rated items is defined by:
       |                                    ^
checkRd: (-1) rrecsys.Rd:76: Lost braces; missing escapes or markup?
    76 |  Where $c_{ij}$ is the number of co-ratings between items $i$ and $j$ and $r_{ui}$ is an existing rating for user $u$ on item $i$. The Weighted Slope One takes into account both, information from users who rated the same item and the number of observed ratings.
       |           ^
checkRd: (-1) rrecsys.Rd:76: Lost braces; missing escapes or markup?
    76 |  Where $c_{ij}$ is the number of co-ratings between items $i$ and $j$ and $r_{ui}$ is an existing rating for user $u$ on item $i$. The Weighted Slope One takes into account both, information from users who rated the same item and the number of observed ratings.
       |                                                                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) lateformeeting.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) regrad.Rd:46: Lost braces; missing escapes or markup?
    46 |  \item \code{x-axis} {1st column: The names of the different institutions}
       |                      ^
checkRd: (-1) regrad.Rd:47: Lost braces; missing escapes or markup?
    47 |  \item \code{y-axis} {2nd column: The value to show completeness}
       |                      ^
checkRd: (-1) rrinf_clust.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{clustering}{A \code{List} that specifies a clustering of datapoint indexes {1, ..., n}. See \link{example_clustering} for details.}
       |                                                                                  ^
checkRd: (-1) rrtest_clust.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{clustering}{A \code{List} that specifies a clustering of datapoint indexes {1, ..., n}.
       |                                                                                  ^
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'RNAPlot.Rd':
  ‘seqTF’
Argument items with no description in Rd file 'aptPlotCT.Rd':
  ‘seqTF’
Found the following files/directories:
  ‘test.bpl’ ‘test.cr’ ‘test.ct’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) mrrr.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:69-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:71-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ordinate.Rd:151-153: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ordinate.Rd:154-160: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ordinate.Rd:161-170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairwise.Rd:82-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairwise.Rd:91-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairwise.Rd:98-105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairwise.Rd:106-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairwise.Rd:146: Lost braces
   146 |  In previous versions of pairwise, code{\link{summary.pairwise}} had three 
       |                                        ^
checkRd: (-1) summary.pairwise.Rd:45-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.pairwise.Rd:54-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.pairwise.Rd:61-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.pairwise.Rd:69-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.pairwise.Rd:88: Lost braces
    88 |  In previous versions of pairwise, code{\link{summary.pairwise}} had three 
       |                                        ^
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file '000-LB-.RspDocument.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'RspEvalDirective.Rd':
  ‘attributes’

Documented arguments not in \usage in Rd file 'RspExpression.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'RspIncludeDirective.Rd':
  ‘attributes’

Documented arguments not in \usage in Rd file 'buildNonSweaveVignette.Rd':
  ‘pathname’

Documented arguments not in \usage in Rd file 'buildNonSweaveVignettes.Rd':
  ‘path’ ‘pattern’

Documented arguments not in \usage in Rd file 'exprToCode.RspSourceCodeFactory.Rd':
  ‘expr’

Documented arguments not in \usage in Rd file 'getContent.RspText.Rd':
  ‘unescaped’

Documented arguments not in \usage in Rd file 'toSourceCode.RspSourceCodeFactory.Rd':
  ‘expr’

Documented arguments not in \usage in Rd file 'trim.RspDocument.Rd':
  ‘envir’

Documented arguments not in \usage in Rd file 'writeResponse.RspResponse.Rd':
  ‘collapse’ ‘sep’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) makedata.Rd:35: Lost braces; missing escapes or markup?
    35 |         {e = (1-h)*N(0, ve) + h*N(0, ve.contam)}.}
       |         ^
checkRd: (-1) landslides.Rd:11-21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) landslides.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) landslides.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) landslides.Rd:22-26: Lost braces
    22 | \item \code{dem} {Digital elevation model given as a .Rd grid, i.e. a list
       |                  ^
checkRd: (-1) landslides.Rd:27-28: Lost braces
    27 | \item \code{study_area} {An \code{sf}-object representing the outlines of
       |                         ^
checkRd: (-1) rsaga.get.modules.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rsaga.get.modules.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rsaga.get.modules.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) rSCA.modeling.Rd:61: Lost braces; missing escapes or markup?
    61 | 		a predefined string to specify how the information of leaf nodes will be stored in the map file. A full list of options for mapvalue is: {mean, max, min, median, interval, radius, variation, random}. Default value is "mean". Use "interval" to get an interval bounded by the minimum and maximum values, (i.e., [min, max]). The option of "radius" will output the mean and the radius [i.e., (max - min) / 2] at the same time. Use "variation" to output the mean and the standard deviation. The option of "random" will output the information as an interval like the "interval" option, but it will use a random value within the interval as the predicted value.
       |                                                                                                                                                          ^
'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) remoteDriver-class.Rd:39-40: Lost braces
    39 | browser being used; should be one of {chrome|firefox|htmlunit|
       |                                      ^
checkRd: (-1) remoteDriver-class.Rd:50: Lost braces; missing escapes or markup?
    50 | of {WINDOWS|XP|VISTA|MAC|LINUX|UNIX}. When requesting a new session,
       |    ^
checkRd: (-1) remoteDriver-class.Rd:194-196: Lost braces
   194 |   element, available schemes: {"class name", "css selector",
       |                               ^
checkRd: (-1) webElement-class.Rd:50-52: Lost braces
    50 |     element, available schemes: {"class name", "css selector",
       |                                 ^
checkRd: (-1) webElement-class.Rd:67-69: Lost braces
    67 |     element, available schemes: {"class name", "css selector",
       |                                 ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  model/variables/BehaviorVariable.cpp:990:55: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘siena::Effect*’ [-Wformat=]
  model/variables/BehaviorVariable.cpp:994:54: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘siena::Effect*’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RSiena.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
Documented arguments not in \usage in Rd file 'ApiRequest.Rd':
  ‘report.description’

Documented arguments not in \usage in Rd file 'BuildLineItemSegment.Rd':
  ‘elements’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
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 significant warnings:
  connection.cpp:61:19: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RSQLite.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simpopmlx.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{fim}{the (\emph{string}) Fisher Information Matrix estimated by Monolix. fim={"sa", "lin"} (default="sa")}
       |                                                                                    ^
checkRd: (-1) writeData.Rd:18: Lost braces; missing escapes or markup?
    18 | It must be one of {"\\t", " ", ";", ","}}
       |                   ^
checkRd: (-1) writeData.Rd:21: Lost braces; missing escapes or markup?
    21 | It must be one of {"csv", "txt"}
       |                   ^
checkRd: (-1) rstanarm-datasets.Rd:81: Lost braces; missing escapes or markup?
    81 | \item \code{age} {in years}
       |                  ^
checkRd: (-1) rstanarm-datasets.Rd:82: Lost braces; missing escapes or markup?
    82 | \item \code{albumin} {serum albumin (g/dl)}
       |                      ^
checkRd: (-1) rstanarm-datasets.Rd:83: Lost braces; missing escapes or markup?
    83 | \item \code{logBili} {logarithm of serum bilirubin}
       |                      ^
checkRd: (-1) rstanarm-datasets.Rd:84: Lost braces; missing escapes or markup?
    84 | \item \code{death} {indicator of death at endpoint} 
       |                    ^
checkRd: (-1) rstanarm-datasets.Rd:85-86: Lost braces
    85 | \item \code{futimeYears} {time (in years) between baseline and  
       |                          ^
checkRd: (-1) rstanarm-datasets.Rd:87: Lost braces; missing escapes or markup?
    87 | \item \code{id} {numeric ID unique to each individual}
       |                 ^
checkRd: (-1) rstanarm-datasets.Rd:88: Lost braces; missing escapes or markup?
    88 | \item \code{platelet} {platelet count}
       |                       ^
checkRd: (-1) rstanarm-datasets.Rd:89: Lost braces; missing escapes or markup?
    89 | \item \code{sex} {gender (m = male, f = female)}
       |                  ^
checkRd: (-1) rstanarm-datasets.Rd:90-91: Lost braces
    90 | \item \code{status} {status at endpoint (0 = censored, 
       |                     ^
checkRd: (-1) rstanarm-datasets.Rd:92-93: Lost braces
    92 | \item \code{trt} {binary treatment code (0 = placebo, 1 = 
       |                  ^
checkRd: (-1) rstanarm-datasets.Rd:94-95: Lost braces
    94 | \item \code{year} {time (in years) of the longitudinal measurements,
       |                   ^
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Found the following significant warnings:
  ../inst/include/rstan/io/r_ostream.hpp:48:20: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
  ../inst/include/rstan/io/r_ostream.hpp:71:21: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rstan.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
GNU make is a SystemRequirements.
checkRd: (-1) rstan_create_package.Rd:33: Lost braces; missing escapes or markup?
    33 | \code{TRUE}. If so, a file `R/{pkgname}-package.R`` is added to the package with
       |                               ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) box_m.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) box_m.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) box_m.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) box_m.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wilcox_test.Rd:91: Lost braces; missing escapes or markup?
    91 |  distribution of \code{(u+v)/2}, where \code{u} and {v} are independent, each
       |                                                     ^
checkRd: (-1) ChangeSpout.Rd:22: Lost braces
    22 | 	a new spout. E.g., a new code{data.frame}.
       |                                      ^
checkRd: (-1) Topology.Rd:11: Lost braces
    11 | By passing a spout (dataframe) to this function and storing its return object you can start building a topology for a RStorm stream. See code{\link{RStorm}} for more detailed examples of the use of Topology. The Topology is the most important concept when defining a RStorm stream.
       |                                                                                                                                              ^
Argument items with no description in Rd file 'SetHash.Rd':
  ‘\dots’
Documented arguments not in \usage in Rd file 'calculate.var.np.Rd':
  ‘sone’ ‘szero’ ‘yone’ ‘yzero’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) datasheet.Rd:153-155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) datasheet.Rd:156-157: Lost braces in \itemize; meant \describe ?
checkRd: (-1) datasheet.Rd:158-159: Lost braces in \itemize; meant \describe ?
checkRd: (-1) datasheet.Rd:162: Lost braces in \itemize; meant \describe ?
checkRd: (-1) datasheet.Rd:163-164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) datasheet.Rd:166-167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) datasheet.Rd:169-170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) project.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) project.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) project.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scenario.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scenario.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scenario.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scenario.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scenario.Rd:71-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssimLibrary.Rd:86-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssimLibrary.Rd:88-89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssimLibrary.Rd:90-93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssimLibrary.Rd:94-96: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
export_as_pdf: no visible global function definition for ‘font_lcpi’
Undefined global functions or variables:
  font_lcpi
checkRd: (-1) list_wrap.Rd:30: Lost braces
    30 | anything else {notably including \code{x}} are passed only the relevant
       |               ^
checkRd: (-1) RTDE.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RTDE.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                              ^
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
checkRd: (-1) article.Rd:414: Lost braces
   414 | \verb{https://uk.sagepub.com/sites/default/files/sage_latex_template_4.zip}{class}.
       |                                                                            ^
GNU make is a SystemRequirements.
checkRd: (-1) tw_options.Rd:22: Lost braces in \itemize; meant \describe ?
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) grapes-.-times-grapes.Rd:6-9: Lost braces
     6 | "round.torch.Tensor" <- function(input) {
       |                                         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) rt_GET.Rd:13: Lost braces
    13 | code{\link[httr]{GET}} (\code{TRUE}) or not (\code{FALSE})}
       |     ^
checkRd: (-1) rt_POST.Rd:13: Lost braces
    13 | code{\link[httr]{POST}} (\code{TRUE}) or not (\code{FALSE})}
       |     ^
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  triangle.c:1428:9: warning: too many arguments for format [-Wformat-extra-args]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RTriangle.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) read_vcv.Rd:10: Lost braces
    10 | \item{file}{\\code{[character]} filename}
       |                   ^
Documented arguments not in \usage in Rd file 'summary.trimbatch.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'trim_workhorse.Rd':
  ‘max_beta’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
Found the following significant warnings:
  Rtsne.cpp:21:37: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  Rtsne.cpp:21:42: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  Rtsne.cpp:63:52: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rtsne.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) Rtsne.Rd:133: Lost braces; missing escapes or markup?
   133 | Given a distance matrix \eqn{D} between input objects (which by default, is the euclidean distances between two objects), we calculate a similarity score in the original space p_ij. \deqn{ p_{j | i} = \frac{\exp(-\|D_{ij}\|^2 / 2 \sigma_i^2)}{\sum_{k \neq i} \exp(-\|D_{ij}\|^2 / 2 \sigma_i^2)} } which is then symmetrized using: \deqn{ p_{i j}=\frac{p_{j|i} + p_{i|j}}{2n}.} The \eqn{\sigma} for each object is chosen in such a way that the perplexity of p_{j|i} has a value that is close to the user defined perplexity. This value effectively controls how many nearest neighbours are taken into account when constructing the embedding in the low-dimensional space.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                           ^
checkRd: (-1) rts.Rd:32: Lost braces
    32 | If a name of a raster time series file is provided for the \code{x} argument, it acts the same as code{\link[rts]{read.rts}}.
       |                                                                                                       ^
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘Tsttwalk.dat’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'tidy_pi_traces.Rd':
  ‘mix_indiv_tib’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) starspace.Rd:108: Lost braces; missing escapes or markup?
   108 | \item loss:            loss function {hinge, softmax} [hinge]
       |                                      ^
checkRd: (-1) starspace_dictionary.Rd:15: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) starspace_dictionary.Rd:16: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) starspace_dictionary.Rd:17: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) starspace_dictionary.Rd:18: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) starspace_dictionary.Rd:19: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) starspace_dictionary.Rd:20-21: Lost braces in \enumerate; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) rules.Rd:24: Lost braces; missing escapes or markup?
    24 | \item Absent names are replaced with the 'rule__\\{ind\\}' where \\{ind\\} is the
       |                                                   ^
checkRd: (-1) rules.Rd:24: Lost braces; missing escapes or markup?
    24 | \item Absent names are replaced with the 'rule__\\{ind\\}' where \\{ind\\} is the
       |                                                                    ^
Documented arguments not in \usage in Rd file 'MEM_MIDAS_lr_pred_no_skew.Rd':
  ‘daily_ret’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
S3 methods shown with full name in Rd file 'printHTML.trackinfo.Rd':
  ‘printHTML.trackInfo’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘results’
checkRd: (-1) max_run.Rd:57: Lost braces; missing escapes or markup?
    57 | max {numeric} vector of length equals length of \code{x}.
       |     ^
checkRd: (-1) mean_run.Rd:48: Lost braces; missing escapes or markup?
    48 | mean {numeric} vector of length equals length of \code{x}.
       |      ^
checkRd: (-1) min_run.Rd:57: Lost braces; missing escapes or markup?
    57 | min {numeric} vector of length equals length of \code{x}.
       |     ^
checkRd: (-1) runner.Rd:160-165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runner.Rd:166-172: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runner.Rd:173-182: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runner.Rd:183-194: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'dot-is_datetime_valid.Rd':
  ‘(`character`)’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^
Package which this enhances but not available for checking: ‘glmmADMB’
checkRd: (-1) Valpha.Rd:15: Lost braces; missing escapes or markup?
    15 |   \item{V}{a numeric vector with (i,j) entry: V[i,j] = P(theta_{i} >= theta[alpha_{j}]|data) }
       |                                                                ^
checkRd: (-1) Valpha.Rd:15: Lost braces; missing escapes or markup?
    15 |   \item{V}{a numeric vector with (i,j) entry: V[i,j] = P(theta_{i} >= theta[alpha_{j}]|data) }
       |                                                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gpuR’
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'summary.rv.Rd':
  ‘all.levels’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'matmult.Rd':
  ‘%*%.rv’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) HardThresh.Rd:15: Lost braces; missing escapes or markup?
    15 | \code{x} filtered result (y 1_{|y|>t}).
       |                               ^
checkRd: (-1) SoftThresh.Rd:15: Lost braces; missing escapes or markup?
    15 | \code{x} filtered result (y 1_{|y|>t}).
       |                               ^
checkRd: (-1) dGenWish.Rd:48: Lost braces
    48 |   -df/2*log|L(2*Sigma)L'| -1/2*tr{ (L(2*Sigma)L')^-1 L(-D)L' }
       |                                  ^
checkRd: (-1) get.Q.Rd:9: Lost braces
     9 |   equal to exp{b1*x_1ij + ... + bp*x_pij}, where beta=(b1,b2,...,bp) is
       |               ^
checkRd: (-1) get.Q.Rd:10: Lost braces; missing escapes or markup?
    10 |   a vector of log-conductance values of the covariates {x_kij}.  Each
       |                                                        ^
checkRd: (-1) mcmc.wish.icar.Rd:73: Lost braces; missing escapes or markup?
    73 |   a vector of log-conductance values of the covariates {x_kij}.  Each
       |                                                        ^
Package suggested but not available for checking: ‘rWCVPdata’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'wind.fit_int.Rd':
  ‘X’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Malformed Title field: should not end in a period.
checkRd: (-1) s_crandb_tvdb.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) s_crandb_tvdb.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) s_crandb_tvdb.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) s_crandb_tvdb.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) s_crandb_tvdb.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) s_crandb_tvdb.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) s_crandb_tvdb.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wtss_to_ts.Rd:31: Lost braces; missing escapes or markup?
    31 | This period can be either {"month", "week", "day"}, 
       |                           ^
checkRd: (-1) wtss_to_ts.Rd:32: Lost braces; missing escapes or markup?
    32 | {"months", "weeks", "days"} or
       | ^
checkRd: (-1) wtss_to_ts.Rd:33: Lost braces; missing escapes or markup?
    33 | {12, 52, 365}. This function creates a new time series with the required 
       | ^
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  checkmate_stub.c:44:68: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
  checkmate_stub.c:50:65: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
  checkmate_stub.c:60:65: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
  checkmate_stub.c:65:103: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rxode2random.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) cvPost.Rd:33: Lost braces
    33 | the Cholesky decomposition. This is only used when code{type="invWishart"}}
       |                                                        ^
checkRd: (-1) cvPost.Rd:36: Lost braces
    36 | covariance matrix sample. This is only used when code{type="invWishart"}}
       |                                                      ^
checkRd: (-1) invWR1d.Rd:15: Lost braces
    15 | the Cholesky decomposition. This is only used when code{type="invWishart"}}
       |                                                        ^
checkRd: (-1) rxCompile.Rd:95: Lost braces
    95 | \item \code{dll}{DLL path}
       |                 ^
checkRd: (-1) rxCompile.Rd:96: Lost braces
    96 | \item \code{model}{model specification}
       |                   ^
checkRd: (-1) rxCompile.Rd:97-98: Lost braces
    97 | \item \code{.c}{A function to call C code in the correct context from the DLL
       |                ^
checkRd: (-1) rxCompile.Rd:99-100: Lost braces
    99 | \item \code{.call}{A function to call C code in the correct context from the DLL
       |                   ^
checkRd: (-1) rxCompile.Rd:101: Lost braces
   101 | \item \code{args}{A list of the arguments used to create the rxDll object.}
       |                  ^
checkRd: (-1) rxModelVars.Rd:24: Lost braces
    24 | \item \code{params}{ a character vector of names of the model parameters}
       |                    ^
checkRd: (-1) rxModelVars.Rd:25: Lost braces
    25 | \item \code{lhs}{ a character vector of the names of the model calculated parameters}
       |                 ^
checkRd: (-1) rxModelVars.Rd:26: Lost braces
    26 | \item \code{state}{ a character vector of the compartments in rxode2 object}
       |                   ^
checkRd: (-1) rxModelVars.Rd:27-29: Lost braces
    27 | \item \code{trans}{ a named vector of translated model properties
       |                   ^
checkRd: (-1) rxModelVars.Rd:30-31: Lost braces
    30 | \item \code{md5}{a named vector that gives the digest of the model (\code{file_md5}) and the parsed model
       |                 ^
checkRd: (-1) rxModelVars.Rd:32-34: Lost braces
    32 | \item \code{model}{ a named vector giving the input model (\code{model}),
       |                   ^
checkRd: (-1) plot.eff.ridge.Rd:6: Lost braces
     6 |  emph{Single Interior Knot} at the MSE Optimal m-Extent of Shrinkage. The
       |      ^
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ZigZagLogistic.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                   ^
checkRd: (-1) ZigZagLogistic.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                                 ^
checkRd: (-1) ZigZagLogistic.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{dataY}{Vector of length n containing {0, 1}-valued observations of the dependent variable y.}
       |                                            ^
checkRd: (-1) ciReg.Rd:10: Lost braces
    10 | \item{fit}{an object of class{lm}, i.e. the output from \code{\link{lm}}.}
       |                              ^
Documented arguments not in \usage in Rd file 'LoadDataFile.Rd':
  ‘remapcells’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) s2Data.Rd:33: Lost braces
    33 | \code{TRUE}{ (default) The data is converted to a matrix. Factor variables are automatically coded using \code{\link{model.matrix}}. The data is scaled, and constant columns are removed.}
       |            ^
checkRd: (-1) s2Data.Rd:35: Lost braces
    35 | \code{FALSE}{ Do nothing. Keep in mind that the theoretical framework assumes that \code{xL} is centered. Unless you are absolutely sure, avoid this.}
       |             ^
Argument items with no description in Rd file 'predict.s2netR.Rd':
  ‘...’
Argument items with no description in Rd file 'print_misc.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) plotprofmle.Rd:20: Lost braces
    20 | \item{code{signature(object="profile.mle2")}}{The preferred invocation for these methods.}
       |           ^
checkRd: (-1) plotprofmle.Rd:21: Lost braces
    21 | \item{code{signature(object="mle2")}}{A convenience wrapper that calls \code{profile} on the mle2 object and runs the former method.}
       |           ^
checkRd: (-1) default.saemix.plots.Rd:21-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) default.saemix.plots.Rd:26-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) default.saemix.plots.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) default.saemix.plots.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) default.saemix.plots.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) sim_setup_preconfigured.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:31: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'file_status.Rd':
  ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) sf_get_all_jobs_bulk.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_jobs_bulk.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_query_jobs_bulk.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_query_jobs_bulk.Rd:45-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_query_jobs_bulk.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) valid_metadata_list.Rd:10: Lost braces
    10 | code{list}; contains name and valid inputs for data types
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd file 'SAMM-package.Rd':
  \seealso: ‘~~ Optional links to other man pages, e.g. ~~’
checkRd: (-1) binaryChoice.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:111: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:113: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:114: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
checkRd: (-1) ModelHMMR-class.Rd:37: Lost braces; missing escapes or markup?
    37 |         class {StatHMMR}).
       |               ^
Package suggested but not available for checking: ‘networkTomography’
checkRd: (-1) vcovBS.Rd:123: Lost braces
   123 |   \code{\link[stats]{glm.fit}} instead of code{update}.
       |                                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) santaR_auto_summary.Rd:54: Lost braces; missing escapes or markup?
    54 | A list: \code{result$pval.all} \code{data.frame} of \emph{p}-values, with all variables as rows and different \emph{p}-value corrections as columns. \code{result$pval.summary} \code{data.frame} of number of variables with a \emph{p}-value inferior to a cut-off. Different metric and {p}-value correction as rows, different cut-off (\emph{Inf 0.05}, \emph{Inf 0.01}, \emph{Inf 0.001}) as columns.
       |                                                                                                                                                                                                                                                                                            ^
'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: ‘FitARMA’
Specified C++11: please drop specification unless essential
checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
Argument items with no description in Rd file 'creer_graphe.Rd':
  ‘groupes’
Argument items with no description in Rd file 'fichiers.Rd':
  ‘groupes’
'library' or 'require' call to ‘progress’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) sassy.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sassy.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sassy.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sassy.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sassy.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sassy.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gen.ds.Rd:43-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gen.ds.Rd:50-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gen.ds.Rd:64-65: Lost braces
    64 |    \item{the dependence parameter \code{dep} or the vector of dependence parameters \code{dep}. When missing, these coefficients are obtained from independent standard uniform sampling.
       |         ^
checkRd: (-1) gen.ds.Rd:66: Lost braces
    66 |    \item{the list \code{asy} of asymmetric weights \eqn{\beta_{i,b}} for \eqn{b \in B}  and \eqn{i \in b}. When missing, these coefficients are obtained from independent standard uniform sampling followed by renormalization in order to satisfy the sum-to-one constraints.}
       |         ^
Package suggested but not available for checking: ‘rgdal’
'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) OTC.Rd:42: Lost braces; missing escapes or markup?
    42 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
checkRd: (-1) OTC.Rd:83: Lost braces; missing escapes or markup?
    83 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
checkRd: (-1) OTHist.Rd:29: Lost braces; missing escapes or markup?
    29 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
checkRd: (-1) dOTC.Rd:72: Lost braces; missing escapes or markup?
    72 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) setData.ReducedRankRegressions.Rd:14-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setData.ReducedRankRegressions.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:42-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:45-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:55: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) session_details.Rd:17: Lost braces; missing escapes or markup?
    17 | authenticated file downloads by appending josso={'jossoSessionId'} to the 
       |                                                 ^
Documented arguments not in \usage in Rd file 'item_rm_recursive.Rd':
  ‘sb_id’

Documented arguments not in \usage in Rd file 'session_age.Rd':
  ‘sb_id’ ‘...’

Documented arguments not in \usage in Rd file 'session_expired.Rd':
  ‘sb_id’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages which this enhances but not available for checking:
  'gurobi', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
License stub is invalid DCF.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) shape.constrained.smooth.terms.Rd:11-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:16-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:26-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:35-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shape.constrained.smooth.terms.Rd:69-70: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) getSigmaR.Rd:13-14: Lost braces
    13 |   \item{digits}{digits}{number of decimal places to use when rounding,
       |                        ^
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
checkRd: (-1) get.events.Rd:51: Lost braces
    51 |   code{\link[deSolve]{events}}
       |       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) scatterD3.Rd:209: Lost braces; missing escapes or markup?
   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       | ^
checkRd: (-1) scatterD3.Rd:209: Lost braces
   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       |                                              ^
checkRd: (-1) PermBiclust.beta.ks.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.beta.ks.Rd:30: Lost braces
    30 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
checkRd: (-1) PermBiclust.sigclust.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.sigclust.Rd:33: Lost braces
    33 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
checkRd: (-1) PermBiclust.sigclust_stop.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.sigclust_stop.Rd:36: Lost braces
    36 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) scdensity.Rd:119-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:121-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:124-126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:127-130: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:131-135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:136-138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:139-142: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:143-144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) scdensity.Rd:145-147: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'sceasy', 'SeuratDisk', 'SeuratWrappers'
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_profile.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) schoRsch.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:45: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'plot.Rd':
  ‘plot.discretization’

S3 methods shown with full name in Rd file 'predict.Rd':
  ‘predict.discretization’ ‘predict.reject_infered’

S3 methods shown with full name in Rd file 'summary.Rd':
  ‘summary.discretization’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) reduce_dimensionality.Rd:19: Lost braces
    19 | \item{ndim}{the maximum dimension of the space which the data are to be represented in; must be in {1, 2, \ldots, n-1}.}
       |                                                                                                    ^
checkRd: (-1) ti_scorpius.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{distance_method}{A character string indicating which correlationcoefficient (or covariance) is to be computed. One of "pearson", "spearman" (default), or "cosine". Domain: {spearman, pearson, cosine}. Default: spearman. Format: character.}
       |                                                                                                                                                                                   ^
checkRd: (-1) ti_scorpius.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{smoother}{\code{principal_curve} parameter; choice of smoother. Domain: {smooth_spline, lowess, periodic_lowess}. Default: smooth_spline. Format: character.}
       |                                                                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
checkRd: (-1) scriptloc.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Get location of script in a fashion analagous to ${BASH_SOURCE[0]}}
       |                                                          ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘untitled_consensus_cluster’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmGamPoi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                  ^
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                                         ^
checkRd: (-1) geom_flat_violin.Rd:7: Lost braces
     7 | url{https://gist.github.com/dgrtwo/eb7750e74997891d7c20}
       |    ^
checkRd: (-1) sda.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:24: Lost braces in \itemize; meant \describe ?
Running examples in ‘sdcLog-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sdc_descriptives
> ### Title: Disclosure control for descriptive statistics
> ### Aliases: sdc_descriptives
> 
> ### ** Examples
> 
> sdc_descriptives(
+   data = sdc_descriptives_DT,
+   id_var = "id",
+   val_var = "val_1"
+ )
Error in `[.data.table`(dt, id_na == TRUE, list(value_share_na = value_share),  : 
  'by' or 'keyby' must evaluate to a vector or a list of vectors (where 'list' includes data.table and data.frame which are lists, too)
Calls: sdc_descriptives -> check_dominance -> [ -> [.data.table
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘FAQ.Rmd’ using rmarkdown
--- finished re-building ‘FAQ.Rmd’

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

Quitting from lines 115-116 [descriptives_simple] (intro.Rmd)
Error: processing vignette 'intro.Rmd' failed with diagnostics:
'by' or 'keyby' must evaluate to a vector or a list of vectors (where 'list' includes data.table and data.frame which are lists, too)
--- failed re-building ‘intro.Rmd’

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

Quitting from lines 52-53 [example1_sdc.n_ids] (options.Rmd)
Error: processing vignette 'options.Rmd' failed with diagnostics:
'by' or 'keyby' must evaluate to a vector or a list of vectors (where 'list' includes data.table and data.frame which are lists, too)
--- failed re-building ‘options.Rmd’

SUMMARY: processing the following files failed:
  ‘intro.Rmd’ ‘options.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Suda2.h:772:68: warning: format ‘%f’ expects argument of type ‘double’, but argument 3 has type ‘int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sdcMicro.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) sdc_extabs.Rd:59: Lost braces
    59 | (including ]code{forcelist} variables) that can be used to form tables.}
       |                 ^
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'rgdal', 'rgeos'
Packages suggested but not available for checking: 'maptools', 'rgdal'
Specified C++11: please drop specification unless essential
checkRd: (-1) msdpd.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hyperpar.Rd:17: Lost braces
    17 | \item{c}{denotes the expected range of eqn{f} .}
       |                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) errors.Rd:180: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:181: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:182: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:183: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:184: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:185: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:186: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:187: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:188: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:189: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) errors.Rd:190: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'parse_search_analytics.Rd':
  ‘pn’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'pipe.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) seas.check.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:58: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) seedCCA.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{u}{numeric, maximum number of projections. The default is 10. This is used for \code{type="seed1"}, \code{type="seed2"} and {tyepe="pls"}.}
       |                                                                                                                                   ^
checkRd: (-1) Gmixt_simultanee.Rd:21: Lost braces
    21 | { \\sum{p=1 -> P} log( \\pi{p} f( y{ij} ; \\theta{p} ) ) }
       | ^
checkRd: (-1) Gmixt_simultanee.Rd:21: Lost braces
    21 | { \\sum{p=1 -> P} log( \\pi{p} f( y{ij} ; \\theta{p} ) ) }
       |        ^
checkRd: (-1) Gmixt_simultanee.Rd:21: Lost braces
    21 | { \\sum{p=1 -> P} log( \\pi{p} f( y{ij} ; \\theta{p} ) ) }
       |                            ^
checkRd: (-1) Gmixt_simultanee.Rd:21: Lost braces
    21 | { \\sum{p=1 -> P} log( \\pi{p} f( y{ij} ; \\theta{p} ) ) }
       |                                    ^
checkRd: (-1) Gmixt_simultanee.Rd:21: Lost braces
    21 | { \\sum{p=1 -> P} log( \\pi{p} f( y{ij} ; \\theta{p} ) ) }
       |                                                  ^
checkRd: (-1) segclust2d.Rd:37: Lost braces
    37 | Patin, R., Etienne, M. P., Lebarbier, E., Chamaill{\'e}-Jammes, S., 
       |                                                   ^
Packages suggested but not available for checking: 'spgrass6', 'rgdal'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) SVbound.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{RR_UY_T1}{Input value. The sensitivity parameter RR_{UY|T=1}. Must be
       |                                                           ^
checkRd: (-1) SVbound.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{RR_UY_T0}{Input value. The sensitivity parameter RR_{UY|T=0}. Must be
       |                                                           ^
checkRd: (-1) SVbound.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{RR_SU_T1}{Input value. The sensitivity parameter RR_{SU|T=1}. Must be
       |                                                           ^
checkRd: (-1) SVbound.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{RR_SU_T0}{Input value. The sensitivity parameter RR_{SU|T=0}. Must be
       |                                                           ^
checkRd: (-1) SVbound.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{RR_UY_S1}{Input value. The sensitivity parameter RR_{UY|S=1}. Must be
       |                                                           ^
checkRd: (-1) SVbound.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{RR_TU_S1}{Input value. The sensitivity parameter RR_{TU|S=1}. Must be
       |                                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SEMrun.Rd:57: Lost braces; missing escapes or markup?
    57 | \code{start = 0.1} generally performs well with {-1, 0, 1} weights.}
       |                                                 ^
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) convert2snafu.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) correct.changes.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) textcleaner.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) textcleaner.Rd:100-101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:116: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:119: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:130: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) append.dictionary.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:44-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:89-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:95-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NRW.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NRW.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.compareShiny.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.compareShiny.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.compareShiny.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) information.criteria.Rd:33: Lost braces
    33 | 	\emph{Psychometrika}  bold{52}, 345--370.
       |                                   ^
checkRd: (-1) specifyModel.Rd:49: Lost braces
    49 |     to specifying the ]code{file} argument or reading the model specification from
       |                            ^
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
checkRd: (-1) markupConvert.Rd:16: Lost braces
    16 | \item{table.float}{TRUE if you want insertion of '\\begin{table}'}
       |                                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) PAVranking.Rd:77-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:80-82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:83-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sendmail_options.Rd:32-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:38-39: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) match_dataphy.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_dataphy.Rd:39-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_dataphy.Rd:42-44: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Auto-generated content requiring editing in Rd file 'seqCBS-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Specified C++14: please drop specification unless essential
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                               ^
checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                                                          ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                              ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                                                     ^
Found the following files/directories:
  ‘assocpointpair_result.csv’ ‘foundereffectfinder_result.csv’
  ‘getfreqs_result.csv’ ‘getfreqs_result.png’ ‘orPlot.pdf1_1.pdf’
  ‘orPlot.pdf2_1.pdf’ ‘orPlot.pdf3_1.pdf’ ‘orPlot.pdf4_1.pdf’
  ‘orPlot.pdf5_1.pdf’ ‘orPlot.pdf6_1.pdf’ ‘orPlot.pdf7_1.pdf’
  ‘orPlot.pdf8_1.pdf’ ‘q-values_result.csv’ ‘rewritetuple_result.csv’
  ‘tartan_plot.pdf’ ‘vispair_plot.pdf’ ‘vispairfeat_plot.pdf’
  ‘volcano_plot.pdf’
checkRd: (-1) poisthin.Rd:82-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) poisthin.Rd:84-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) poisthin.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) poisthin.Rd:87-88: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  getzlibsock.c:145:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/seqinr.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'sequential.design.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BPCells’
Packages suggested but not available for checking:
  'BPCells', 'monocle', 'presto'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) kernels.Rd:28: Lost braces; missing escapes or markup?
    28 | \item \code{guassian}: K(z) = (2pi)^{1/2} * exp(-z^2/2)
       |                                     ^
Documented arguments not in \usage in Rd file 'jc_clc_perm_impl.Rd':
  ‘a’

Documented arguments not in \usage in Rd file 'local_g_spt.Rd':
  ‘n_sim’

Documented arguments not in \usage in Rd file 'permute_listw.Rd':
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) spatial_morphers.Rd:112: Lost braces
   112 | geospatial features as object of class code{\link[sf]{sf}} or
       |                                            ^
checkRd: (-1) st_relate.Rd:19: Lost braces; missing escapes or markup?
    19 | In case \code{pattern} is not given, \code{st_relate} returns a dense \code{character} matrix; element [i,j] has nine characters, referring to the DE9-IM relationship between x[i] and y[j], encoded as IxIy,IxBy,IxEy,BxIy,BxBy,BxEy,ExIy,ExBy,ExEy where I refers to interior, B to boundary, and E to exterior, and e.g. BxIy the dimensionality of the intersection of the the boundary of x[i] and the interior of y[j], which is one of {0,1,2,F}, digits denoting dimensionality, F denoting not intersecting. When \code{pattern} is given, a dense logical matrix or sparse index list returned with matches to the given pattern; see \link{st_intersection} for a description of the returned matrix or list. See also \url{https://en.wikipedia.org/wiki/DE-9IM} for further explanation.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                ^
Found the following significant warnings:
  c_functions.c:279:32: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long long int’ [-Wformat=]
  c_functions.c:288:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long long int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SFSI.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
Specified C++11: please drop specification unless essential
checkRd: (-1) st_as_sftime.Rd:71: Lost braces
    71 | remove these columns from code{data.frame}?}
       |                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) bisee.Rd:127: Lost braces
   127 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) hisee.Rd:101: Lost braces
   101 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) isee.Rd:116: Lost braces
   116 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) see.Rd:98: Lost braces
    98 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) sgl_predict.Rd:38-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:40-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:44-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:50-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:52-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:56-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_predict.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:73-84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:79-82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:85-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:87-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:91-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgl_subsampling.Rd:106: Lost braces in \itemize; meant \describe ?
Invalid package aliases in Rd file 'package_sgmodel.Rd':
  ‘package_sgmodel-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) generate_toy_data.Rd:35: Lost braces
    35 | \item{groups}{If item{grouped=TRUE}, the grouping structure is required. Each input variable should have a group id.}
       |                      ^
checkRd: (-1) generate_toy_data.Rd:58: Lost braces
    58 | \item{true_grp_id}{Indices of which groups are non-zero in item{true_beta}.}
       |                                                                ^
checkRd: (-1) predict.sgs.Rd:18: Lost braces
    18 | item{response}{The predicted response. In the logistic case, this represents the predicted class probabilities.}
       |     ^
checkRd: (-1) predict.sgs.Rd:18: Lost braces
    18 | item{response}{The predicted response. In the logistic case, this represents the predicted class probabilities.}
       |               ^
checkRd: (-1) predict.sgs.Rd:19: Lost braces
    19 | item{class}{The predicted class assignments. Only returned if type = "logistic" in the \code{"sgs"} object.}
       |     ^
checkRd: (-1) predict.sgs.Rd:19: Lost braces
    19 | item{class}{The predicted class assignments. Only returned if type = "logistic" in the \code{"sgs"} object.}
       |            ^
checkRd: (-1) calculate_sampsize.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculate_sampsize.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculate_sampsize.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                   ^
checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) changept.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) changept.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) changept.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:32-33: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCOSA’
Package unavailable to check Rd xrefs: ‘rCOSA’
Package suggested but not available for checking: ‘hydromad’
checkRd: (-1) monthlyWB.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) monthlyWB.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) monthlyWB.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) monthlyWB.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) monthlyWB.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) monthlyWB.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) monthlyWB.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) monthlyWB.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) age_corr.Rd:15: Lost braces
    15 | \item{plot}{Should the results be plotted? (/code{TRUE/FALSE})}
       |                                                  ^
checkRd: (-1) age_corr.Rd:17: Lost braces
    17 | \item{agecorrection}{Correct for jumps in age (/code{TRUE}) or
       |                                                     ^
checkRd: (-1) age_corr.Rd:18: Lost braces
    18 | only for starting time (/code{FALSE})}
       |                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) shiftrPrepare.Rd:37: Lost braces
    37 |     See code{\link{shiftrPermBinary}} function and the respective example.
       |             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) shinyalert.Rd:159: Lost braces; missing escapes or markup?
   159 | Modals created with {shinyalert} have a return value when they exit.
       |                     ^
checkRd: (-1) shinyalert.Rd:180: Lost braces; missing escapes or markup?
   180 | For example, using the following {shinyalert} code will result in a modal with
       |                                  ^
checkRd: (-1) useShinyalert.Rd:21: Lost braces; missing escapes or markup?
    21 | The first time a {shinyalert} message is shown, the required scripts are
       |                  ^
checkRd: (-1) useShinyalert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{force}{Set to \code{TRUE} to force pre-loading the {shinyalert} scripts. If
       |                                                          ^
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) js_calls.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pickCheckboxNamesAndLabels.Rd:14: Lost braces
    14 | \item{choices}{link{pickCheckboxInput} choices list.}
       |                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) display.Rd:17: Lost braces; missing escapes or markup?
    17 | div which wraps your message to display it in the {position} corner of your shiny app.
       |                                                   ^
checkRd: (-1) info_value.Rd:15: Lost braces; missing escapes or markup?
    15 | div which wraps rendered value to display it in the {position} corner of your shiny app.
       |                                                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) shinyjs-defunct.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shinyjs-defunct.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shinyjs-defunct.Rd:20: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) store_googledrive.Rd:19: Lost braces; missing escapes or markup?
    19 | See the {gargle} package to manage authentication, and especially
       |         ^
checkRd: (-1) store_googledrive.Rd:20: Lost braces; missing escapes or markup?
    20 | \href{https://gargle.r-lib.org/articles/articles/managing-tokens-securely.html}{this vignette from {gargle} package} to manage the process.
       |                                                                                                    ^
checkRd: (-1) custom-labels.Rd:7: Lost braces; missing escapes or markup?
     7 | \title{Modify {shinymanager} labels to use custom text}
       |               ^
checkRd: (-1) use_language.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Use {shinymanager} labels}
       |            ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘uchardet’
'LazyData' is specified without a 'data' directory
checkRd: (-1) messages.Rd:40: Lost braces
    40 | \item{id}{Reference to link{f7Messages} container.}
       |                            ^
checkRd: (-1) plot_multiclass_obs_pred.Rd:23: Lost braces; missing escapes or markup?
    23 | {tidymodels} results for a multi-class classification model.
       | ^
checkRd: (-1) plot_multiclass_pred_factorcol.Rd:43: Lost braces; missing escapes or markup?
    43 | {tidymodels} results for a multi-class classification model.
       | ^
checkRd: (-1) plot_multiclass_pred_numcol.Rd:43: Lost braces; missing escapes or markup?
    43 | on {tidymodels} results for a multi-class classification model.
       |    ^
checkRd: (-1) plot_numeric_obs_pred.Rd:27: Lost braces; missing escapes or markup?
    27 | {tidymodels} results for a regression model.
       | ^
checkRd: (-1) plot_numeric_res_factorcol.Rd:36: Lost braces; missing escapes or markup?
    36 | {tidymodels} results for a regression model.
       | ^
checkRd: (-1) plot_numeric_res_numcol.Rd:36: Lost braces; missing escapes or markup?
    36 | {tidymodels} results for a regression model.
       | ^
checkRd: (-1) plot_numeric_res_pred.Rd:25: Lost braces; missing escapes or markup?
    25 | {tidymodels} results for a regression model.
       | ^
checkRd: (-1) plot_twoclass_obs_pred.Rd:25: Lost braces; missing escapes or markup?
    25 | {tidymodels} results for a two-class classification model.
       | ^
checkRd: (-1) plot_twoclass_pred_factorcol.Rd:46: Lost braces; missing escapes or markup?
    46 | {tidymodels} results for a two-class classification model.
       | ^
checkRd: (-1) plot_twoclass_pred_numcol.Rd:46: Lost braces; missing escapes or markup?
    46 | on {tidymodels} results for a two-class classification model.
       |    ^
Documented arguments not in \usage in Rd file 'shiny_models.Rd':
  ‘original_data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘uchardet’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) shiny_pivot_table.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:64: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) addValidationSuffix.Rd:13: Lost braces; missing escapes or markup?
    13 | A string `"{tagId}-shinyreforms-validation"`.
       |            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) checkbox.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkbox.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkbox.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiple_checkbox.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiple_checkbox.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiple_checkbox.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_selection_api.Rd:27-70: Lost braces
    27 | if (interactive()) {
       |                    ^
checkRd: (-1) search_selection_api.Rd:33-42: Lost braces
    33 |    ui <- function() {
       |                     ^
checkRd: (-1) search_selection_api.Rd:44-67: Lost braces
    44 |   server <- shinyServer(function(input, output, session) {
       |                                                          ^
checkRd: (-1) search_selection_api.Rd:46-58: Lost braces
    46 |    search_api <- function(gapminder, q) {
       |                                         ^
checkRd: (-1) search_selection_api.Rd:47-49: Lost braces
    47 |      has_matching <- function(field) {
       |                                      ^
checkRd: (-1) text_input.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) text_input.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) text_input.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) text_input.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) text_input.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) text_input.Rd:55: 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:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
checkRd: (-1) add_class.Rd:18: Lost braces; missing escapes or markup?
    18 | Custom function for adding a CSS class used in {shinysurveys}.
       |                                                ^
checkRd: (-1) disable_element.Rd:16: Lost braces; missing escapes or markup?
    16 | Custom function for disabling an HTML element in {shinysurveys}.
       |                                                  ^
checkRd: (-1) enable_element.Rd:16: Lost braces; missing escapes or markup?
    16 | Custom function for disabling an HTML element in {shinysurveys}.
       |                                                  ^
checkRd: (-1) extendInputType.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{extension}{A shiny input type not natively supported by {shinysurveys}. See the examples section for more information.}
       |                                                               ^
checkRd: (-1) getSurveyData.Rd:15: Lost braces; missing escapes or markup?
    15 | default, and the built-in {shinysurveys} userID will be used.}
       |                           ^
checkRd: (-1) radioMatrixInput.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{...}{Additional arguments specific to {shinysurveys} required questions.}
       |                                             ^
checkRd: (-1) remove_class.Rd:18: Lost braces; missing escapes or markup?
    18 | Custom function for removing a CSS class used in {shinysurveys}.
       |                                                  ^
checkRd: (-1) toggle_element.Rd:18: Lost braces; missing escapes or markup?
    18 | Custom function for toggling enable/disable state of HTML element in {shinysurveys}.
       |                                                                      ^
checkRd: (-1) AppDriver.Rd:1087: Lost braces; missing escapes or markup?
  1087 | _snaps/{variant}/{test.md}\verb{, so }variant` must be a single
       |        ^
checkRd: (-1) AppDriver.Rd:1087: Lost braces; missing escapes or markup?
  1087 | _snaps/{variant}/{test.md}\verb{, so }variant` must be a single
       |                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) run_shinytitle_example.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) run_shinytitle_example.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pickerOptions.Rd:81: Lost braces; missing escapes or markup?
    81 | \item{noneResultsText}{The text displayed when a search doesn't return any results. Type: string; Default: 'No results matched {0}'.}
       |                                                                                                                                ^
checkRd: (-1) setBackgroundColor.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{shinydashboard}{Set to \code{TRUE} if in a {shinydasboard} application.}
       |                                                  ^
checkRd: (-1) setBackgroundImage.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{shinydashboard}{Set to \code{TRUE} if in a {shinydasboard} application.}
       |                                                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) MrBayes.Rd:24: Lost braces
    24 | \item{contype}{A character string; the type of consensus tree calculated from the posterior distribution of trees}{either "halfcompat" (majority-rule consensus tree) or "allcombat" (strict consensus tree)}
       |                                                                                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) shutterplot.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.'
       |                       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) pop.dist.Rd:41: Lost braces; missing escapes or markup?
    41 | where \emph{dist(i,j)} represents the distance between populations \emph{i} and \emph{j}, \emph{m} and \emph{n} are the number of sequences in populations \emph{i} and \emph{j}, respectively, and \emph{dist(H_{ki},H_{lj})} is the distance between the \emph{k-th} sequence found in population \emph{i} and the \emph{l-th} sequence found in population \emph{j}. 
       |                                                                                                                                                                                                                  ^
checkRd: (-1) pop.dist.Rd:41: Lost braces; missing escapes or markup?
    41 | where \emph{dist(i,j)} represents the distance between populations \emph{i} and \emph{j}, \emph{m} and \emph{n} are the number of sequences in populations \emph{i} and \emph{j}, respectively, and \emph{dist(H_{ki},H_{lj})} is the distance between the \emph{k-th} sequence found in population \emph{i} and the \emph{l-th} sequence found in population \emph{j}. 
       |                                                                                                                                                                                                                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) drr.Rd:36: Lost braces; missing escapes or markup?
    36 |   \code{drr} {is Rosin - Rammler probability density function}\cr
       |              ^
checkRd: (-1) drr.Rd:37: Lost braces; missing escapes or markup?
    37 |   \code{urr} {is Rosin - Rammler cumulative distribution function (CDF) representing undersize mass fraction}\cr
       |              ^
checkRd: (-1) drr.Rd:38: Lost braces
    38 |   \code{orr} {is Rosin - Rammler complementary CDF representing oversize mass fraction ie. relative remainder on the sieve with the mesh size \code{x}}\cr
       |              ^
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'ggseqlogo', 'qlcMatrix'
Unknown package ‘ggseqlogo’ in Rd xrefs
checkRd: (-1) add_k_mer_state.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) sig.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
Found the following files/directories:
  ‘ExportFigtree1.tre’
checkRd: (-1) siland.Rd:64: Lost braces; missing escapes or markup?
    64 | \item x_{l,i}, local variable l,
       |         ^
checkRd: (-1) siland.Rd:70: Lost braces; missing escapes or markup?
    70 | \item d_{r,i} the distance between the center of pixel r and the observation at site i.
       |         ^
checkRd: (-1) inlandwaters.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_Y_Binary_X.Rd:51: Lost braces
    51 |     \item \code{dist = "binomial"} is drawn from eqn{Bin(XB, XB(1-XB))}
       |                                                     ^
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'estThetaRow.Rd':
  ‘theta’
'LazyData' is specified without a 'data' directory
checkRd: (-1) fptsde1d.Rd:69: Lost braces; missing escapes or markup?
    69 | \code{dfptsde1d} {gives the density estimate of fpt.}
       |                  ^
checkRd: (-1) fptsde1d.Rd:70: Lost braces; missing escapes or markup?
    70 | \code{fptsde1d} {generates random of fpt.}
       |                 ^
checkRd: (-1) fptsde2d.Rd:75: Lost braces; missing escapes or markup?
    75 | \code{dfptsde2d} {gives the kernel density approximation for fpt.}
       |                  ^
checkRd: (-1) fptsde2d.Rd:76: Lost braces; missing escapes or markup?
    76 | \code{fptsde2d} {generates random of fpt.}
       |                 ^
checkRd: (-1) fptsde3d.Rd:77: Lost braces; missing escapes or markup?
    77 | \code{dfptsde3d} {gives the marginal kernel density approximation for fpt.}
       |                  ^
checkRd: (-1) fptsde3d.Rd:78: Lost braces; missing escapes or markup?
    78 | \code{fptsde3d} {generates random of fpt.}
       |                 ^
checkRd: (-1) rsde1d.Rd:54: Lost braces
    54 | \code{dsde1d} {gives the transition density estimate of \code{X(t-s) | X(s)=x0}.}
       |               ^
checkRd: (-1) rsde1d.Rd:55: Lost braces
    55 | \code{rsde1d} {generates random of \code{X(t-s) | X(s)=x0}.}
       |               ^
checkRd: (-1) rsde2d.Rd:46: Lost braces
    46 | \code{dsde2d} {gives the bivariate density approximation for \code{(X(t-s),Y(t-s) | X(s)=x0,Y(s)=y0)}.}
       |               ^
checkRd: (-1) rsde2d.Rd:47: Lost braces
    47 | \code{rsde2d} {generates random of the couple \code{(X(t-s),Y(t-s) | X(s)=x0,Y(s)=y0)}.}
       |               ^
checkRd: (-1) rsde3d.Rd:46: Lost braces
    46 | \code{dsde3d} {gives the trivariate density approximation \code{(X(t-s),Y(t-s),Z(t-s) | X(s)=x0,Y(s)=y0,Z(s)=z0)}.}
       |               ^
checkRd: (-1) rsde3d.Rd:47: Lost braces
    47 | \code{rsde3d} {generates random of the \code{(X(t-s),Y(t-s),Z(t-s) | X(s)=x0,Y(s)=y0,Z(s)=z0)}.}
       |               ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) create_modelDF.Rd:25-38: Lost braces
    25 | convert_xlsx_to_csv<-function(xlsx_file){
       |                                         ^
checkRd: (-1) create_modelDF.Rd:33-36: Lost braces
    33 |   for (i in Sheetnames) {
       |                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  misc/SimInf_clean_raw_events.c:192:66: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
  misc/SimInf_clean_raw_events.c:194:65: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
  misc/SimInf_clean_raw_events.c:196:65: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
  misc/SimInf_clean_raw_events.c:198:65: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
  misc/SimInf_clean_raw_events.c:207:31: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
  misc/SimInf_distance_matrix.c:47:55: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
  misc/SimInf_distance_matrix.c:47:64: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
  misc/SimInf_distance_matrix.c:99:61: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SimInf.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) abc.Rd:102: Lost braces
   102 | argument of type code{SimInf_abc} with the current state of
       |                      ^
checkRd: (-1) continue.Rd:38: Lost braces
    38 | argument of type code{SimInf_abc} with the current state of
       |                      ^
checkRd: (-1) events_SISe3.Rd:25: Lost braces
    25 | 182685), sQuote{Internal transfer} events move individuals between
       |                ^
checkRd: (-1) internal.statistics.one.lm.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) internal.statistics.one.lm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'make_kernel_dist.Rd':
  ‘Umax’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
Packages suggested but not available for checking: 'Rcgmin', 'Rvmmin'
Unknown packages ‘Rvmmin’, ‘Rcgmin’ in Rd xrefs
checkRd: (-1) coxsimSpline.Rd:93: Lost braces; missing escapes or markup?
    93 | {FD(h[i](t)) = (exp(g(x[j]) - g(x[l])) - 1) * 100}
       | ^
checkRd: (-1) simPH.Rd:16-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:20-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:25-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:34-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:50-53: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rgdal', 'rgeos'
Documented arguments not in \usage in Rd file 'interval_labels.Rd':
  ‘format’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'SimplifyStats-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
checkRd: (-1) cross.Rd:11: Lost braces
    11 | \item{x}{\code{\link{Pop-class}} or code{\link{Colony-class}} or \code{\link{MultiColony-class}},
       |                                         ^
Found the following significant warnings:
  calibPop.cpp:198:126: warning: format ‘%g’ expects argument of type ‘double’, but argument 4 has type ‘int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/simPop.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) utility.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) utility.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) utility.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) utility.Rd:30: Lost braces in \itemize; meant \describe ?
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘fg_step_tab_pp’
Invalid package aliases in Rd file 'SimReg-package.Rd':
  ‘SimReg3-package’
Documented arguments not in \usage in Rd file 'sim_founderRVstatus.Rd':
  ‘intro_RV’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) SimDataDist-class.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SimDataDist-class.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) createData.Rd:7: Lost braces
     7 | 	This function can be used to create data from a set of parameters created from \code{\link{draw}}, called a code{paramSet}. This function is used internally to create data, and is available publicly for accessibility and debugging.
       |                                                                                                                         ^
checkRd: (-1) exportData.Rd:7: Lost braces
     7 | 	This function can be used to export data created from a set of parameters created from \code{\link{draw}}, called a code{paramSet}. This function can export data to be analyzed with either Mplus or LISREL.
       |                                                                                                                                 ^
Package suggested but not available for checking: ‘INLA’
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
checkRd: (-1) make_one_dataset.Rd:67: Lost braces; missing escapes or markup?
    67 |  \code{within.SD} to be extremely small (e.g., $1 * 10^{-7}$) and all corresponding correlations in matrix
       |                                                        ^
checkRd: (-1) add_bold.Rd:15: Lost braces; missing escapes or markup?
    15 | For example, in latex it would take "2" and output "{\\bf 2}"; in html
       |                                                     ^
checkRd: (-1) NAP.Rd:109: Lost braces
   109 | bounds for P{X<Y}, based on two independent samples. \emph{The Annals of
       |             ^
Specified C++11: please drop specification unless essential
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) noharm.sirt.Rd:263: Lost braces; missing escapes or markup?
   263 | is available as freeware ({http://noharm.niagararesearch.ca/};
       |                           ^
checkRd: (-1) person.parameter.rasch.copula.Rd:22: Lost braces
    22 | Object which is generated by the code{rasch.copula2} function.
       |                                      ^
checkRd: (-1) rasch.jml.jackknife1.Rd:32: Lost braces; missing escapes or markup?
    32 |             \item \code{b.JML}: {Item difficulty from JML estimation}
       |                                 ^
checkRd: (-1) rasch.jml.jackknife1.Rd:33-34: Lost braces
    33 |             \item \code{b.JMLcorr}: {Item difficulty from JML estimation by
       |                                     ^
checkRd: (-1) rasch.jml.jackknife1.Rd:35: Lost braces; missing escapes or markup?
    35 |             \item \code{b.jack}: {Item difficulty from Jackknife estimation}
       |                                  ^
checkRd: (-1) rasch.jml.jackknife1.Rd:36-39: Lost braces
    36 |             \item \code{b.jackse}: {Standard error of Jackknife estimation
       |                                    ^
checkRd: (-1) rasch.jml.jackknife1.Rd:40-41: Lost braces
    40 |             \item \code{b.JMLse}: {Standard error for item difficulties
       |                                   ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) sitar-package.Rd:27: Lost braces; missing escapes or markup?
    27 | individual curves, adjusted for {abcd} to lie on top of (i.e. be
       |                                 ^
checkRd: (-1) sitar.Rd:110: Lost braces; missing escapes or markup?
   110 | \code{\link{nlme}}) (default {nlmeControl(returnObject = TRUE)}).}
       |                              ^
checkRd: (-1) rawCCD.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{distr.type}{school district type (constructed for illustration purposes; (values={"A", "B", "C", "D"})).}
       |                                                                                          ^
checkRd: (-1) selectMatch.Rd:61: Lost braces; missing escapes or markup?
    61 | \item{replacementUnitsFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "replacementUnits.csv"}
       |                                                                    ^
checkRd: (-1) selectMatch.Rd:63: Lost braces; missing escapes or markup?
    63 | \item{subUnitTableFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "subUnitTable.csv"}
       |                                                                ^
checkRd: (-1) selectMatch.Rd:66: Lost braces; missing escapes or markup?
    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                  ^
checkRd: (-1) selectMatch.Rd:66: Lost braces; missing escapes or markup?
    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                                                                                  ^
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
checkRd: (-1) OU_14.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OU_14.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OU_14.Rd:17: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) grow.dbhinc.hgtinc.Rd:29: Lost braces; missing escapes or markup?
    29 |   {dbh.inc.mm } {DBH increment in mm}
       |   ^
checkRd: (-1) grow.dbhinc.hgtinc.Rd:29: Lost braces; missing escapes or markup?
    29 |   {dbh.inc.mm } {DBH increment in mm}
       |                 ^
checkRd: (-1) grow.dbhinc.hgtinc.Rd:30: Lost braces; missing escapes or markup?
    30 |   {hgt.inc.dm } {Height increment in dm}
       |   ^
checkRd: (-1) grow.dbhinc.hgtinc.Rd:30: Lost braces; missing escapes or markup?
    30 |   {hgt.inc.dm } {Height increment in dm}
       |                 ^
Argument items with no description in Rd file 'management.prob.Rd':
  ‘...’
Argument items with no description in Rd file 'mng.tree.removal.Rd':
  ‘\dots’
Argument items with no description in Rd file 'prep.common.vars.fun.Rd':
  ‘\dots’
Argument items with no description in Rd file 'recr.BBG2008.Rd':
  ‘common.vars’
checkRd: (-1) ss.cc.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ss.ci.Rd:26: Lost braces
    26 | \item{alpha}{The eqn{\\alpha} error used to compute the \eqn{100*(1-\\alpha)\%} confidence interval}
       |                     ^
checkRd: (-1) ss.rr.Rd:84: Lost braces; missing escapes or markup?
    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |     ^
checkRd: (-1) ss.rr.Rd:84: Lost braces; missing escapes or markup?
    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |                 ^
checkRd: (-1) ss.rr.Rd:87: Lost braces; missing escapes or markup?
    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                            ^
checkRd: (-1) ss.rr.Rd:87: Lost braces; missing escapes or markup?
    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                                        ^
checkRd: (-1) alvm.fit.Rd:48: Lost braces
    48 | the basic or na{\" i}ve ALVM, and \code{"homoskedastic"} for the
       |                ^
checkRd: (-1) avm.ci.Rd:51: Lost braces
    51 | interval. \code{"stdnorm"} corresponds to a na{\" i}ve standard normal
       |                                               ^
checkRd: (-1) avm.ci.Rd:163: Lost braces
   163 |    The third is the na{\" i}ve standard normal interval, which takes
       |                       ^
Documented arguments not in \usage in Rd file 'to_shiny_tag.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'calculate_gefficiency.Rd':
  ‘RunMatrix’

Documented arguments not in \usage in Rd file 'constructRunMatrix.Rd':
  ‘Levelvector’

Documented arguments not in \usage in Rd file 'effectpower.Rd':
  ‘X’

Documented arguments not in \usage in Rd file 'gen_momentsmatrix.Rd':
  ‘Levelvector’

Documented arguments not in \usage in Rd file 'generate_noise_block.Rd':
  ‘RunMatrix’

Documented arguments not in \usage in Rd file 'genhypmatrix.Rd':
  ‘Parameters’ ‘Levels’ ‘G’

Documented arguments not in \usage in Rd file 'genparammatrix.Rd':
  ‘Parameters’ ‘Levels’ ‘G’

Documented arguments not in \usage in Rd file 'priorlevels.Rd':
  ‘Levelvector’

Documented arguments not in \usage in Rd file 'reduceRunMatrix.Rd':
  ‘ModelMatrix’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘texPreview’
Unknown package ‘texPreview’ in Rd xrefs
Specified C++11: please drop specification unless essential
checkRd: (-1) outliers.hdts.Rd:44: Lost braces; missing escapes or markup?
    44 |   \item I.cov.rob - The matrix (V'GnV)^{-1} used to compute the statistics to detect the idiosyncratic outliers.
       |                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ex0723.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ex0915.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) ex1515.Rd:4: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘captioner’
checkRd: (-1) nba_team_logo.Rd:22: Lost braces; missing escapes or markup?
    22 | https://i.cdn.turner.com/nba/nba/.element/img/4.0/global/logos/512x512/bg.white/svg/{team_short_name}.svg
       |                                                                                     ^
checkRd: (-1) fit_slim.Rd:24: Lost braces; missing escapes or markup?
    24 | sum(x' V^{-1} (y - x beta)) = 0 as the covariance V tends from V[, , 1] +
       |          ^
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) morsescales.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) morsescales.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) morsescales.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) morsescales.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) morsescales.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bcmds.Rd:111: Lost braces; missing escapes or markup?
   111 | This function minimizes the Box-Cox Stress of Chen & Buja (2013) via gradient descent. This is a ratio metric scaling method. The transformations are not straightforward to interpret but mu is associated with fitted distances in the configuration and lambda with the dissimilarities. Concretely for fitted distances (attraction part) it is BC_{mu+lambda}(d(X)) and for the repulsion part it is delta^lambdaBC_{mu}(d(X)) with BC being the one-parameter Box Cox transformation.
       |                                                                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) bcmds.Rd:111: Lost braces; missing escapes or markup?
   111 | This function minimizes the Box-Cox Stress of Chen & Buja (2013) via gradient descent. This is a ratio metric scaling method. The transformations are not straightforward to interpret but mu is associated with fitted distances in the configuration and lambda with the dissimilarities. Concretely for fitted distances (attraction part) it is BC_{mu+lambda}(d(X)) and for the repulsion part it is delta^lambdaBC_{mu}(d(X)) with BC being the one-parameter Box Cox transformation.
       |                                                                                                                                                                                                                                                                                                                                                                                                                          ^
checkRd: (-1) aggrtab.Rd:14: Lost braces
    14 | \item{d}{A list d{[[j]]} whose elements are vectors of variable names from A defining marginal tables/cubes 
       |                  ^
checkRd: (-1) aggrtab.Rd:24: Lost braces; missing escapes or markup?
    24 | D = {D[[j]]} of marginal tables/cubes of A spesified by the list d = d{[[j]]} generated 
       |     ^
checkRd: (-1) aggrtab.Rd:24: Lost braces
    24 | D = {D[[j]]} of marginal tables/cubes of A spesified by the list d = d{[[j]]} generated 
       |                                                                       ^
checkRd: (-1) makeroundtabs.Rd:31: Lost braces
    31 | \item{d}{A list d{[[j]]} whose elements are vectors of variable names from A defining marginal tables/cubes D
       |                  ^
checkRd: (-1) redcube.Rd:15: Lost braces
    15 | \item{d}{A list d{[[j]]} whose elements are vectors of variable names from A defining marginal tables/cubes D
       |                  ^
Package suggested but not available for checking: ‘gurobi’
Auto-generated content requiring editing in Rd file 'smallstuff-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rgdal’
'LazyData' is specified without a 'data' directory
Unknown package ‘InformationValue’ in Rd xrefs
checkRd: (-1) cities_lon_lat.Rd:6: Lost braces
     6 | A subset of world.cities{maps}. Extracted in order to shink number of dependencies. 
       |                         ^
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
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checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) trlong.Rd:17: Lost braces
    17 |     \item{\code{resp}}{a factor indicating the transport mode choice, and \code{B} denotes taking the bus, code{D} denotes driving one's own vehicle, \code{F} denotes getting a ride with a friend, \code{O} denotes other, and \code{W} denotes walking}
       |                                                                                                                ^
checkRd: (-1) smdi_diagnose.Rd:49: Lost braces; missing escapes or markup?
    49 | \item asmd_{mean/median}: average/median absolute standardized mean difference (and min, max) of patient characteristics between those without (1) and with (0) observed covariate
       |            ^
checkRd: (-1) smdocker_log.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:35-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:19: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                  ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                            ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                          ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                                    ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                              ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                        ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                      ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                                ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) fit_spm.Rd:73: Lost braces; missing escapes or markup?
    73 | algorithm to be used. For details, see {optim}.}
       |                                        ^
checkRd: (-1) fit_spm.Rd:76: Lost braces; missing escapes or markup?
    76 | the optimization algorithm to be used. For details, see {optim}.}
       |                                                         ^
checkRd: (-1) fit_spm.Rd:101: Lost braces; missing escapes or markup?
   101 | the control parameters from the {optim} function through the argument
       |                                 ^
Documented arguments not in \usage in Rd file 'aux_cs.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gauss.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gw.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_mat.Rd':
  ‘mat_list1’ ‘mat_list2’ ‘x’ ‘y’ ‘return_single’

Documented arguments not in \usage in Rd file 'aux_matern.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_pexp.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_spher.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_tapmat.Rd':
  ‘dists’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'SMLE-package.Rd':
  ‘smle-package’
Specified C++11: please drop specification unless essential
checkRd: (-1) SMMA.Rd:115: Lost braces
   115 |  is the empirical explained variance from \cite{Meinshausen and B{u}hlmann, 2015}.  See \cite{Lund et al., 2020} for more details and references.
       |                                                                  ^
checkRd: (-1) SMMA.Rd:170: Lost braces
   170 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
Specified C++11: please drop specification unless essential
checkRd: (-1) estimMk.Rd:44: Lost braces; missing escapes or markup?
    44 | estimMk returns the transition probability matrix of size (S^{k})xS (with S = length(E)) 
       |                                                              ^
Specified C++11: please drop specification unless essential
checkRd: (-1) getKernel.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getKernel.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
Found the following significant warnings:
  glog.cpp:151:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  glog.cpp:253:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  glog.cpp:286:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  glog.cpp:320:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  glog.cpp:369:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smog.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'smoke-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
checkRd: (-1) getGlobalOptimum.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smoof_function.Rd:10: Lost braces
    10 | or code{smoof_multi_objective_function}. Both single- and multi-objective functions share the following attributes.
       |        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) hoods2dsmooth.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dmeitsjer.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dsmooth.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) smoothie-package.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) cma.Rd:53: Lost braces; missing escapes or markup?
    53 | phi_i = {0.5,1,1,...,0.5} / order
       |         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) smoothtail-package.Rd:63: Lost braces
    63 | Kaspar Ru{f}{i}bach (maintainer), \email{kaspar.rufibach@gmail.com} , \cr \url{http://www.kasparrufibach.ch}
       |          ^
checkRd: (-1) smoothtail-package.Rd:63: Lost braces
    63 | Kaspar Ru{f}{i}bach (maintainer), \email{kaspar.rufibach@gmail.com} , \cr \url{http://www.kasparrufibach.ch}
       |             ^
Problems with news in ‘NEWS.md’:
No news entries found.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
Auto-generated content requiring editing in Rd file 'smotefamily-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Found the following files/directories:
  ‘my_new_social_media_plot.png’
checkRd: (-1) sm.rm.Rd:50-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sm.rm.Rd:55-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sm.rm.Rd:60-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sm.rm.Rd:64-67: Lost braces in \itemize; meant \describe ?
Objects in \usage without \alias in Rd file 'sm-internal.Rd':
  ‘sm.check.data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) SnakesAndLaddersGame.Rd:25: Lost braces; missing escapes or markup?
    25 | {Hector Haffenden} {haffendenh@cardiff.ac.uk}
       |                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                  ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                           ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                                      ^
checkRd: (-1) sk_GLS.Rd:40: Lost braces; missing escapes or markup?
    40 | Operations with V^{-1} are computed using the factorization \code{fac} (see \code{sk_var}), or
       |                   ^
checkRd: (-1) sk_LL.Rd:37: Lost braces; missing escapes or markup?
    37 | \code{quad_form} is z^T V^{-1} z, for the observed response vector z, which is constructed
       |                           ^
checkRd: (-1) sk_var.Rd:41: Lost braces; missing escapes or markup?
    41 | returns the quadratic form X^T V^{-1} X.
       |                                  ^
checkRd: (-1) sk_var.Rd:33: Lost braces; missing escapes or markup?
    33 | either matrix \code{V}, or X^T V^{-1} X, or a factorization ('chol' or 'eigen')
       |                                  ^
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) knockoffGenotypes.Rd:32: Lost braces; missing escapes or markup?
    32 | This function efficiently constructs group-knockoffs of {0,1,2} variables distributed
       |                                                         ^
checkRd: (-1) knockoffGenotypes.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{X}{a {0,1,2} matrix of size n-by-p containing the original variables.}
       |            ^
checkRd: (-1) knockoffGenotypes.Rd:29: Lost braces; missing escapes or markup?
    29 | A {0,1,2} matrix of size n-by-p containing the knockoff variables.
       |   ^
checkRd: (-1) maize.line.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maize.line.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maize.line.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maize.line.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) raw.data.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{call.rate}{\code{numeric}. Threshold for removing marker by missing genotype rate. SNP with \code{call rate} below threshold are removed from dataset. Must be between {0, 1}}
       |                                                                                                                                                                              ^
checkRd: (-1) raw.data.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{maf}{Threshold for removing SNP by minor allele frequency. Must be between {0, 1}}
       |                                                                                  ^
checkRd: (-1) plot.selm.Rd:101: Lost braces
   101 | data. Default value for code{which} is \code{2:4} if \code{p>1}, otherwise
       |                             ^
Found the following calls to attach():
File ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘.R_Test’
'LazyData' is specified without a 'data' directory
checkRd: (-1) map.active.Rd:82: Lost braces
    82 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.add.Rd:99: Lost braces
    99 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.csa.mca.Rd:35: Lost braces
    35 | \link{soc.csa}, \link{map.csa.all}, link{map.csa.mca.array}
       |                                         ^
checkRd: (-1) map.ctr.Rd:85: Lost braces
    85 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.ind.Rd:80: Lost braces
    80 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.mod.Rd:82: Lost braces
    82 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.sup.Rd:82: Lost braces
    82 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                          ^
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                                                        ^
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                                                                     ^
checkRd: (-1) s_soda_pred.Rd:8: Lost braces; missing escapes or markup?
     8 | S-SODA assumes within each slice the X vector follow multivariate normal distribution. This function predicts the response y by reverting the P(X | slice(y)) to P(slice(y) | X), and estimates the E(y|X) as sum_{h} E(y | slice(y)=h, X) P (slice(y)=h | X)
       |                                                                                                                                                                                                                   ^
checkRd: (-1) db_compact.Rd:41: Lost braces; missing escapes or markup?
    41 | database structure will be set to true. See GET /{db}. You can also obtain a list of
       |                                                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) solr_mlt.Rd:70: Lost braces; missing escapes or markup?
    70 | TermVector DEFAULT_FIELD_NAMES = new String[] {"contents"}
       |                                               ^
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.solveEnv’
checkRd: (-1) solve_pH_from_AT.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) superClass.Rd:92-93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) superClass.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) superClass.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trainSOM.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trainSOM.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trainSOM.Rd:42-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trainSOM.Rd:45-47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trainSOM.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trainSOM.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'som.nn.do.train.Rd':
  ‘model’

Documented arguments not in \usage in Rd file 'som.nn.som.internal.Rd':
  ‘rlen’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'plot.predictions.Rd':
  ‘plot.predictions’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.som.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) som.Rd:128: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
checkRd: (-1) spe.Rd:101: Lost braces
   101 | code{spe} command; (4) \code{alpha} stores significance level as in
       |     ^
checkRd: (-1) load_sorvi_data.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findFn.Rd:101-102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:103-109: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:110-116: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:117-120: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:121-124: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:126-130: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:131-133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:134-137: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:144-150: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:151-157: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:158-161: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findFn.Rd:162: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'path2name.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
checkRd: (-1) sound.Rd:16: Lost braces
    16 | The replacement form can be used to reset the waveform of a sample object. Here, filenames are not accepted for code{s}.
       |                                                                                                                     ^
checkRd: (-1) stereo.Rd:18: Lost braces
    18 | If the samples have different sample parameters (bits, rate and channels), the command code{\link{fitSampleParameters}} is called to adjust them before the two samples are combined.
       |                                                                                            ^
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
checkRd: (-1) SpaceTimeBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entity_extract.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entity_extract.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entity_extract.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entity_extract.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nounphrase_extract.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nounphrase_extract.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nounphrase_extract.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nounphrase_extract.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘NLMR’
Package suggested but not available for checking: ‘NLMR’
'LazyData' is specified without a 'data' directory
Running examples in ‘spaMM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoregressive
> ### Title: Fitting autoregressive models
> ### Aliases: autoregressive adjacency CAR AR1
> ### Keywords: models spatial ts
> 
> ### ** Examples
> 
> ##### AR1 random effect:
> ts <- data.frame(lh=lh,time=seq(48)) ## using 'lh' data from stats package
> fitme(lh ~ 1 +AR1(1|time), data=ts, method="REML")
Error in if (processed$augZXy_cond && resu > processed$augZXy_env$objective) { : 
  missing value where TRUE/FALSE needed
Calls: fitme ... .safe_opt -> <Anonymous> -> eval_f -> do.call -> HLCor.obj
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sdf_unnest.Rd:20: Lost braces
    20 | \code{a1, a2, a3}, then code{sdf_explode(df, a)} will produce output with each record replicated
       |                             ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) xgboost_classifier.Rd:92: Lost braces; missing escapes or markup?
    92 | \item{tree_method}{The tree construction algorithm used in XGBoost. options: {'auto', 'exact', 'approx'} [default='auto']}
       |                                                                              ^
checkRd: (-1) xgboost_classifier.Rd:100: Lost braces; missing escapes or markup?
   100 | \item{normalize_type}{Parameter of Dart booster. type of normalization algorithm, options: {'tree', 'forest'}. [default="tree"]}
       |                                                                                            ^
checkRd: (-1) xgboost_classifier.Rd:116: Lost braces; missing escapes or markup?
   116 | \item{use_external_memory}{The tree construction algorithm used in XGBoost. options: {'auto', 'exact', 'approx'} [default='auto']}
       |                                                                                      ^
checkRd: (-1) xgboost_regressor.Rd:88: Lost braces; missing escapes or markup?
    88 | \item{tree_method}{The tree construction algorithm used in XGBoost. options: {'auto', 'exact', 'approx'} [default='auto']}
       |                                                                              ^
checkRd: (-1) xgboost_regressor.Rd:96: Lost braces; missing escapes or markup?
    96 | \item{normalize_type}{Parameter of Dart booster. type of normalization algorithm, options: {'tree', 'forest'}. [default="tree"]}
       |                                                                                            ^
checkRd: (-1) xgboost_regressor.Rd:112: Lost braces; missing escapes or markup?
   112 | \item{use_external_memory}{The tree construction algorithm used in XGBoost. options: {'auto', 'exact', 'approx'} [default='auto']}
       |                                                                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) counterfactual_yhat.Rd:47: Lost braces; missing escapes or markup?
    47 | We want the counterfactual Yhat_{g' <- G} |X=x,G=g (or alternatively
       |                                 ^
checkRd: (-1) counterfactual_yhat.Rd:48: Lost braces; missing escapes or markup?
    48 | Yhat_{g' <- G} |G=g).
       |      ^
checkRd: (-1) counterfactual_yhat.Rd:58: Lost braces; missing escapes or markup?
    58 | To estimate Y'=Yhat_{g' <- G} | G=g, we need to
       |                     ^
checkRd: (-1) counterfactual_yhat.Rd:65: Lost braces; missing escapes or markup?
    65 | To estimate Y'=Yhat_{g' <- G} |X=x, G=g, we need to
       |                     ^
checkRd: (-1) counterfactual_yhat.Rd:27: Lost braces; missing escapes or markup?
    27 | indices representing sample(s) from counterfactual  Yhat_{g' <- G} |X=x,G=g
       |                                                          ^
Unknown package ‘sparsebn’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  grad_est.cpp:33:19: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  grad_est.cpp:98:19: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  grad_est.cpp:116:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  grad_est.cpp:133:19: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  grad_est.cpp:160:20: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  hmc4sfa.cpp:45:14: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  test_gamma_pois.cpp:30:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SparseFactorAnalysis.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) plot.sfa.Rd:21-22: Lost braces
    21 | \env{type}{ Either \env{"dim"} or \env{"scatter"}.  Whether to return a summary of dimensionality or scatterplot between two dimensions.
       |           ^
checkRd: (-1) plot.sfa.Rd:24: Lost braces
    24 | \env{main, ylabel, xlabel}{ Main title, y axis label, and x axis label.}
       |                           ^
checkRd: (-1) plot.sfa.Rd:26: Lost braces
    26 | \env{dims.scatter}{ Which two dimensions to plot against each other.}
       |                   ^
checkRd: (-1) plot.sfa.Rd:28: Lost braces
    28 | \env{scatter.by}{ Either \env{row} or \env{col}.  Whether to produce scatterplot of two rows or of two columns.}
       |                 ^
checkRd: (-1) plot.sfa.Rd:30-31: Lost braces
    30 | \env{topbottom}{ Number of points to label at the extreme of each dimension.  Only used for 
       |                ^
checkRd: (-1) summary.sfa.Rd:26-27: Lost braces
    26 | \env{interval}{
       |               ^
checkRd: (-1) summary.sfa.Rd:29: Lost braces
    29 | \env{topbottom}{ A positive integer.  How many observations at the top and bottom of each dimension to print.}
       |                ^
checkRd: (-1) summary.sfa.Rd:31: Lost braces
    31 | \env{print.dims}{ Optional. Additional dimensions besides the first two for which to return the top and bottom \env{topbottom} observations.}
       |                 ^
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
checkRd: (-1) Coord.to.Pointers.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{triangle=TRUE}{Input \code{rows} and {cols} represent lower
       |                                            ^
checkRd: (-1) Coord.to.Pointers.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{triangle=FALSE}{Input \code{rows} and {cols} represent a full
       |                                             ^
checkRd: (-1) cholsolveAQinvAT.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Solve the equation X = AQ^{-1}t(A) under permutations}
       |                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |    ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |             ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                      ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                   ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                            ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                                     ^
checkRd: (-1) lsq.Rd:12-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lsq.Rd:26-27: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.sparsereg.Rd:22-23: Lost braces
    22 | \env{main1, main2, main3}{
       |                          ^
checkRd: (-1) plot.sparsereg.Rd:25-27: Lost braces
    25 | \env{xlabel}{
       |             ^
checkRd: (-1) plot.sparsereg.Rd:29-31: Lost braces
    29 | \env{plot.one}{
       |               ^
checkRd: (-1) summary.sparsereg.Rd:27-29: Lost braces
    27 | \env{interval}{
       |               ^
checkRd: (-1) summary.sparsereg.Rd:31-33: Lost braces
    31 | \env{ci}{
       |         ^
checkRd: (-1) summary.sparsereg.Rd:35-37: Lost braces
    35 | \env{order}{
       |            ^
checkRd: (-1) summary.sparsereg.Rd:39-41: Lost braces
    39 | \env{normal}{
       |             ^
checkRd: (-1) summary.sparsereg.Rd:43-45: Lost braces
    43 | \env{select}{
       |             ^
checkRd: (-1) summary.sparsereg.Rd:47-48: Lost braces
    47 | \env{printit}{
       |              ^
checkRd: (-1) summary.sparsereg.Rd:50-52: Lost braces
    50 | \env{stage}{
       |            ^
checkRd: (-1) elasticNetSEMcv.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) elasticNetSEMcv.Rd:71-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) elasticNetSEMcv.Rd:75-82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) elasticNetSEMcv.Rd:83-92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) elasticNetSEMcv.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) elasticNetSEMcv.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'logit.Rd':
  ‘theta’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SpatialBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SpatialBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SpatialBSS-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SpatialBSS-package.Rd:28: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) distSG.Rd:40: Lost braces; missing escapes or markup?
    40 |   matrix and weight matrix (plus a matrix with {eID} identifiers
       |                                                ^
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'binarizer.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat.linnet', 'spatstat.data', 'spatstat',
  'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'spatstat.model', 'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  nonSpGLM_AMCMC.cpp:251:44: warning: unknown conversion type character ‘\x09’ in format [-Wformat=]
  spPPLM.cpp:543:40: warning: unknown conversion type character ‘\x09’ in format [-Wformat=]
  spPPLM.cpp:545:42: warning: unknown conversion type character ‘\x09’ in format [-Wformat=]
  spPPLM.cpp:547:37: warning: unknown conversion type character ‘\x09’ in format [-Wformat=]
  spPPLM.cpp:549:38: warning: unknown conversion type character ‘\x09’ in format [-Wformat=]
  spPPMvLM.cpp:807:46: warning: unknown conversion type character ‘\x09’ in format [-Wformat=]
  spPPMvLM.cpp:813:48: warning: unknown conversion type character ‘\x09’ in format [-Wformat=]
  spPPMvLM.cpp:818:50: warning: unknown conversion type character ‘\x09’ in format [-Wformat=]
  spPPMvLM.cpp:824:43: warning: unknown conversion type character ‘\x09’ in format [-Wformat=]
  spPPMvLM.cpp:829:44: warning: unknown conversion type character ‘\x09’ in format [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spBayes.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
'LazyData' is specified without a 'data' directory
checkRd: (-1) NEWS.Rd:137: Escaped LaTeX specials: \&
checkRd: (-1) dphat.Rd:25: Lost braces
    25 | These results were heavily used in Krumbholz/Z\"{o}ller (1995) for Shewhart and in Knoth/Steinmetz (2013) for EWMA control charts.
       |                                                 ^
checkRd: (-1) dphat.Rd:38: Lost braces
    38 | W. Krumbholz and A. Z\"{o}ller (1995),
       |                        ^
checkRd: (-1) dphat.Rd:39: Lost braces
    39 | \code{p}-Karten vom Shewhartschen Typ f\"{u}r die messende Pr\"{u}fung,
       |                                          ^
checkRd: (-1) dphat.Rd:39: Lost braces
    39 | \code{p}-Karten vom Shewhartschen Typ f\"{u}r die messende Pr\"{u}fung,
       |                                                                ^
checkRd: (-1) xshewhartrunsrules.arl.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) xshewhartrunsrules.arl.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) xshewhartrunsrules.arl.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) xshewhartrunsrules.arl.Rd:43-44: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘spDataLarge’
Documented arguments not in \usage in Rd file 'hazard.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) findRef.Rd:39: Lost braces
    39 | Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemi\`{e}re F, Verschoren A, Goethals B, Laukens K. (2011) An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics. 2011 Oct 20;12:405.
       |                                                              ^
checkRd: (-1) hClustAlign.Rd:70: Lost braces
    70 | Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemi\`{e}re F, Verschoren A, Goethals B, Laukens K. (2011) An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics. 2011 Oct 20;12:405.
       |                                                              ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'grapes-matches-grapes.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) FitAkdParameters.Rd:23: Lost braces; missing escapes or markup?
    23 |       p(y|ens) = 1 / K * sum {dnorm(y, z.i, s)} \cr
       |                              ^
checkRd: (-1) australia.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) australia.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) australia.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) australia.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) australia.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SpectraInTime-class.Rd:66: Lost braces
    66 | \item{colors}{colorblind friendly palettes are used from the de \code{\link[viridis]{viridis_pal}} choice between code{"A"} (magna),
       |                                                                                                                       ^
checkRd: (-1) SpectraInTime-class.Rd:67: Lost braces
    67 | code{"B"} (inferno),  \code{"C"} (plasma) and \code{"D"} the default viridis color palette}
       |     ^
checkRd: (-1) addPreprocessingStep.Rd:17: Lost braces
    17 | code{\link{SpectraInTime-class}}
       |     ^
checkRd: (-1) baselineCorrect.Rd:24: Lost braces
    24 | \item{degree}{numeric value, degree of the polynomial used only if \code{method} is code{'modpolyfit'}}
       |                                                                                         ^
checkRd: (-1) scatterCorrect.Rd:19: Lost braces
    19 | \item{referenceSpectra}{the reference spectra when not derived from the current data, defaults to code{NULL} when \code{referenceMethod} is used 
       |                                                                                                       ^
checkRd: (-1) spectralIntegration.Rd:19: Lost braces
    19 | \item{smoothingValue}{numeric value between 0 and 1, amount of code{\link[stats]{lowess}}-smoothing,
       |                                                                    ^
Documented arguments not in \usage in Rd file 'changeDevSettings.Rd':
  ‘defaultsSettings’

Documented arguments not in \usage in Rd file 'checkMethod.Rd':
  ‘allowedMethod’

Documented arguments not in \usage in Rd file 'convertListToS4.Rd':
  ‘names’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'i_is_index.Rd':
  ‘max_length’

Documented arguments not in \usage in Rd file 'i_read_asd_spectra.Rd':
  ‘format’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) speech_recompiler.Rd:25: Lost braces; missing escapes or markup?
    25 | The default compilation is that of \ code {speech_build (., compiler = TRUE}).
       |                                           ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.neig’
checkRd: (-1) moment_empirical_var.Rd:15: Lost braces; missing escapes or markup?
    15 | {alpha, alpha_I, beta, gamma}.
       | ^
Objects in \usage without \alias in Rd file 'add_details.Rd':
  ‘\S4method{add_details}{spflow_model}’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
    61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc}, 
       |                                                   ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) adaptIntegrateSpherePolar.Rd:14: Lost braces
    14 | code{adaptIntegrateBallPolar()} will likely miss these abrupt changes and give
       |     ^
Found the following files/directories:
  ‘AlphaGA_3.txt’ ‘AlphaML_3.txt’ ‘BetaGA_3.txt’ ‘BetaML_3.txt’
  ‘Performance_GA_ML_ 3 .pdf’ ‘SPIGA_3Pmon.Pm_St1.pdf’
  ‘SPIGA_3Pmon.Pm_St2.pdf’ ‘SPI_AG_3.txt’ ‘SPI_ML_3.txt’
  ‘SPI_ML_3Pm_St1.pdf’ ‘SPI_ML_3Pm_St2.pdf’ ‘SPI_ML_3Pm_St3.pdf’
  ‘SPI_ML_3Pm_St4.pdf’ ‘SPI_PARAM_3.txt’ ‘SPI_PARAM_3Pm_St1.pdf’
  ‘SPI_PARAM_3Pm_St2.pdf’ ‘SPI_PARAM_3Pm_St3.pdf’
  ‘SPI_PARAM_3Pm_St4.pdf’
Specified C++11: please drop specification unless essential
checkRd: (-1) BVCfit.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BVCfit.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BVCfit.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BVCfit.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BVCfit.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BVCfit.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PimaIndiansDiabetes_long.Rd:14: Escaped LaTeX specials: \^
checkRd: (-1) PimaIndiansDiabetes_wide.Rd:16: Escaped LaTeX specials: \^
checkRd: (-1) cartesian_to_xy.Rd:21: Lost braces; missing escapes or markup?
    21 | in the polar coordinate system, r_k and r_{k+1} are the radius of the two loops at theta + 2*pi*a and theta + 2*pi*(a+1) that below and above the data point,
       |                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) wood_inv_solve.Rd:7: Lost braces; missing escapes or markup?
     7 | using the Woodbury formula. The function \code{mmqn_step} invokes \code{wood_inv_solve} instead of {ddg} if the argument
       |                                                                                                    ^
checkRd: (-1) wood_inv_solve.Rd:26: Lost braces; missing escapes or markup?
    26 | using the Woodbury formula. The function \code{mmqn_step} invokes \code{wood_inv_solve} instead of {ddg} if the argument
       |                                                                                                    ^
Invalid package aliases in Rd file 'split_feasibility.Rd':
  ‘split_feasibility-package’
'LazyData' is specified without a 'data' directory
checkRd: (-1) speedtestdata.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ds_aat.Rd:16: Lost braces
    16 | \doi{10.1111/add.14071}{Boffo et al., 2018}. Participants were presented stimuli from a "test"
       |                        ^
checkRd: (-1) ds_gng.Rd:16: Lost braces
    16 | described in detail in \doi{10.1016/j.tate.2019.102887}{Hedge, Powell, and Sumner (2018)}. 
       |                                                        ^
checkRd: (-1) ds_iat.Rd:19: Lost braces
    19 | \doi{10.1016/j.tate.2019.102887}{Abacioglu and colleagues (2019)}. 
       |                                 ^
checkRd: (-1) ds_rapi.Rd:15: Lost braces
    15 | problems within the last year (\doi{https://doi.org/10.15288/jsa.1989.50.30}{White & Labouvie, 1989}).
       |                                                                             ^
checkRd: (-1) ds_sst.Rd:17: Lost braces
    17 | described in detail in \doi{10.1016/j.tate.2019.102887}{Hedge, Powell, and Sumner (2018)}. 
       |                                                        ^
checkRd: (-1) ds_vpt.Rd:22: Lost braces
    22 | \doi{10.1111/acer.12853}{(Pronk, Deursen, Beraha, Larsen, & Wiers, 2015)}.
       |                         ^
checkRd: (-1) splithalfr.Rd:15: Lost braces
    15 |   \item \code{vignette("rapi_sum")} Sum-score for data of the 23-item version of the Rutgers Alcohol Problem Index (\doi{https://doi.org/10.15288/jsa.1989.50.30}{White & Labouvie, 1989})
       |                                                                                                                                                                  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) softening.optimized.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) softening.optimized.Rd:44: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
Specified C++11: please drop specification unless essential
checkRd: (-1) gbmidwcv.Rd:118: Lost braces
   118 | rfcv{randomForest} and gbm
       |     ^
checkRd: (-1) gbmokgbmidwcv.Rd:108: Lost braces
   108 | variable and anisotropy parameters. see notes vgm{gstat} for details.
       |                                                  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) spnn-package.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spnn-package.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spnn-package.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spnn-package.Rd:18: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'obis_search.Rd':
  ‘scientificname’

Documented arguments not in \usage in Rd file 'spocc_objects.Rd':
  ‘n’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ratings.cpp:9:28: warning: format ‘%p’ expects argument of type ‘void*’, but argument 3 has type ‘SEXP’ {aka ‘SEXPREC*’} [-Wformat=]
  ratings.cpp:9:28: warning: format ‘%p’ expects argument of type ‘void*’, but argument 4 has type ‘Rcpp::NumericVector*’ {aka ‘Rcpp::Vector<14, Rcpp::PreserveStorage>*’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sport.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
Specified C++11: please drop specification unless essential
checkRd: (-1) hockey_goaltenders_restricted_area.Rd:38: Lost braces; missing escapes or markup?
    38 | "has_trapezoid" key in the \code{rink_params} passed to geom_{league}
       |                                                              ^
Documented arguments not in \usage in Rd file 'basketball_center_circle_fill.Rd':
  ‘linethickness’

Documented arguments not in \usage in Rd file 'basketball_free_throw_circle_dash.Rd':
  ‘end_angleThe’

Documented arguments not in \usage in Rd file 'basketball_painted_area.Rd':
  ‘free_throw_lane_boundary_line_thickness’

Documented arguments not in \usage in Rd file 'curling_features_set_colors.Rd':
  ‘sheet’ ‘ring_1’ ‘ring_2’ ‘ring_3’

Documented arguments not in \usage in Rd file 'football_field_border.Rd':
  ‘boundary_thickness’

Documented arguments not in \usage in Rd file 'football_field_border_outline.Rd':
  ‘boundary_thickness’

Documented arguments not in \usage in Rd file 'hockey_features_set_colors.Rd':
  ‘boards_color’ ‘center_line_color’ ‘blue_line_color’
  ‘goal_line_color’ ‘goalkeepers_restricted_area_color’
  ‘goal_crease_outline_color’ ‘goal_crease_fill_color’
  ‘referee_crease_color’ ‘center_faceoff_spot_color’
  ‘faceoff_spot_outer_ring_color’ ‘faceoff_spot_fill_color’
  ‘center_faceoff_circle_color’ ‘non_center_faceoff_circle_color’
  ‘faceoff_line_color’ ‘goal_color’ ‘goal_fill_color’

Documented arguments not in \usage in Rd file 'lacrosse_off_field_officials_box.Rd':
  ‘feature_thickness’

Documented arguments not in \usage in Rd file 'lacrosse_penalty_box_outline.Rd':
  ‘feature_thickness’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_my_currently_playing.Rd:15: Lost braces
    15 | href{https://developer.spotify.com/documentation/general/guides/track-relinking-guide/}{Track Relinking}}
       |     ^
checkRd: (-1) get_my_currently_playing.Rd:15: Lost braces
    15 | href{https://developer.spotify.com/documentation/general/guides/track-relinking-guide/}{Track Relinking}}
       |                                                                                        ^
Documented arguments not in \usage in Rd file 'checkFunEvalsDesignSize.Rd':
  ‘fun’ ‘upper’

Documented arguments not in \usage in Rd file 'print.spotBOModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotGaussianProcessModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotLOESS.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotLassoModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotLinearModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotRSM.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotRandomForest.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotRanger.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotSeverity.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotTreeModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'simulationSpectral.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Specified C++11: please drop specification unless essential
checkRd: (-1) shpdata1.Rd:7: Lost braces
     7 | \format{An object of class /code{"list"}.}
       |                                 ^
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
checkRd: (-1) sncFun.01110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-C1 in insertRef{Streck.2020}{spsh} using eq 21 which can be used
       |                                            ^
checkRd: (-1) sncFun.01110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-C1 in insertRef{Streck.2020}{spsh} using eq 21 which can be used
       |                                                         ^
checkRd: (-1) sncFun.02110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-B in insertRef{Streck.2020}{spsh}
       |                                           ^
checkRd: (-1) sncFun.02110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-B in insertRef{Streck.2020}{spsh}
       |                                                        ^
checkRd: (-1) sncFun.04110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-A  in insertRef{Streck.2020}{spsh}
       |                                            ^
checkRd: (-1) sncFun.04110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-A  in insertRef{Streck.2020}{spsh}
       |                                                         ^
checkRd: (-1) impactspsur.Rd:42: Lost braces; missing escapes or markup?
    42 | and a matching \code{Qres} list attribute if {Q} was given.
       |                                              ^
checkRd: (-1) spsur3sls.Rd:158: Lost braces; missing escapes or markup?
   158 |   the matrix of regressors, of order \emph{(Nxp_{g})}. Moreover, 
       |                                                 ^
checkRd: (-1) spsurgs3sls.Rd:67: Lost braces; missing escapes or markup?
    67 | \item{het}{default {FALSE}: if {TRUE} uses the methods 
       |                    ^
checkRd: (-1) spsurgs3sls.Rd:67: Lost braces; missing escapes or markup?
    67 | \item{het}{default {FALSE}: if {TRUE} uses the methods 
       |                                ^
checkRd: (-1) power_dsgn.Rd:138-139: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) spsOption.Rd:29: Lost braces; missing escapes or markup?
    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                   ^
checkRd: (-1) spsOption.Rd:29: Lost braces; missing escapes or markup?
    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                              ^
checkRd: (-1) spsOption.Rd:29: Lost braces; missing escapes or markup?
    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                                             ^
checkRd: (-1) predict.spT.Rd:36: Lost braces
    36 | \item{...}{Other values "obsData", "fittedData" and "residuals" are provided only for temporal prediction. This is to analyse the code{spTimer} forecast output using package \code{forecast} through function \code{\link{as.forecast.object}}.}
       |                                                                                                                                       ^
Argument items with no description in Rd file 'sim.kong.Rd':
  ‘gamma’ ‘beta’ ‘design’ ‘rho’ ‘seed’ ‘impute’ ‘ppi’
'LazyData' is specified without a 'data' directory
checkRd: (-1) vol.m3.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vol.m3.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vol.m3.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sqldf.Rd:248: Lost braces
   248 | and code{port} arguments of sqldf.
       |         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{ - a small, positive scalar that determines when iterations 
       |               ^
checkRd: (-1) fpiter.Rd:60-61: Lost braces
    60 |     \code{maxiter}{ - an integer denoting the maximum limit on the number of 
       |                   ^
checkRd: (-1) fpiter.Rd:63-65: Lost braces
    63 |     \code{trace}{ - a logical variable denoting whether some of the intermediate 
       |                 ^
checkRd: (-1) fpiter.Rd:67-70: Lost braces
    67 |     \code{intermed}}{ - a logical variable denoting whether the intermediate 
       |                     ^
checkRd: (-1) squarem.Rd:134: Lost braces
   134 |       along with the corresponding log-likelihood value.  When the code{objfn} is not specified it will return the fixed-point residual instead of the objective function values. 
       |                                                                        ^
checkRd: (-1) squidR.Rd:83: Lost braces; missing escapes or markup?
    83 |   \item \code{X1_sto_shared} (default \code{TRUE}): {logical}; if \code{TRUE}, the stochastic environmental effect included in the environmental effect x1 will be shared between individuals. If \code{FALSE}, each individual will experience a different stochastic environmental effect x1 (i.e. a new stochastic environmental effect is generated for each individual).
       |                                                     ^
Documented arguments not in \usage in Rd file 'sraAutoregTimeseries.Rd':
  ‘logs2’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) plot.SRCS.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:55: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) plot.SRCS.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:77-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:87-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:143-144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:145: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:146-148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:149: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) ssaBSS-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sscor.Rd:33: Lost braces; missing escapes or markup?
    33 | Otherwise, if {pdim=TRUE}, the pxp SSCM is computed, and then from the SSCM an estimator of the correlation matrix, which is done by the function \code{\link{SSCM2Shape}}, see there for details.
       |               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) new.distance.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:35-36: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) new.distance.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:30-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:38-40: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                   ^
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                              ^
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                                      ^
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                                                ^
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'namesMultiple.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) SRanalysis.Rd:100: Lost braces
   100 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
checkRd: (-1) StabilizedRegression.Rd:109: Lost braces
   109 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
'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) stabsel_parameters.Rd:42: Lost braces
    42 |     always use code{"none"}.}
       |                    ^
checkRd: (-1) stabsel_stabsel.Rd:25: Lost braces
    25 |     always use code{"none"}.}
       |                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) stackExample.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stackExample.Rd:11: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'connect-report_mig-method.Rd':
  ‘h’ ‘...’

Documented arguments not in \usage in Rd file 'print-report_mig-method.Rd':
  ‘h’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'which_class.Rd':
  ‘character’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) stamppFst.Rd:20: Lost braces
    20 | \code{Fsts}{a matrix of pairwise Fst values between populations}
       |            ^
checkRd: (-1) stamppFst.Rd:21: Lost braces
    21 | \code{Pvalues}{a matrix of p-values for each of the pairwise Fst values containined in the 'Fsts' matrix}
       |               ^
checkRd: (-1) stamppFst.Rd:22: Lost braces
    22 | \code{Bootstraps}{a dataframe of each Fst value generated during Bootstrapping and the associated confidence intervals}
       |                  ^
Found the following significant warnings:
  include/rstan/io/r_ostream.hpp:49:20: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
  include/rstan/io/r_ostream.hpp:72:21: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
  include/rstan/io/r_ostream.hpp:49: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
  include/rstan/io/r_ostream.hpp:72: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
  stan_sampler.cpp:359: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/stan4bart.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) standardize.Rd:94: Lost braces; missing escapes or markup?
    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                ^
checkRd: (-1) standardize.Rd:94: Lost braces; missing escapes or markup?
    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                                           ^
checkRd: (-1) alertify.Rd:69: Lost braces
    69 | \item{closable}{Logical; if \code{TRUE} (the default), a |code{Close} button is displayed in the header of the dialog.}
       |                                                               ^
checkRd: (-1) notify.Rd:47: Lost braces
    47 | \item{hide}{Logical; if \code{TRUE} (the default), notice is closed after |code{delay} specified in milliseconds.}
       |                                                                                ^
checkRd: (-1) CxxFlags.Rd:27: Lost braces; missing escapes or markup?
    27 |   PKG_CXXFLAGS += $(shell "${R_HOME}/bin/Rscript" -e "StanHeaders:::CxxFlags()")
       |                             ^
checkRd: (-1) CxxFlags.Rd:28: Lost braces; missing escapes or markup?
    28 |   PKG_LDLIBS += $(shell "${R_HOME}/bin/Rscript" -e "StanHeaders:::LdFlags()")
       |                           ^
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_fields.Rd:27: Lost braces
    27 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
checkRd: (-1) identify_form_fields.Rd:34: Lost braces
    34 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
checkRd: (-1) abs_parms.Rd:67: Lost braces; missing escapes or markup?
    67 |    \item $S_{275-295}$ slope between 275 and 295 nm calculated with nonlinear regression
       |             ^
checkRd: (-1) abs_parms.Rd:68: Lost braces; missing escapes or markup?
    68 |    \item $S_{350-400}$ slope between 350 and 400 nm calculated with nonlinear regression
       |             ^
checkRd: (-1) abs_parms.Rd:69: Lost braces; missing escapes or markup?
    69 |    \item $S_{300-700}$ slope between 275 and 295 nm calculated with nonlinear regression
       |             ^
checkRd: (-1) abs_parms.Rd:70: Lost braces; missing escapes or markup?
    70 |    \item SR slope ratio, calculated by $S_{275-295}$/$S_{350-400}$
       |                                           ^
checkRd: (-1) abs_parms.Rd:70: Lost braces; missing escapes or markup?
    70 |    \item SR slope ratio, calculated by $S_{275-295}$/$S_{350-400}$
       |                                                         ^
checkRd: (-1) abs_parms.Rd:71: Lost braces; missing escapes or markup?
    71 |    \item E2:E3 ratio $a_{250}$/$a_{365}$
       |                         ^
checkRd: (-1) abs_parms.Rd:71: Lost braces; missing escapes or markup?
    71 |    \item E2:E3 ratio $a_{250}$/$a_{365}$
       |                                   ^
checkRd: (-1) abs_parms.Rd:72: Lost braces; missing escapes or markup?
    72 |    \item E4:E6 ratio $a_{465}$/$a_{665}$
       |                         ^
checkRd: (-1) abs_parms.Rd:72: Lost braces; missing escapes or markup?
    72 |    \item E4:E6 ratio $a_{465}$/$a_{665}$
       |                                   ^
checkRd: (-1) abs_parms.Rd:73: Lost braces; missing escapes or markup?
    73 |    \item $a_{254}$ absorbance at 254 nm
       |             ^
checkRd: (-1) abs_parms.Rd:74: Lost braces; missing escapes or markup?
    74 |    \item $a_{300}$ absorbance at 300 nm
       |             ^
checkRd: (-1) stargazer.Rd:229: Lost braces
   229 |   \item{report}{a character string containing only elements of {\code{"v"}, \code{"c"}, \code{"s"},\code{"t"}, \code{"p"}, \code{"*"}} that determines whether, and in which order, variable names (\code{"v"}), coefficients (\code{"c"}), standard errors/confidence intervals (\code{"s"}), test statistics (\code{"t"}) and p-values (\code{"p"}) should be reported in regression tables. If one of the aforementioned letters is followed by an asterisk (\code{"*"}), significance stars will be reported next to the corresponding statistic.}
       |                                                                ^
checkRd: (-1) stargazer.Rd:246: Lost braces
   246 |   \item{table.placement}{a character string containing only elements of {\code{"h"}, \code{"t"},\code{"b"}, \code{"p"}, \code{"!"}, \code{"H"}} that determines the table placement in its LaTeX floating environment.}
       |                                                                         ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    To do
checkRd: (-1) normalize_2d.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{The dimensions are spatial, named \code{x} and {y} (in that order).}
       |                                                      ^
checkRd: (-1) normalize_3d.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{The first two dimensions are spatial, named \code{x} and {y} (in that order).}
       |                                                                ^
Package suggested but not available for checking: ‘starsdata’
checkRd: (-1) Start.Rd:654: Lost braces
   654 | chooses the first). Because /code{*} is not the tag, which means it cannot
       |                                  ^
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) AutoPollution.Rd:16: Lost braces
    16 |     \code{Side} \tab {Side of vehicle: code{1}=right or \code{2}=left}\cr
       |                                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) statcan_data.Rd:22: Lost braces; missing escapes or markup?
    22 | \code{statcan_data()} function has 2 arguments to fulfill to get data: {tableNumber} & {lang}.
       |                                                                        ^
checkRd: (-1) statcan_data.Rd:22: Lost braces; missing escapes or markup?
    22 | \code{statcan_data()} function has 2 arguments to fulfill to get data: {tableNumber} & {lang}.
       |                                                                                        ^
checkRd: (-1) statcan_search.Rd:18: Lost braces; missing escapes or markup?
    18 | The \code{statcan_search()} function has 2 arguments to fulfill to find a database: {keywords} and {lang}.
       |                                                                                     ^
checkRd: (-1) statcan_search.Rd:18: Lost braces; missing escapes or markup?
    18 | The \code{statcan_search()} function has 2 arguments to fulfill to find a database: {keywords} and {lang}.
       |                                                                                                    ^
Invalid package aliases in Rd file 'statcheck-package.Rd':
  ‘{statcheck}-package’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘asreml’
checkRd: (-1) gxeFw.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gxeFw.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gxeFw.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gxeFw.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gxeFw.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gxeFw.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gxeFw.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gxeFw.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gxeFw.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gxeFw.Rd:64-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gxeFw.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gxeFw.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘asreml’
checkRd: (-1) plot.IBDprob.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.IBDprob.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.IBDprob.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.IBDprob.Rd:51-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.IBDprob.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.QTLMPP.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.QTLMPP.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.QTLMPP.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.QTLMPP.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.gDataMPP.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.gDataMPP.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.gDataMPP.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.gDataMPP.Rd:45-46: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'estEffsCPP.Rd':
  ‘y’ ‘w’ ‘x’ ‘ncores’

Documented arguments not in \usage in Rd file 'updateFA.Rd':
  ‘Y’ ‘WStart’ ‘m’ ‘PStart’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: ‘networksis’
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp_get_codelist_file.Rd:29: Lost braces; missing escapes or markup?
    29 | finer-grained control of intermediate outputs is needed, e.g. in a {targets} workflow.
       |                                                                    ^
checkRd: (-1) sp_get_codelist_url.Rd:19: Lost braces; missing escapes or markup?
    19 | finer-grained control of intermediate outputs is needed, e.g. in a {targets} workflow.
       |                                                                    ^
checkRd: (-1) sp_get_table_file.Rd:21: Lost braces; missing escapes or markup?
    21 | finer-grained control of intermediate outputs is needed, e.g. in a {targets} workflow.
       |                                                                    ^
checkRd: (-1) sp_load_codelist.Rd:19: Lost braces; missing escapes or markup?
    19 | finer-grained control of intermediate outputs is needed, e.g. in a {targets} workflow.
       |                                                                    ^
checkRd: (-1) sp_load_table.Rd:19: Lost braces; missing escapes or markup?
    19 | finer-grained control of intermediate outputs is needed, e.g. in a {targets} workflow.
       |                                                                    ^
checkRd: (-1) ci.agree.3rater.Rd:13: Lost braces
    13 | f = {\code{[}}f111, f112, f121, f122, f211, f212, f221, f222{\verb{]}}
       |                                                             ^
checkRd: (-1) ci.agree.3rater.Rd:24: Lost braces
    24 | \item G(1,2)-G(1,3): difference in G{1,2} and G{1,3}
       |                                     ^
checkRd: (-1) ci.agree.3rater.Rd:24: Lost braces
    24 | \item G(1,2)-G(1,3): difference in G{1,2} and G{1,3}
       |                                                ^
checkRd: (-1) ci.agree.3rater.Rd:25: Lost braces
    25 | \item G(1,2)-G(2,3): difference in G{1,2} and G{2,3}
       |                                     ^
checkRd: (-1) ci.agree.3rater.Rd:25: Lost braces
    25 | \item G(1,2)-G(2,3): difference in G{1,2} and G{2,3}
       |                                                ^
checkRd: (-1) ci.agree.3rater.Rd:26: Lost braces
    26 | \item G(2,3)-G(1,3): difference in G{2,3} and G{1,3}
       |                                     ^
checkRd: (-1) ci.agree.3rater.Rd:26: Lost braces
    26 | \item G(2,3)-G(1,3): difference in G{2,3} and G{1,3}
       |                                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) sample2indp.pow.Rd:48: Lost braces
    48 | Pooled standard deviation= \code{sp} = sqrt{((n1 - 1) sigma1^2 +(n2 - 1) sigma2^2) / (n1 + n2 - 2)}
       |                                            ^
Package suggested but not available for checking: ‘imputeMissings’
checkRd: (-1) rankSTB.Rd:31: Lost braces; missing escapes or markup?
    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                        ^
checkRd: (-1) rankSTB.Rd:31: Lost braces; missing escapes or markup?
    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                                                                  ^
checkRd: (-1) rankSTB.Rd:31: Lost braces; missing escapes or markup?
    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                                                                      ^
checkRd: (-1) stb.default.Rd:43: Lost braces
    43 | sampling from the standard normal distribution. Another example is defining func=function(n){rchisq(n=n, df=3, ncp=2)}
       |                                                                                             ^
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) keypoints.Rd:35-36: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:37-39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:40-44: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:45-48: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:49-50: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:63-65: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:66-67: Lost braces in \enumerate; meant \describe ?
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) STEPCAM_ABC.Rd:19: Lost braces
    19 |   \code{rows}{ every row corresponds to a different plot or community} \cr
       |              ^
checkRd: (-1) STEPCAM_ABC.Rd:20: Lost braces
    20 |   \code{columns}{ every column corresponds to a different species.} \cr
       |                 ^
checkRd: (-1) STEPCAM_ABC.Rd:25: Lost braces
    25 |   \code{rows}{ every row corresponds to a different species} \cr
       |              ^
checkRd: (-1) STEPCAM_ABC.Rd:26: Lost braces
    26 |   \code{columns}{ the first column contains the name of the species, every consecutive column corresponds to a different trait} \cr
       |                 ^
checkRd: (-1) plotSTEPCAM.Rd:16: Lost braces
    16 |             - \code{DA}{ a vector containing the posterior distribution for the parameter dispersal assembly} \cr
       |                        ^
checkRd: (-1) plotSTEPCAM.Rd:17: Lost braces
    17 |             - \code{HF}{ a vector containing the posterior distribution for the parameter habitat filtering} \cr
       |                        ^
checkRd: (-1) plotSTEPCAM.Rd:18: Lost braces
    18 |             - \code{LS}{ a vector containing the posterior distribution for the parameter limiting similarity} \cr
       |                        ^
checkRd: (-1) tuneParam.Rd:28: Lost braces; missing escapes or markup?
    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
checkRd: (-1) tuneParamCL2.Rd:28: Lost braces; missing escapes or markup?
    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) landmarkMatrixToList.Rd:10: Lost braces
    10 |   \item{semilandmark.pattern}{a regular expression pattern passed to \code{sub()} for identifying and grouping curve points. The default is landmark names ending in one or more numbers. To disable grouping, set to code{''}.}
       |                                                                                                                                                                                                                           ^
checkRd: (-1) docker_config_collection.Rd:11: Lost braces; missing escapes or markup?
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("config")}
       | ^
checkRd: (-1) docker_container.Rd:13: Lost braces
    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_container")}
       | ^
checkRd: (-1) docker_image_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("image")}
       | ^
checkRd: (-1) docker_plugin_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("plugin")}
       | ^
checkRd: (-1) docker_service_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("service")}
       | ^
checkRd: (-1) docker_task.Rd:13: Lost braces
    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_task")}
       | ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Medellin.Rd:8: Lost braces
     8 | This dataset represents the spatio-temporal locations of traffic accidents in an area near the pontifical bolivarian university in Medell\'{i}n (Colombia) during 2016. The entire data were published in the OpenData portal of Medell\'{i}n Town Hall at https://www.medellin.gov.co/geomedellin/index.hyg.
       |                                                                                                                                            ^
checkRd: (-1) Medellin.Rd:8: Lost braces
     8 | This dataset represents the spatio-temporal locations of traffic accidents in an area near the pontifical bolivarian university in Medell\'{i}n (Colombia) during 2016. The entire data were published in the OpenData portal of Medell\'{i}n Town Hall at https://www.medellin.gov.co/geomedellin/index.hyg.
       |                                                                                                                                                                                                                                          ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘corrviz.html’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'd.sum.of.mixtures.EXPLN.Rd':
  ‘p.vector’
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_proposal_votes.Rd:24: Lost braces; missing escapes or markup?
    24 | \item \strong{$proposal_by_parties${proposal_id}} (what parties (id) stood behind proposal(s))
       |                                    ^
checkRd: (-1) geo_toptail.Rd:26: Lost braces; missing escapes or markup?
    26 | in {stplanr} v0.8.5 for an implementation that uses the geosphere
       |    ^
checkRd: (-1) powderymildew.Rd:14-16: Lost braces
    14 | \code{$demographic.coord}{
       |                          ^
checkRd: (-1) powderymildew.Rd:18-20: Lost braces
    18 | \code{$genetic.coord}{
       |                      ^
checkRd: (-1) powderymildew.Rd:22-24: Lost braces
    22 | \code{$demographic.measures}{
       |                             ^
checkRd: (-1) powderymildew.Rd:26-28: Lost braces
    26 | \code{$genetic.frequencies}{
       |                            ^
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'strategicplayers-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
  \references: ‘~~ Literature or other references for background information ~~’
Found the following files/directories:
  ‘myNewStrat.R’
Package suggested but not available for checking: ‘StrathE2E2examples’
checkRd: (-1) StrathE2E2-package.Rd:70: Lost braces; missing escapes or markup?
    70 | {Basic model operations:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:79: Lost braces; missing escapes or markup?
    79 | {Parameter estimation:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:88: Lost braces; missing escapes or markup?
    88 | {Sensitivity and Monte Carlo analyses:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:98: Lost braces; missing escapes or markup?
    98 | {Compare model runs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:105: Lost braces; missing escapes or markup?
   105 | {Fishery yield analysis:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:111: Lost braces; missing escapes or markup?
   111 | {Visualize model inputs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:117: Lost braces; missing escapes or markup?
   117 | {Visualize model outputs:} \cr
       | ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgeos’
Specified C++11: please drop specification unless essential
checkRd: (-1) isle.Rd:38: Lost braces
    38 | \code{\link[streamDAG]{stream.order}}, \code{\link[igraph]{delete.vertices}}, code{\link[igraph]{add.vertices}}, code{\link[igraph]{add.edges}}
       |                                                                                   ^
checkRd: (-1) isle.Rd:38: Lost braces
    38 | \code{\link[streamDAG]{stream.order}}, \code{\link[igraph]{delete.vertices}}, code{\link[igraph]{add.vertices}}, code{\link[igraph]{add.edges}}
       |                                                                                                                      ^
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get_groups.Rd':
  ‘groups’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  stri_messages.h:95:4: warning: '0' flag ignored with precision and ‘%x’ gnu_printf format [-Wformat=]
  stri_messages.h:119:4: warning: '0' flag ignored with precision and ‘%x’ gnu_printf format [-Wformat=]
  stri_messages.h:122:4: warning: '0' flag ignored with precision and ‘%x’ gnu_printf format [-Wformat=]
  stri_messages.h:125:4: warning: '0' flag ignored with precision and ‘%x’ gnu_printf format [-Wformat=]
  stri_messages.h:128:4: warning: '0' flag ignored with precision and ‘%x’ gnu_printf format [-Wformat=]
  stri_messages.h:116:4: warning: '0' flag ignored with precision and ‘%x’ gnu_printf format [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/stringi.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) string_magic.Rd:176: Lost braces; missing escapes or markup?
   176 | each of them. Do you think we can do that? Of course yes: string_magic("hello {upper, ''s, c ? x}"). And that's it.
       |                                                                               ^
checkRd: (-1) string_magic.Rd:186: Lost braces; missing escapes or markup?
   186 | The syntax is always the same: {operations ? expression}, where the operations section
       |                                ^
checkRd: (-1) string_magic.Rd:213: Lost braces; missing escapes or markup?
   213 | expression only begins after it. Ex: "{upper! hi}" leads to " HI" while \code{"{upper ! hi}"}
       |                                       ^
checkRd: (-1) string_magic.Rd:751: Lost braces
   751 | Ex.3: string_magic("I {'can {write} {{what}} I want'}") leads to \code{"I can {write} {{what}} I want"}.
       |                       ^
checkRd: (-1) string_magic.Rd:751: Lost braces; missing escapes or markup?
   751 | Ex.3: string_magic("I {'can {write} {{what}} I want'}") leads to \code{"I can {write} {{what}} I want"}.
       |                             ^
checkRd: (-1) string_magic.Rd:751: Lost braces
   751 | Ex.3: string_magic("I {'can {write} {{what}} I want'}") leads to \code{"I can {write} {{what}} I want"}.
       |                                     ^
checkRd: (-1) string_magic_alias.Rd:98: Lost braces
    98 | if you want the interpolation to be done with "{{}}" (instead of \code{{}}) or if you want the
       |                                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
checkRd: (-1) Grossarl.Rd:53: Lost braces
    53 | \emph{Festschrift 50 Jahre \"{O}sterreichische Statistische Gesellschaft}, 133-146,
       |                              ^
checkRd: (-1) Grossarl.Rd:54: Lost braces
    54 | \"{O}sterreichische Statistische Gesellschaft.
       |   ^
checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) breakpoints.Rd:223: Lost braces
   223 | Zeileis A., Kleiber C., Kr\"{a}mer W., Hornik K. (2003), Testing and Dating of
       |                             ^
checkRd: (-1) efp.Rd:109: Lost braces
   109 | Kr\"{a}mer W., Ploberger W., Alt R. (1988), Testing for structural change in
       |     ^
checkRd: (-1) efp.Rd:119: Lost braces
   119 | Ploberger W., Kr\"{a}mer W. (1992), The CUSUM test with OLS residuals,
       |                   ^
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'StructFDR-package.Rd':
  ‘TreeFDR-package’
checkRd: (-1) calculateStatistics.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{quant}{numeric quantile to calculate {0,1}, default 0.95.}
       |                                            ^
checkRd: (-1) cmss.Rd:21: Lost braces
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                        ^
checkRd: (-1) cmss.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                            ^
checkRd: (-1) cmss.Rd:21: Lost braces
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                        ^
checkRd: (-1) cmss.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                            ^
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'size.penalize.Rd':
  ‘size.penalize’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) subdetect-package.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subdetect-package.Rd:12: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘maptools’
Documented arguments not in \usage in Rd file 'subsamp.Rd':
  ‘x:’ ‘y:’ ‘s:’ ‘m:’ ‘qnum:’ ‘wplot:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) P3C.Rd:18: Lost braces; missing escapes or markup?
    18 |  used for this will be 1.00*10^{-PoissonThreshold}.}
       |                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) fp19.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:12-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) suggests.Rd:14: Lost braces; missing escapes or markup?
    14 | {suggests} aims to make that workflow as minimal and painless as possible,
       | ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) plot.SUMMERproj.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SUMMERproj.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SUMMERproj.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sunburst.Rd:30: Lost braces; missing escapes or markup?
    30 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{csvdata}
       |                                ^
checkRd: (-1) sunburst.Rd:88: Lost braces; missing escapes or markup?
    88 | \item{jsondata}{\code{deprecated} use data argument instead; data in nested d3 JSON hierarchy with `{name:...,  children:[];}`}
       |                                                                                                     ^
checkRd: (-1) sund2b.Rd:22: Lost braces; missing escapes or markup?
    22 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{list}, \code{character},
       |                                ^
Auto-generated content requiring editing in Rd file 'supcluster-package.Rd':
  \references: ‘~~ Literature or other references for background information ~~’
Specified C++11: please drop specification unless essential
checkRd: (-1) plot.supc.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BiclustSet-class.Rd:19: Lost braces
    19 |     \item{\code{Number}:}{code{"numeric"}, number of biclusters in the set}
       |                               ^
checkRd: (-1) plot.Rd:42: Lost braces; missing escapes or markup?
    42 |  \item{color.off}{color code; specifying the color for set(s) which are "{absent}" for an intersection.}
       |                                                                          ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘extraTrees’
checkRd: (-1) SL.bartMachine.Rd:41: Lost braces; missing escapes or markup?
    41 | contained in the interval (y_{min}, y_{max}), based on a normal
       |                              ^
checkRd: (-1) SL.bartMachine.Rd:41: Lost braces; missing escapes or markup?
    41 | contained in the interval (y_{min}, y_{max}), based on a normal
       |                                       ^
checkRd: (-1) SL.cforest.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{cforest {party}}
       |                ^
Unknown package ‘extraTrees’ in Rd xrefs
Package suggested but not available for checking: ‘extraTrees’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'check_package.Rd':
  ‘X’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Specified C++11: please drop specification unless essential
checkRd: (-1) getFittedProbs.Rd:6-8: Lost braces
     6 | getFittedValues <- function(object) {
       |                                     ^
checkRd: (-1) getFittedProbs.Rd:14-16: Lost braces
    14 | getFittedValues <- function(object) {
       |                                     ^
surfaceSimulate : phytransform: no visible global function definition
  for ‘rescale’
Undefined global functions or variables:
  rescale
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) svyquantile.Rd:58: Lost braces; missing escapes or markup?
    58 | quantile interval; \code{"hf1"} to {"hf9"} are weighted analogues of
       |                                    ^
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'
checkRd: (-1) tprob.Rd:138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:141: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:142: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:145: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:146: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘distr6’
checkRd: (-1) set_seed.Rd:19: Lost braces; missing escapes or markup?
    19 | using \link{set.seed} as usual but also in {numpy} and {torch} via {reticulate}.
       |                                            ^
checkRd: (-1) set_seed.Rd:19: Lost braces; missing escapes or markup?
    19 | using \link{set.seed} as usual but also in {numpy} and {torch} via {reticulate}.
       |                                                        ^
checkRd: (-1) set_seed.Rd:19: Lost braces; missing escapes or markup?
    19 | using \link{set.seed} as usual but also in {numpy} and {torch} via {reticulate}.
       |                                                                    ^
Unknown package ‘distr6’ in Rd xrefs
checkRd: (-1) coxph_mpl_dc.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{mpl_h0t}{MPL estimates of the baseline hazard for T, i.e. h_{0T}(x_i)}
       |                                                                   ^
checkRd: (-1) coxph_mpl_dc.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{mpl_h0c}{MPL estimates of the baseline hazard for C, i.e. h_{0C}(x_i)}
       |                                                                   ^
checkRd: (-1) coxph_mpl_dc.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{mpl_H0t}{MPL estimates of the baseline cumulative hazard for T, i.e. H_{0T}(x_i)}
       |                                                                              ^
checkRd: (-1) coxph_mpl_dc.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{mpl_H0c}{MPL estimates of the baseline cumulative hazard for C, i.e. H_{0c}(x_i)}
       |                                                                              ^
checkRd: (-1) coxph_mpl_dc.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{mpl_S0t}{MPL estimates of the baseline survival for T, i.e. S_{0T}(x_i)}
       |                                                                     ^
checkRd: (-1) coxph_mpl_dc.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{mpl_S0c}{MPL estimates of the baseline survival for C, i.e. S_{0C}(x_i)}
       |                                                                     ^
checkRd: (-1) hoel.Rd:14: Lost braces
    14 |     \item{\code{outcome}}{outcome: code{censor}, \code{thymic
       |                                        ^
checkRd: (-1) tmerge.Rd:42-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tmerge.Rd:57: Lost braces
    57 |  \item{newname = cumtdc(y,x, init)}{ Similar to tdc, except that the event
       |       ^
checkRd: (-1) tmerge.Rd:57-60: Lost braces
    57 |  \item{newname = cumtdc(y,x, init)}{ Similar to tdc, except that the event
       |                                    ^
checkRd: (-1) tmerge.Rd:62: Lost braces
    62 |  \item{newname = event(y,x)}{ Mark an event at time y.
       |       ^
checkRd: (-1) tmerge.Rd:62-65: Lost braces
    62 |  \item{newname = event(y,x)}{ Mark an event at time y.
       |                             ^
checkRd: (-1) tmerge.Rd:66: Lost braces
    66 |  \item{newname = cumevent(y,x)}{ Cumulative events}.
       |       ^
checkRd: (-1) tmerge.Rd:66: Lost braces
    66 |  \item{newname = cumevent(y,x)}{ Cumulative events}.
       |                                ^
Specified C++11: please drop specification unless essential
Unknown package ‘survJamda’ in Rd xrefs
checkRd: (-1) fullKernel.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullKernel.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullKernel.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullKernel.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullKernel.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullKernel.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullKernel.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) halfKernel.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) halfKernel.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) halfKernel.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) halfKernel.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) halfKernel.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) halfKernel.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) halfKernel.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lastValue.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lastValue.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lastValue.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lastValue.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nearValue.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nearValue.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nearValue.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nearValue.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) sf.Rd:66: Lost braces; missing escapes or markup?
    66 | A {data.table} which is stored as an attribute of
       |   ^
checkRd: (-1) stackG.Rd:79: Lost braces
    79 | estimating coefficients for the Super Learner, defaults to \code{"method.NNLS"}), code{stratifyCV}
       |                                                                                       ^
checkRd: (-1) stackG.Rd:87: Lost braces
    87 | estimate the survival function of \code{tau - time}. Defaults to code{NULL},
       |                                                                      ^
checkRd: (-1) stackL.Rd:68: Lost braces
    68 | code{stratifyCV} (logical indicating whether to stratify by outcome in \code{SuperLearner}'s cross-validation
       |     ^
checkRd: (-1) stackL.Rd:75: Lost braces
    75 | estimate the survival function of \code{tau - time}. Defaults to code{NULL},
       |                                                                      ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) coxDT.Rd:76: Lost braces; missing escapes or markup?
    76 | The estimation procedure here is performed using coxph {survival} and inserting these estimated
       |                                                        ^
checkRd: (-1) predict.DNFOptim.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.DNFOptim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.DNFOptim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.DNFOptim.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.DNFOptim.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.DNFOptim.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary.DNFOptim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary.DNFOptim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary.DNFOptim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary.DNFOptim.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
'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) koInstall.Rd:24: Lost braces; missing escapes or markup?
    24 | set, svKomodo loads {svSocket}, starts the socket server listening to the
       |                     ^
checkRd: (-1) svKomodo-package.Rd:18: Lost braces; missing escapes or markup?
    18 | Komodo and (2) the present {svKomodo} R package that work hand in hand to
       |                            ^
checkRd: (-1) svKomodo-package.Rd:28: Lost braces; missing escapes or markup?
    28 | Nevertheless, the SciViews-K Komodo addin and the {svKomodo} R package
       |                                                   ^
checkRd: (-1) svKomodo-package.Rd:31: Lost braces; missing escapes or markup?
    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                          ^
checkRd: (-1) svKomodo-package.Rd:31: Lost braces; missing escapes or markup?
    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                                         ^
checkRd: (-1) svKomodo-package.Rd:37: Lost braces; missing escapes or markup?
    37 | Both SciViews-K and {svKomodo} should be considered archived items. I keep
       |                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) svSocket-package.Rd:12: Lost braces; missing escapes or markup?
    12 | The SciViews {svSocket} package provides a stateful, multi-client and
       |              ^
checkRd: (-1) svSocket-package.Rd:16: Lost braces; missing escapes or markup?
    16 | thus, it needs a working version of Tcl/Tk (>= 8.4) and of the {tcltk} R
       |                                                                ^
checkRd: (-1) svSocket-package.Rd:33: Lost braces; missing escapes or markup?
    33 | efficient as, say {Rserver} ({Rserver} exchanges R objects in binary format,
       |                   ^
checkRd: (-1) svSocket-package.Rd:33: Lost braces; missing escapes or markup?
    33 | efficient as, say {Rserver} ({Rserver} exchanges R objects in binary format,
       |                              ^
checkRd: (-1) svSocket-package.Rd:34: Lost braces; missing escapes or markup?
    34 | but {Rserver} is not stateful, clients do not share the same global workspace
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) eff_n.Rd:32: Lost braces; missing escapes or markup?
    32 | \code{\link[survey:surveysummary]{survey::svymean()}} and related functions from the {survey}
       |                                                                                      ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) swDsn.Rd:28: Lost braces
    28 | numeric (scalar or vector): Relative treatment effect upon crossing over from control. Note that this is not the treatment effect (the treatment effect is specified in the call to other functions such as \code{swPwr} or \code{swSim})!  If \code{tx.effect.frac} is set to a scalar with value of 1, the standard SW CRT treatment effect will be presumed. If code{tx.effect.frac} is set to a scalar with a fractional value between 0 and 1, then only the first time point upon crossing over from control will have fractional relative treatment effect; the remaining exposure times will have a relative treatment effect of 1. If a vector of fractional treatment effect is specified, each element of the vector corresponds to the (fractional) treatment effect upon crossing over from control; if the length of the vector is less than total number of exposure times, the remaining time points will have a relative treatment effect value of 1; if the length of the vector is greater than total number of time points after crossing over, not all elements of \code{tx.effect.frac} will be used. The default value is (scalar) 1.
       |                                                                                                                                                                                                                                                                                                                                                                        ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘swephRdata’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  include/reactor.h:176:67: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
  include/reactor.h:176:67: warning: ‘%s’ directive argument is null [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sylcount.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) hyph.support.en.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hyph.support.en.Rd:20: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
checkRd: (-1) kRp.hyphen-methods.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kRp.hyphen-methods.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kRp.hyphen-methods.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kRp.hyphen-methods.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manage.hyph.pat.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manage.hyph.pat.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manage.hyph.pat.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manage.hyph.pat.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elliptical.ts.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{epsilon}{positive convergence tolerance \emph{e}; the iterations converge when |fit - fit_{old}|/|fit| < \emph{e}. Default is \emph{e=1e-04}.}
       |                                                                                                   ^
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rbinding.cpp:964:46: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  rbinding.cpp:964:52: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  rbinding.cpp:975:46: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  rbinding.cpp:975:52: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/symengine.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) coord2dist.Rd:14: Lost braces; missing escapes or markup?
    14 | \code{n} x 4 matrix of coordinates consisting of {lat or y, lon or x} pairs for each each site
       |                                                  ^
Invalid package aliases in Rd file 'syncrng-package.Rd':
  ‘syncrng-package’
checkRd: (-1) create_synthetic_example.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_synthetic_example.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_synthetic_example.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initial_estimates_example.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initial_estimates_example.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initial_estimates_example.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) robCov.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robCov.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robCov.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robCov.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) slice.Rd:28: Lost braces
    28 | before plotting {ex: \code{trans = c(s = "exp", d = "exp")}}/}
       |                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.csv’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'table_params_circle.Rd':
  ‘d’

Documented arguments not in \usage in Rd file 'table_params_rect.Rd':
  ‘d’ ‘scale_breaks’ ‘r_max’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) table_ester.Rd:32: Lost braces; missing escapes or markup?
    32 | inside of curly brackets, i.e., { } . For instance, if estimate = 1.23
       |                                 ^
checkRd: (-1) table_ester.Rd:33: Lost braces; missing escapes or markup?
    33 | and error = 0.45, then \code{form} = "{estimate} ({error})" will return
       |                                       ^
checkRd: (-1) table_ester.Rd:33: Lost braces; missing escapes or markup?
    33 | and error = 0.45, then \code{form} = "{estimate} ({error})" will return
       |                                                   ^
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'plot.prEntries.Rd':
  ‘plot.margin’ ‘sizeAdjust’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) tabmulti.Rd:68: Lost braces
    68 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
checkRd: (-1) tabmulti.svy.Rd:67: Lost braces
    67 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) parse_logs.Rd:38: Lost braces
    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |   ^
checkRd: (-1) parse_logs.Rd:38: Lost braces
    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |                      ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'designMatrices.Rd':
  ‘print.designMatrices’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) SKPar.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) TAQ-functions.Rd:119: Lost braces
   119 | Brownlees, C. T., and Gallo, G. M. (2006). Financial Econometric Analysis at Ultra{--}High Frequency: Data Handling Concerns, \emph{Computational Statistics and Data Analysis} \bold{51}, 2232--2245.
       |                                                                                   ^
checkRd: (-1) TAQ-package.Rd:59: Lost braces
    59 | Brownlees, C. T., and Gallo, G. M. (2006). Financial Econometric Analysis at Ultra{--}High Frequency: Data Handling Concerns, \emph{Computational Statistics and Data Analysis} \bold{51}, 2232--2245.
       |                                                                                   ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) NB-class.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NB-class.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calibration-class.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calibration-class.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calibration-class.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cross_validated-class.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cross_validated-class.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cross_validated-class.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) specify_ode.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) specify_ode.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) specify_ode.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) specify_ode.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) targeted-class.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) targeted-class.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) targeted-class.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) targeted-class.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) targeted-class.Rd:32: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
'LazyData' is specified without a 'data' directory
checkRd: (-1) pDisHoeffInd.Rd:24: Lost braces
    24 | eqn{P(X = u_i)}.}
       |    ^
Documented arguments not in \usage in Rd file 'default_db_ref.Rd':
  ‘name’ ‘url’ ‘desc’ ‘id_regex’

Documented arguments not in \usage in Rd file 'limited_print.Rd':
  ‘trunc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) mean_ci.Rd:24: Lost braces
    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
checkRd: (-1) median_ci.Rd:24: Lost braces
    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
       |                                                                                                                                                                                                                                                                                                                                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
checkRd: (-1) diagram_mds.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{k}{the dimension of the space which the data are to be represented in; must be in {1,2,...,n-1}.}
       |                                                                                         ^
checkRd: (-1) silhouette.Rd:10: Lost braces; missing escapes or markup?
    10 |   The function {silhouette} computes the silhouette function corresponding to a given persistence diagram.
       |                ^
checkRd: (-1) silhouette.Rd:38: Lost braces; missing escapes or markup?
    38 |   The function {silhouette} returns a numeric matrix of with the number of row as the length of \code{tseq} and the number of column as the length of \code{p}. The value at ith row and jth column represents the value of the \code{p[j]}-th power silhouette function evaluated at \code{tseq[i]}.
       |                ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  node_categorical.cpp:46:16: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  node_categorical.cpp:49:19: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  node_categorical.cpp:56:16: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  node_categorical.cpp:59:19: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  node_continuous.cpp:41:16: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  node_continuous.cpp:47:16: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDboost.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
Specified C++11: please drop specification unless essential
checkRd: (-1) teachingApp.Rd:66: Lost braces
    66 | code{link{create_logo}}
       |     ^
checkRd: (-1) teachingApp.Rd:66: Lost braces
    66 | code{link{create_logo}}
       |          ^
checkRd: (-1) teachingApp.Rd:68: Lost braces
    68 | code{link{add_logo}}
       |     ^
checkRd: (-1) teachingApp.Rd:68: Lost braces
    68 | code{link{add_logo}}
       |          ^
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'maptools', 'R2wd'
checkRd: (-1) R2txt.Rd:164: Escaped LaTeX specials: \#
checkRd: (-1) bct.Rd:18: Escaped LaTeX specials: \^
checkRd: (-1) bct.Rd:19: Escaped LaTeX specials: \^
checkRd: (-1) ineq.Rd:10: Escaped LaTeX specials: \&
checkRd: (-1) put.points.demo.Rd:39: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:10: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:31: Escaped LaTeX specials: \^
checkRd: (-1) crossEntropy.Rd:32: Lost braces
    32 | link{squaredError}
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) sendChatAction.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:25: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgdal’
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) estimate_template.Rd:238: Lost braces; missing escapes or markup?
   238 | the type of scaling and detrending performed; the {dat_struct} which can be
       |                                                   ^
checkRd: (-1) make_mask.Rd:15: Lost braces; missing escapes or markup?
    15 | {varTol}.}
       | ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) tcata.line.plot.Rd:72: Lost braces; missing escapes or markup?
    72 | \item{las}{numeric in {0,1,2,3}; the style of the axis labels. See \code{\link[graphics]{par}}.}
       |                       ^
checkRd: (-1) tds.plot.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{las}{numeric in {0,1,2,3}; the style of the axis labels. See: \code{\link[graphics]{par}}}
       |                       ^
checkRd: (-1) Tendril.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) Tendril.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) Tendril.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) choltensor.Rd:28-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) invtensor.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) normtensor.Rd:39-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) normtensor.Rd:42-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reptensor.Rd:31: Lost braces; missing escapes or markup?
    31 |   case of {rep(x,c(3,2))}. If the second is wanted it can be forced by
       |           ^
checkRd: (-1) solvetensor.Rd:32-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) svdtensor.Rd:28-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tenFM.rank.Rd:31: Lost braces; missing escapes or markup?
    31 | \item{penalty}{takes value in {1,2,3,4,5}, decides which penalty function to use for each tesnor mode \eqn{k}. Here \eqn{\nu} is a tuning parameter defined in the argument "\code{delta1}", and \eqn{d=\prod_{i=1}^{K} d_k }.
       |                               ^
'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
Package suggested but not available for checking: ‘gurobi’
checkRd: (-1) getSolution-methods.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{index_only}{if \code{TRUE}, only print item indices. if \code{FALSE}, print all item attributes. (default = {TRUE})}
       |                                                                                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) permucycle.Rd:37: Lost braces; missing escapes or markup?
    37 |  {The 2 in the first row means there are two cycles;}
       |  ^
checkRd: (-1) permucycle.Rd:38: Lost braces; missing escapes or markup?
    38 |   {The second row means there is a cycle of length 2, with members  (1,3);}
       |   ^
checkRd: (-1) permucycle.Rd:39: Lost braces; missing escapes or markup?
    39 |  {The third row means  there is a cycle of length 1, with member  (2);}
       |  ^
checkRd: (-1) permucycle.Rd:40: Lost braces; missing escapes or markup?
    40 |  {The fourth row is redundant for this specific case.}
       |  ^
checkRd: (-1) permucycle.Rd:41: Lost braces; missing escapes or markup?
    41 |  {One can read from the output of permucycle() to obtain cycle notation (13)(2) of the permutation, and other information.}
       |  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) DivideFile.Rd:16: Lost braces
    16 | \item{document}{A character vector that includes \emph{every line} from \\begin{document} to the first \\end\{document\}} }
       |                                                                                ^
Documented arguments not in \usage in Rd file 'CompileLatexDir.Rd':
  ‘engine:’ ‘compile.dir:’

Documented arguments not in \usage in Rd file 'GetLayerSampleIndexes.Rd':
  ‘NamesOfListToSample’ ‘isRandomized’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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}}
       |                                                       ^
Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
checkRd: (-1) lexicon_afinn.Rd:48: Lost braces; missing escapes or markup?
    48 | ``A new {ANEW:} Evaluation of a word list for sentiment analysis in
       |         ^
checkRd: (-1) lexicon_afinn.Rd:54: Lost braces; missing escapes or markup?
    54 | title     = \{A new {ANEW:} Evaluation of a word list for sentiment analysis in microblogs\}, \cr
       |                     ^
checkRd: (-1) infer_Z.Rd:16: Lost braces; missing escapes or markup?
    16 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variatioanl approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
checkRd: (-1) sibp.Rd:26: Lost braces
    26 | It is recommended to use link{sibp_param_search} instead of this function to search over multiple configurations of the most important parameters.  So long as only the training data is used, the analyst can freely experimient with as many parameter configurations as he likes without corrupting his causal inferences.  Once a parameter configuration is chosen, the user can then use \link{sibp_amce} on the test set to estimate the average marginal component effect (AMCE) for each treatment.}
       |                              ^
checkRd: (-1) sibp.Rd:28: Lost braces; missing escapes or markup?
    28 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variational approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
checkRd: (-1) sibp_amce.Rd:19: Lost braces
    19 |   \item{sibp.amce}{The table returned by code{sibp_amce}.}
       |                                              ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Rd file 'textEmbedReduce.Rd':
  \usage lines wider than 90 characters:
         "https://raw.githubusercontent.com/adithya8/ContextualEmbeddingDR/master/models/fb20/scalar.csv",
         "https://raw.githubusercontent.com/adithya8/ContextualEmbeddingDR/master/models/fb20/rpca_roberta_768_D_20.csv"

These lines will be truncated in the PDF manual.
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
Unknown package ‘textreadr’ in Rd xrefs
'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
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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
       |                           ^
Objects in \usage without \alias in Rd file 'timeSeries.Rd':
  ‘tbind.timeSeries’

Objects in \usage without \alias in Rd file 'tis.Rd':
  ‘tfstart.tis’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) shoulders.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) shoulders.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) shoulders.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) resampled_ttest.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Compute correlated t-statistic and p-value for resampled data from {correctR} package}
       |                                                                           ^
checkRd: (-1) resampled_ttest.Rd:24: Lost braces; missing escapes or markup?
    24 | Compute correlated t-statistic and p-value for resampled data from {correctR} package
       |                                                                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'witcher.Rd':
  ‘palettes’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'poisson_likelihood.Rd':
  ‘rate_exp’ ‘rate_ref’ ‘rate_pla’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
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checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
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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: \&
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checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) 01-dataObjects.Rd:18-19: Lost braces
    18 |   \item \code{sigma}{: A list of length five; each entry is a covariance matrix
       |                     ^
checkRd: (-1) 01-dataObjects.Rd:20-23: Lost braces
    20 |   \item \code{savedSims}{: A list of length five; each entry is a
       |                         ^
checkRd: (-1) 01-dataObjects.Rd:24-26: Lost braces
    24 |   \item \code{savedReap}{: A list of length five; each entry is a
       |                         ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) bin_cols.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bin_cols.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bin_cols.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bin_cols.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bin_cols.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bin_cols.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bin_cols.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bin_cols.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bin_cols.Rd:58: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) to_survey.Rd:25: Lost braces
    25 | Currently the only option is code{"rep_weights"}/.}
       |                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'gate_interactive_chr_int.Rd':
  ‘gate_list’

Documented arguments not in \usage in Rd file 'gate_programmatic.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'gate_programmatic_chr_int.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                    ^
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                           ^
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                                          ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
checkRd: (-1) single_imputation.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) single_imputation.Rd:23-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) separate_genes.Rd:14: Lost braces
    14 | microbial genes like AbcD, default [A-Za-z][a-z]{2}[A-Z0-9]+}
       |                                                 ^
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'deprecated-se.Rd':
  ‘expand_cols’

Documented arguments not in \usage in Rd file 'tidyr_legacy.Rd':
  ‘nm’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'vars_select.Rd':
  ‘args’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) get_tidysq_options.Rd:37: Lost braces
    37 | \item tidysq_pillar_max_width [code{integer(1)}]\cr
       |                                    ^
checkRd: (-1) read_fasta.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_fasta.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) stops_as_sf.Rd:28: Lost braces
    28 | code{\link{gtfs_as_sf}}
       |     ^
Specified C++11: please drop specification unless essential
checkRd: (-1) graphics-plot.Rd:69: Lost braces; missing escapes or markup?
    69 |     an integer code, one of {0,1,2}. If
       |                             ^
Auto-generated content requiring editing in Rd file 'timeperiodsR-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'timeSeq_1.0.4-package.Rd':
  ‘timeSeq_1.0.4-package’
checkRd: (-1) setup_sql_functions.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} System Functions}
       |                ^
checkRd: (-1) setup_sql_functions.Rd:17: Lost braces; missing escapes or markup?
    17 | Installs functions needed to operated {timeseriesdb} in
       |                                       ^
checkRd: (-1) setup_sql_grant_rights.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Grant execute on {timeseriesdb} functions}
       |                         ^
checkRd: (-1) setup_sql_grant_rights.Rd:17: Lost braces; missing escapes or markup?
    17 | Grant execute on {timeseriesdb} functions
       |                  ^
checkRd: (-1) setup_sql_tables.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} System Tables}
       |                ^
checkRd: (-1) setup_sql_tables.Rd:17: Lost braces; missing escapes or markup?
    17 | Installs tables needed to operated {timeseriesdb} in
       |                                    ^
checkRd: (-1) setup_sql_triggers.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} Triggers}
       |                ^
checkRd: (-1) methods-plot.Rd:166: Lost braces; missing escapes or markup?
   166 |        an integer code, one of {0,1,2}. If
       |                                ^
checkRd: (-1) POSIXst-class.Rd:247: Lost braces
   247 |   do any conversion on the POSIX{l,c}t objects).
       |                                 ^
checkRd: (-1) alcohol.Rd:16-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:22-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) add_md.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{body}{an XML object generated via {tinkr}}
       |                                         ^
checkRd: (-1) md_ns.Rd:13: Lost braces; missing escapes or markup?
    13 | The {commonmark} package is used to translate markdown to XML, but it does
       |     ^
checkRd: (-1) md_ns.Rd:14: Lost braces; missing escapes or markup?
    14 | not assign a namespace prefix, which means that {xml2} will auto-assign a
       |                                                 ^
checkRd: (-1) stylesheet.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{The {tinkr} stylesheet}
       |            ^
checkRd: (-1) stylesheet.Rd:14: Lost braces; missing escapes or markup?
    14 | This function returns the path to the {tinkr} stylesheet
       |                                       ^
checkRd: (-1) stylesheet.Rd:11: Lost braces; missing escapes or markup?
    11 | stylesheet used by {tinkr}.
       |                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) partition_undirected_graph.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{cutoff}{Numeric. The value max(0, g_{i,j} - cutoff) so that there are <\code{.num_components}> components in the graph.}
       |                                           ^
GNU make is a SystemRequirements.
checkRd: (-1) tierChart.Rd:332: Lost braces
   332 |   If the input argument code{boxes} is \code{F}, the \code{lBox},
       |                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
checkRd: (-1) tLagData.Rd:12: Lost braces; missing escapes or markup?
    12 |     \item{A:}{The treatment received, where A={0,1}.}
       |                                               ^
Specified C++11: please drop specification unless essential
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 ?
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checkRd: (-1) pmvt.Rd:23: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) pmvt.Rd:25: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) tv_episode_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the episode_id value found in the change entries.
       |                                                 ^
checkRd: (-1) tv_season_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the season_id value found in the change entries.
       |                                                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) estimateQ.Rd:22: Lost braces
    22 |   \item{SL.library}{specification of prediction algorithms, default is {(\sQuote{SL.glm}, \sQuote{SL.glmnet}, \sQuote{tmle.SL.dbarts2})}. In practice, including more prediction algorithms in the library improves results.}
       |                                                                        ^
checkRd: (-1) tmle.Sl.dbarts2.Rd:26: Lost braces
    26 | \item{id}{id}{id to group observations, not used}
       |              ^
checkRd: (-1) tmle.Sl.dbarts2.Rd:51: Lost braces
    51 | {object}{an object of type tmle.SL.dbarts2 used internally by \code{Super Learner}}
       |         ^
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 ?
Invalid package aliases in Rd file 'tm.plugin.alceste-package.Rd':
  ‘tm.plugin.europresse-package’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'TNRS_core.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) jsonStr.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Format data as a JSON object (like this: {"x": "120"}).}
       |                                                 ^
checkRd: (-1) jsonStr.Rd:18: Lost braces; missing escapes or markup?
    18 | Format data as a JSON object (like this: {"x": "120"}).
       |                                          ^
checkRd: (-1) fixed_width_no_modeling.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.Rd:10: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) Data.Rd:13: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) Data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:17: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^
checkRd: (-1) getSegsExtra.Rd:14: Lost braces
    14 | \item{data}{data.table returned from function /code{tdtr}}
       |                                                    ^
checkRd: (-1) ETM.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ETM.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ETM.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ETM.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ETM.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘corpus.JSS.papers’
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
Specified C++11: please drop specification unless essential
checkRd: (-1) norm_bin.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) norm_bin.Rd:19: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) clean_endPoint_info.Rd:21: Lost braces
    21 | \doi{10.1021/acs.est.7b01613}{Blackwell et al., 2017}.
       |                              ^
Documented arguments not in \usage in Rd file 'createLink.Rd':
  ‘hits’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) layer_templates.Rd:33: Lost braces; missing escapes or markup?
    33 | {param}. Supply as a named list, where the element name is the parameter.}
       | ^
Found the following significant warnings:
  RngStream.c:280:30: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘double’ [-Wformat=]
  RngStream.c:292:30: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘double’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TPmsm.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
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
Package suggested but not available for checking: ‘moveVis’
Unknown package ‘moveVis’ in Rd xrefs
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Enhancements
    Other changes
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 ?
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checkRd: (-1) Sim-Functions.Rd:114-116: Lost braces in \itemize; meant \describe ?
Argument items with no description in Rd file 'abrams.Rd':
  ‘prior’ ‘change’
Argument items with no description in Rd file 'absoluteIncreaseALL.Rd':
  ‘storedev’ ‘\dots’
Argument items with no description in Rd file 'boundaryLineALL.Rd':
  ‘\dots’
Argument items with no description in Rd file 'growthAveragingALL.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plotFirstYears.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plotRelease.Rd':
  ‘\dots’
Argument items with no description in Rd file 'splechtnaALL.Rd':
  ‘\dots’
'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’
Specified C++11: please drop specification unless essential
checkRd: (-1) OCC.Rd:24: Lost braces; missing escapes or markup?
    24 | of assignment to group j is done with $pi_{ik}$, the probability estimate by 
       |                                           ^
Argument items with no description in Rd file 'seqimplic.Rd':
  ‘ylim’
checkRd: (-1) nlp_scores.Rd:31-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nlp_scores.Rd:38-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nlp_scores.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nlp_scores.Rd:47-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nlp_scores.Rd:54-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nlp_scores.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformer_scores.Rd:37-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformer_scores.Rd:44-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformer_scores.Rd:54-57: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) Blavet.Rd:15: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) Blavet.Rd:29: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) Oudon.Rd:15: Lost braces in \itemize; meant \describe ?
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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
Objects in \usage without \alias in Rd file 'transport-internal.Rd':
  ‘gif.generate’ ‘plot_pgrid_wpp’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package which this enhances but not available for checking: ‘fwelnet’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Eunomia', 'CohortGenerator', 'CirceR'
checkRd: (-1) trtsel.Rd:69: Lost braces; missing escapes or markup?
    69 | numeric with two values {0,1} and gaussian(link = "identity") otherwise.
       |                         ^
checkRd: (-1) search_treebase.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) search_treebase.Rd:75: Lost braces; missing escapes or markup?
    75 | such as `{CG}` indicating either a C or G, which is not supported by any R interpreter,
       |          ^
Documented arguments not in \usage in Rd file 'clean_data.Rd':
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'correct_continuous.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'tc_correlation.Rd':
  ‘p’

Documented arguments not in \usage in Rd file 'tc_efunc.Rd':
  ‘p’

Documented arguments not in \usage in Rd file 'tc_mfunc.Rd':
  ‘p’

Documented arguments not in \usage in Rd file 'tc_response.Rd':
  ‘p’

Documented arguments not in \usage in Rd file 'truncate_input.Rd':
  ‘moving’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) HiC2Tree.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) HiC2Tree.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) HiC2Tree.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) HiC2Tree.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) treediff.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) treediff.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) treediff.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) treediff.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) treediff.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘TreeDistData’
Specified C++11: please drop specification unless essential
checkRd: (-1) gen_mease.Rd:19: Lost braces
    19 | column (\code{yprob}) gives the true probabilities (i.e., Pr{Y = 1 | X = x}). 
       |                                                             ^
Auto-generated content requiring editing in Rd file 'treemisc-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
Specified C++11: please drop specification unless essential
checkRd: (-1) ReadTntTree.Rd:37: Lost braces
    37 | \link{TNTOrder}{\code{tnt} order},
       |                ^
checkRd: (-1) random_experiments.Rd:64: Lost braces
    64 | (default: minimum{Number of random experiments K, number of physical cores}).}
       |                  ^
checkRd: (-1) trex.Rd:51: Lost braces
    51 | (default: minimum{Number of random experiments K, number of physical cores}).}
       |                  ^
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) coef.tridim_transformation.Rd:31: Lost braces
    31 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
checkRd: (-1) coef.tridim_transformation.Rd:32: Lost braces
    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
checkRd: (-1) coef.tridim_transformation.Rd:32: Lost braces; missing escapes or markup?
    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
checkRd: (-1) predict.tridim_transformation.Rd:24: Lost braces
    24 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
checkRd: (-1) predict.tridim_transformation.Rd:25: Lost braces
    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
checkRd: (-1) predict.tridim_transformation.Rd:25: Lost braces; missing escapes or markup?
    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
checkRd: (-1) variable_summary.Rd:18: Lost braces; missing escapes or markup?
    18 | data.frame with "{var_name}" column for the mean and
       |                  ^
checkRd: (-1) variable_summary.Rd:19: Lost braces; missing escapes or markup?
    19 | "{var_name}_{prob}" columns for each probability.
       |  ^
checkRd: (-1) variable_summary.Rd:19: Lost braces; missing escapes or markup?
    19 | "{var_name}_{prob}" columns for each probability.
       |             ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
checkRd: (-1) summary.armasubsets.Rd:16: Lost braces
    16 | \item{matrix.logical}{With matrix=TRUE, the matrix is logical TRUE/FALSE or string "*"/code{" "}}
       |                                                                                            ^
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 ?
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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.
       |                      ^
Documented arguments not in \usage in Rd file 'dvinecopula_objective.Rd':
  ‘udata’

Documented arguments not in \usage in Rd file 'wobjective.Rd':
  ‘vt’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) example.database2.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database2.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database3.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database3.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binary_transform.Rd:16: Lost braces; missing escapes or markup?
    16 | Converts any variable with two possible values to a {0,1} binary
       |                                                     ^
checkRd: (-1) binary_transform.Rd:13: Lost braces; missing escapes or markup?
    13 | A vector with values in {0,1}.
       |                         ^
checkRd: (-1) regime.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{discretize}{logical (default TRUE) whether the series are discretized to {1,2}, 
       |                                                                                ^
Objects in \usage without \alias in Rd file 'nlar.struct.Rd':
  ‘getNUsed’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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S3 methods shown with full name in Rd file 'tsibble-vctrs.Rd':
  ‘vec_ptype2.tbl_ts’ ‘vec_cast.tbl_ts’ ‘vec_cast.yearmonth’
  ‘vec_ptype2.yearmonth’ ‘vec_cast.yearquarter’
  ‘vec_ptype2.yearquarter’ ‘vec_cast.yearweek’ ‘vec_ptype2.yearweek’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Invalid package aliases in Rd file 'tsoutliers-package.Rd':
  ‘tsouliers-package’
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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.
       |                                                          ^
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checkRd: (-1) FULLoption.Rd:180: Lost braces; missing escapes or markup?
   180 |  (see the function {selectdirectory} more more informations)
       |                    ^
checkRd: (-1) fixdata.Rd:18: Lost braces; missing escapes or markup?
    18 | fixdata() call the function fix() that act on the rawdata base. The fix() function itself call the function edit() from the package {utils}
       |                                                                                                                                     ^
Invalid package aliases in Rd file 'TTAinterface-package.Rd':
  ‘TTAinterface-package’
'LazyData' is specified without a 'data' directory
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Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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    74 | 	doi{10.1093/biomet/74.2.221}
       |            ^
Specified C++11: please drop specification unless essential
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    25 | \item{xcov}{Either a \[stats]{formula} with an empty left-hand side specifying external covariates
       |                              ^
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    30 | \item{threshold_estimate_explanatory}{Point estimate of d_{0}}
       |                                                           ^
checkRd: (-1) threshold_estimate_ir.Rd:31: Lost braces; missing escapes or markup?
    31 | \item{threshold_estimate_response}{Estimate of f(d_{0}), which may not be 
       |                                                    ^
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    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |     ^
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    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |                                  ^
Package which this enhances but not available for checking: ‘sl3’
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    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |  ^
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    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |               ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |                                ^
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    47 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
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    33 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
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   111 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
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    35 | Lp<- function(a, data, sgl){
       |                            ^
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    38 | sapply(a,FUN=function(a){prod((psip(sgl,a)^ndlt)*((1-psip(sgl,a))^(npt-ndlt)))})
       |                         ^
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    42 | Lt<- function(a, data, sgl){
       |                            ^
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    45 | sapply(a,FUN=function(a){prod((psit(sgl,a)^ndlt)*((1-psit(sgl,a))^(npt-ndlt)))})
       |                         ^
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    49 | Ll<- function(a, data, sgl){
       |                            ^
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    52 | sapply(a,FUN=function(a){prod((psil(sgl,a)^ndlt)*((1-psil(sgl,a))^(npt-ndlt)))})
       |                         ^
GNU make is a SystemRequirements.
Found the following significant warnings:
  interface.c:31:15: warning: too many arguments for format [-Wformat-extra-args]
  interface.c:81:15: warning: too many arguments for format [-Wformat-extra-args]
  interface.c:83:15: warning: too many arguments for format [-Wformat-extra-args]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ucminf.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used Fortran compiler: ‘GNU Fortran (Debian 13.2.0-7) 13.2.0’
Specified C++11: please drop specification unless essential
checkRd: (-1) ggSave.Rd:39: Lost braces; missing escapes or markup?
    39 | to \code{\link[ggplot2:ggsave]{ggplot2::ggsave()}}. This is prevented by default since {gglot} switched
       |                                                                                        ^
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    50 |   In addition to the S3 methods listed under the topic "Methods (by generic)", the \code{predict} and {simulate} methods
       |                                                                                                       ^
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
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Argument items with no description in Rd file 'HC.Rd':
  ‘X’ ‘K’
Argument items with no description in Rd file 'KA.Rd':
  ‘X’ ‘K’ ‘distancemetric’
Argument items with no description in Rd file 'SOMs.Rd':
  ‘X’ ‘K’ ‘topo’ ‘rlen’ ‘alpha’ ‘n.hood’
Argument items with no description in Rd file 'binarise.Rd':
  ‘U’ ‘K’ ‘technique’ ‘parameter’
Argument items with no description in Rd file 'closestToSquareFactors.Rd':
  ‘n’
Argument items with no description in Rd file 'clustDist.Rd':
  ‘U1’ ‘U2’ ‘X’ ‘criterion’
Argument items with no description in Rd file 'clustVec2partMat.Rd':
  ‘C’
Argument items with no description in Rd file 'clusterDataset.Rd':
  ‘X’ ‘K’ ‘D’ ‘methods’
Argument items with no description in Rd file 'factors.Rd':
  ‘n’ ‘primeonly’
Argument items with no description in Rd file 'fixnans.Rd':
  ‘X’ ‘type’
Argument items with no description in Rd file 'fuzzystretch.Rd':
  ‘X’ ‘x0’
Argument items with no description in Rd file 'generateCoPaM.Rd':
  ‘U’ ‘relabel_technique’ ‘w’ ‘X’ ‘distCriterion’ ‘K’ ‘GDM’
Argument items with no description in Rd file 'isValidBPM.Rd':
  ‘U’
Argument items with no description in Rd file 'isempty.Rd':
  ‘X’
Argument items with no description in Rd file 'isnullorempty.Rd':
  ‘X’
Argument items with no description in Rd file 'kmeansKA.Rd':
  ‘X’ ‘K’ ‘distancemetric’ ‘iter.max’ ‘nstart’ ‘algorithm’ ‘trace’
Argument items with no description in Rd file 'mnplots.Rd':
  ‘Vmse’ ‘mseCache’ ‘subplotdim’ ‘subplotind’ ‘minimiseDistance’
Argument items with no description in Rd file 'mseclusters.Rd':
  ‘X’ ‘B’ ‘normalise’
Argument items with no description in Rd file 'normaliseMatrix.Rd':
  ‘X’ ‘type’
Argument items with no description in Rd file 'partMat2clustVec.rd':
  ‘U’ ‘skipValidity’
Argument items with no description in Rd file 'permutations.Rd':
  ‘n’
Argument items with no description in Rd file 'relabelClusts.Rd':
  ‘ref’ ‘input’ ‘technique’ ‘X’ ‘distCriterion’
Documented arguments not in \usage in Rd file 'sqrtm.Rd':
  ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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Rd files without \alias:
  ‘ungroup.Rd’
Documented arguments not in \usage in Rd file 'MortSmooth_tpower.Rd':
  ‘vector’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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    42 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
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    33 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
Specified C++11: please drop specification unless essential
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    45 | link[dlogitnorm]{dlogitnorm}for the normal density.
       |                 ^
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    21 |         \item{\code{Dist_5km}{Proportion of disturbed land in 5 km radius}}
       |                              ^
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    22 |         \item{\code{HDens_5km}{Housing density in 5 km radius}}
       |                               ^
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    23 |         \item{\code{Latitude}{Latitude / 100}}
       |                              ^
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    24 |         \item{\code{Longitude}{Longitude / 100}}
       |                               ^
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    25 |         \item{\code{People_site}{Number of photos of people at site / 1000}}
       |                                 ^
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    26 |         \item{\code{Trail}{1 if camera was on trail, 0 if not}}
       |                           ^
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    48 | data is of this type you should use code{occu} to analyze data. The detection parameter p, which is modeled using the
       |                                         ^
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   263 | \author{Ian Fiske, Richard Chandler, Andy Royle, Marc K\'{e}ry, David
       |                                                          ^
GNU make is a SystemRequirements.
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    59 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}
       |                                  ^
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    60 | \item{\code{sim_CI}}: {vector containing the cluster indices for each generated unimodal reference distribution}
       |                       ^
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    61 | \item{\code{pvalue_emp}}: {the empirical p-value:  the proportion of times the cluster index from the reference
       |                           ^
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    63 | \item{\code{pvalue_norm}}: {the normalized p-value: the simulated p-value based on comparison to a standard normal distribution }
       |                            ^
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    58 | \item{\code{BestK}}: {A matrix with 1 row and 4 columns named: "Max_CI","Max_CI_wi_1SE","Max_scaled_CI" and "Max_logWCSS_wi_1SE".
       |                      ^
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    63 | \item{\code{full_process}}: {A matrix containing the number of clusters, K, evaluated, the CI from the data, the average CI from the null
       |                             ^
checkRd: (-1) UNPaC_num_clust.Rd:66: Lost braces; missing escapes or markup?
    66 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}}
       |                                  ^
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   104 | \item{NW.order}{the value of the input argument code{NW.order}.}
       |                                                     ^
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   109 | \item{type.pvalue}{character, the value of the input argument code{pvalue}.}
       |                                                                   ^
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   176 | \item{type.pvalue}{a character, the value of the input argument code{pvalue}.}
       |                                                                     ^
Package suggested but not available for checking: ‘USA.state.boundaries.data’
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    35 | defaults to "{package name} authors"; you should only change this if you
       |              ^
checkRd: (-1) tidyverse.Rd:54: Lost braces; missing escapes or markup?
    54 | defaults to "{package name} authors"; you should only change this if you
       |              ^
Documented arguments not in \usage in Rd file 'use_course_details.Rd':
  ‘destdir’ ‘zipfile’

Documented arguments not in \usage in Rd file 'write-this.Rd':
  ‘contents’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
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    21 |    \code{train}{The mldr dataset with train examples, that includes all
       |                ^
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    23 |    \code{test}{The mldr dataset with test examples, defined by the
       |               ^
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    25 |    \code{validation}{Optionally, only if \code{has.validation = TRUE}.
       |                     ^
Documented arguments not in \usage in Rd file 'countDNAPatternInAlt.Rd':
  ‘trascriptsTable’

Documented arguments not in \usage in Rd file 'countDNAPatternInAltOneVariant.Rd':
  ‘trascriptsTable’

Documented arguments not in \usage in Rd file 'getAltSequence.Rd':
  ‘trascriptsTable’

Documented arguments not in \usage in Rd file 'getCodonInAlt.Rd':
  ‘trascriptsTable’ ‘codonPositionsColumnn’

Documented arguments not in \usage in Rd file 'getCodonInAltOneVariant.Rd':
  ‘trascriptsTable’ ‘codonPositionsColumnn’

Documented arguments not in \usage in Rd file 'getTSSKozakOneVariant.Rd':
  ‘variantsTable’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
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'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'
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'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
checkRd: (-1) sendTasks.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sendTasks.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'validate_extend.Rd':
  ‘varlist:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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    18 | Generate \code{n} random samples from multivariate Gaussian distribution N(0, (L^TL)^{-1})
       |                                                                                      ^
'LazyData' is specified without a 'data' directory
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    97 | \item{ID_level2}{Optional}{variable for unit ID codes. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                           ^
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.}
       |                        ^
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   124 | \item{use.estVar}{Logical}{value. If value is \code{TRUE}, then \code{R} function \code{estVar} is used for the  estimation of covariance matrix of the residuals. If value is \code{FALSE}, then \code{R} function \code{estVar} is not used for the estimation of covariance matrix of the residuals.}
       |                           ^
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
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     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Burr distribution due to Parana\'{i}ba et al. (2011) given by
       |                                                                                                                        ^
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
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    40 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + exp(2*X22)*e
       |                                ^
checkRd: (-1) simulateDCSIS.Rd:42: Lost braces
    42 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + 6*X22 + e
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get.miniseq.sample.files.Rd:15: Lost braces
    15 | \item{file.suffix}{Regex expression for end of file name. For example, `file.suffix = '_S\\d{1,2}_.*_R1_.*'` will match R1 files.1 files.}
       |                                                                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) Acoef_sh.Rd:23: Lost braces; missing escapes or markup?
    23 | The function returns the K-by-K matrices {A_1, ..., A_p} as a list object.
       |                                          ^
checkRd: (-1) VARshrink.Rd:58: Lost braces; missing escapes or markup?
    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                    ^
checkRd: (-1) VARshrink.Rd:58: Lost braces; missing escapes or markup?
    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) decomposition.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |      ^
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |          ^
checkRd: (-1) moving.estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fsweep.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fsweep.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fsweep.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fsweep.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fsweep.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fsweep.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fsweep.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fsweep.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VCAinference.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VCAinference.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VCAinference.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) anovaMM.Rd:59: Lost braces; missing escapes or markup?
    59 | A Linear Mixed Model, noted in standard matrix notation, can be written as {y = Xb + Zg + e}, where
       |                                                                            ^
checkRd: (-1) getSSQsweep.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getSSQsweep.Rd:21: 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,
       |                                              ^
checkRd: (-1) vcfR_to_tidy_conversion.Rd:115: Lost braces
   115 | \doi{doi.org/10.18637/jss.v059.i10}{this article}.
       |                                    ^
checkRd: (-1) se.meanratio2.Rd:35: Lost braces
    35 | link[vcmeta]{meta.lm.gen} functions in application where compatible
       |             ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) tv.coverperc.Rd:25: Lost braces
    25 | data.frame of observations with additional column #' code{COVER_PERC}
       |                                                          ^
checkRd: (-1) tv.coverperc.Rd:27: Lost braces
    27 | author{Florian Jansen #' email{florian.jansen@uni-rostock.de} }
       |       ^
checkRd: (-1) tv.coverperc.Rd:27: Lost braces
    27 | author{Florian Jansen #' email{florian.jansen@uni-rostock.de} }
       |                               ^
checkRd: (-1) vegdata-package.Rd:26: Lost braces
    26 | Journal of vegetation science, 21(6), 1179-1186. @url{http://dx.doi.org/10.1111/j.1654-1103.2010.01209.x}
       |                                                      ^
S3 methods shown with full name in Rd file 'syntab.Rd':
  ‘print.syntab’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'vein-deprecated.Rd':
  ‘object’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) additiveBeta.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:33: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) predcomp.test.Rd:51: Lost braces; missing escapes or markup?
    51 | S = dbar/sqrt(2*pi*se_{d}(0)/N),
       |                       ^
checkRd: (-1) predcomp.test.Rd:53: Lost braces; missing escapes or markup?
    53 | where d is the loss differential, d = e1 - e2 (e1 = loss(x, xhat1) and e2 = loss(x, xhat2)), dbar is its sample mean, and se_{d}(0) is the standard error for d, which must be estimated, and N is the length of the series investigated.  Let V = 2*pi*se_{d}(0), then V is estimated by
       |                                                                                                                              ^
checkRd: (-1) predcomp.test.Rd:53: Lost braces; missing escapes or markup?
    53 | where d is the loss differential, d = e1 - e2 (e1 = loss(x, xhat1) and e2 = loss(x, xhat2)), dbar is its sample mean, and se_{d}(0) is the standard error for d, which must be estimated, and N is the length of the series investigated.  Let V = 2*pi*se_{d}(0), then V is estimated by
       |                                                                                                                                                                                                                                                            ^
checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex125.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
Found the following significant warnings:
  alike.c:466:68: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  cstringr.c:164:19: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  cstringr.c:220:57: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  cstringr.c:265:60: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  envtrack.c:176:44: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
  eval.c:70:17: warning: format ‘%s’ expects a matching ‘char *’ argument [-Wformat=]
  misc.c:63:27: warning: format ‘%s’ expects a matching ‘char *’ argument [-Wformat=]
  trackinghash.c:110:11: warning: too many arguments for format [-Wformat-extra-args]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vetr.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) veWaning.Rd:60: Lost braces; missing escapes or markup?
    60 | of {'lin', 'piece', 'splin', 'spcub'} for the linear,
       |    ^
Specified C++11: please drop specification unless essential
checkRd: (-1) veWaningVariant.Rd:94: Lost braces; missing escapes or markup?
    94 | Must be one of {'lin', 'piece', 'splin', 'spcub'} for the linear,
       |                ^
'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) CommonVGAMffArguments.Rd:597: Lost braces
   597 |   Changes relating to the code{lss} argument have very important
       |                               ^
checkRd: (-1) ucberk.Rd:20: Lost braces
    20 |                 called \code{A}, code{B}, \dots, code{F}.
       |                                      ^
checkRd: (-1) ucberk.Rd:20: Lost braces
    20 |                 called \code{A}, code{B}, \dots, code{F}.
       |                                                      ^
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
Malformed Title field: should not end in a period.
Argument items with no description in Rd file 'learnPartitionWithLLR.Rd':
  ‘type’ ‘procedure’ ‘ql’ ‘qq’ ‘BinaryLearningProcedure’
Argument items with no description in Rd file 'plotClassifRule.Rd':
  ‘object’
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.}
       |                    ^
Documented arguments not in \usage in Rd file 'boxplot_VICI.Rd':
  ‘res_2plot’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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 ?
Documented arguments not in \usage in Rd file 'draw_map_shiny.Rd':
  ‘rigth.lim’

Documented arguments not in \usage in Rd file 'map_summary.Rd':
  ‘rigth.lim’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
'LazyData' is specified without a 'data' directory
checkRd: (-1) viridis.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:24-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:31-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePopulation.Rd:75: Lost braces; missing escapes or markup?
    75 |   \item \strong{Pollen productivity}: In each time step the model computes the pollen productivity (in relative values) of the population using the equation \eqn{P_{t} = \sum x_{it} \times max(S_{t}, B)}, where \emph{t} is time (a given simulation time step), \emph{P} is the pollen productivity of the population at a given time, \emph{x_{i}} represents the biomass of every adult individual, \emph{S} is the environmental suitability at the given time, \emph{B} is the contribution of biomass to pollen productivity regardless of environmental suitability (\emph{pollen.control} parameter in the simulation, 0 by default). If \emph{B} equals 1, \emph{P} is equal to the total biomass sum of the adult population, regardless of the environmental suitability. If \emph{B} equals 0, pollen productivity depends entirely on environmental suitability values.
       |                                                                                                                                                                                                                                                                                                                                                    ^
checkRd: (-1) NSpec.DB.Rd:16: Lost braces; missing escapes or markup?
    16 |   ...{currently not used}
       |      ^
checkRd: (-1) wavelength-methods.Rd:32: Lost braces; missing escapes or markup?
    32 | A call to {new} returns a newly allocated object from the class identified by the first argument.
       |           ^
checkRd: (-1) phasePortrait.Rd:350: Lost braces; missing escapes or markup?
   350 |   \code{vMod = xMod^(1/lambda)} and {vArg = xArg^(1/lambda)}\cr\cr
       |                                     ^
checkRd: (-1) compdesc.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) ViSiElse.Rd:101-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:105-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:108-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:114-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:116: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:128-134: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:135-147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:148-157: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:152-153: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:154-155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dim-ViSibook-methods.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dim-ViSibook-methods.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary-ViSigrid-methods.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary-ViSigrid-methods.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  heap.h:198:28: warning: too many arguments for format [-Wformat-extra-args]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vistla.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) aminoAcidFun.Rd:37: Lost braces
    37 | \item{ownVLFreduced}{ownVLFMatrix}{A matrix containing only those specimen that have VLFs as well as the amino acids at the positions that contain VLFs and NAs in all other positions of the sequence.  Only appears if own is not NULL.}
       |                                   ^
checkRd: (-1) vlfFun.Rd:36: Lost braces
    36 | \item{ownVLFreduced}{ownVLFMatrix}{A matrix containing only those specimen that have VLFs as well as the nucleotides at the positions that contain VLFs and NAs in all other positions of the sequence.  Only appears if own is not NULL.}
       |                                   ^
Specified C++11: please drop specification unless essential
checkRd: (-1) getTurnType.Rd:38: Lost braces; missing escapes or markup?
    38 | Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
       |               ^
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Documented arguments not in \usage in Rd file 'cpp_vol2bird_version.Rd':
  ‘path’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'blendColor.Rd':
  ‘color’ ‘percent’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Data-Examples.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data-Examples.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data-Examples.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aquaporin.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vsts_create_release.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vsts_create_release.Rd:34: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) WACS.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACSreadAgroclim.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) WACSreadAgroclim.Rd:16-17: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get.wal.mipmap.heights.Rd':
  ‘height_mm’

Documented arguments not in \usage in Rd file 'get.wal.mipmap.widths.Rd':
  ‘width_mm’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dyad.Rd:6: Lost braces; missing escapes or markup?
     6 | Returns a vector of integers $2^j+1,...,2^{j+1}$.
       |                                           ^
checkRd: (-1) dyad.Rd:19: Lost braces; missing escapes or markup?
    19 | Returns a vector of integers $2^j+1,...,2^{j+1}$.
       |                                           ^
checkRd: (-1) dyadjk.Rd:20: Lost braces; missing escapes or markup?
    20 | of the wavelet coefficient $w_{j,k}$ in a vector of wavelet 
       |                               ^
Documented arguments not in \usage in Rd file 'WaveDjF.Rd':
  ‘y_fft’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Auto-generated content requiring editing in Rd file 'maxithresh.Rd':
  \details: ‘~~ If necessary, more details than the description above ~~’
  \arguments: data: ‘~~Describe \code{data} here~~’
  \arguments: g: ‘~~Describe \code{g} here~~’
  \arguments: L: ‘~~Describe \code{L} here~~’
  \arguments: F: ‘~~Describe \code{F} here~~’
  \arguments: eta: ‘~~Describe \code{eta} here~~’
'LazyData' is specified without a 'data' directory
checkRd: (-1) anchor_points_grey.Rd:9: Lost braces
     9 | Zeeden et al., (2013) and anchored to the code{\link{astrosignal_example}} \cr
       |                                               ^
checkRd: (-1) retrack_wt_MC.Rd:206: Lost braces
   206 | be off in certain intervals. the link[WaverideR]{retrack_wt_MC} mitigates
       |                                                 ^
checkRd: (-1) retrack_wt_MC.Rd:40: Lost braces
    40 | link[WaverideR]{analyze_wavelet} wavelet function
       |                ^
checkRd: (-1) retrack_wt_MC.Rd:41: Lost braces
    41 | To create a list use the link[base]{list} function}
       |                                    ^
checkRd: (-1) retrack_wt_MC.Rd:44: Lost braces
    44 | To create the matrix use the link[base]{cbind} function and only add the
       |                                        ^
Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'train_spectra.Rd':
  ‘save.model’ ‘vector.input’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
checkRd: (-1) plot_wbaconmv.Rd:23: Lost braces
    23 |     \item{pch}{plot character of outliers, code{[integer]} (default:
       |                                                ^
Invalid package aliases in Rd file 'wce-package.Rd':
  ‘wce-package’
'LazyData' is specified without a 'data' directory
checkRd: (-1) centrality.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) centrality.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) centrality.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) centrality.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) centrality.Rd:55-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) centrality.Rd:57-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) centrality.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) centrality.Rd:67-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) centrality.Rd:70-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clustcoef.Rd:67: Lost braces
    67 |   \item Barrat, A., Barth\'{e}lemy, M., Pastor-Satorras,
       |                            ^
checkRd: (-1) dprewire.Rd:37-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dprewire.Rd:41-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dprewire.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dprewire.Rd:45-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dprewire.Rd:48-50: Lost braces
    48 | is provided.} \item{\code{cvxr_control} {A list of parameters passed to
       |                                         ^
checkRd: (-1) rpa_control_preference.Rd:69-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpa_control_preference.Rd:77-87: Lost braces in \itemize; meant \describe ?
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
checkRd: (-1) image_func.Rd:20: Lost braces; missing escapes or markup?
    20 | This is a convenience function for applying {magick} functions that take an image as the first argument and return an image. It's fully vectorised, so you can set separate argument values for each image.
       |                                             ^
Documented arguments not in \usage in Rd file 'read_img.Rd':
  ‘imgfile’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
checkRd: (-1) predict.SDMfit.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.SDMfit.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) busTrace.Rd:15: Lost braces
    15 | /href{https://crawdad.org/coppe-ufrj/RioBuses/20180319/}
       |      ^
Specified C++11: please drop specification unless essential
checkRd: (-1) WeightedROC.Rd:10: Lost braces; missing escapes or markup?
    10 | integer/numeric with values all in {0=negative,1=positive} or
       |                                    ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       | ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       |                            ^
checkRd: (-1) CLIC.Rd:149: Lost braces
   149 | Composite likelihood {E}{M} algorithm with applications to
       |                         ^
Argument items with no description in Rd file 'zdifference_ordinal.Rd':
  ‘na.rm’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  corFunctions.c:166:15: warning: too many arguments for format [-Wformat-extra-args]
  corFunctions.c:410:15: warning: too many arguments for format [-Wformat-extra-args]
  corFunctions.c:727:15: warning: too many arguments for format [-Wformat-extra-args]
  corFunctions.c:1152:15: warning: too many arguments for format [-Wformat-extra-args]
  networkFunctions.c:322:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  networkFunctions.c:322:73: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  networkFunctions.c:366:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  networkFunctions.c:366:73: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  networkFunctions.c:391:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/WGCNA.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-7) 13.2.0’
Argument items with no description in Rd file 'sampledHierarchicalConsensusModules.Rd':
  ‘consensusTOMFilePattern’
S3 methods shown with full name in Rd file 'QIC.gee.Rd':
  ‘QIC.gee’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
Documented arguments not in \usage in Rd file 'remove_empty.Rd':
  ‘quiet’

Documented arguments not in \usage in Rd file 'undoHistory.Rd':
  ‘class’ ‘btn_class’ ‘back_text’ ‘fwd_text’ ‘back_title’ ‘fwd_title’
  ‘back_icon’ ‘fwd_icon’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) get.deriv.smooth.hist.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Gets $n^{th}$ derivative of smoothed histogram}
       |                ^
Package suggested but not available for checking: ‘rgdal’
Documented arguments not in \usage in Rd file 'displayDataTable.Rd':
  ‘id’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pageviews’
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 ?
Package suggested but not available for checking: ‘pageviews’
'LazyData' is specified without a 'data' directory
checkRd: (-1) secondDerivative.Rd:14: Lost braces
    14 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
checkRd: (-1) windAC.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) windAC.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) windAC.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Hoover.Rd:21: Lost braces; missing escapes or markup?
    21 | Let x_{i} be the income of the i-th person and \eqn{\overline{x}} be the mean income. Then the Hoover index H is:
       |       ^
checkRd: (-1) RicciSchutz.Rd:21: Lost braces; missing escapes or markup?
    21 | In the case of an empirical distribution with n elements where y_{i} denotes the wealth of household i and \eqn{\overline{y}} the sample average, the Ricci and Schutz coefficient can be expressed as:
       |                                                                  ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) word2vec_similarity.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) word2vec_similarity.Rd:31: Lost braces in \itemize; meant \describe ?
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 ?
checkRd: (-1) WFO.match.Rd:128: Lost braces
   128 | Function \code{WFO.one} finds one unique matching name for each submitted name. Via \code{priority = "Accepted"}, it first limits candidates to accepted names, with a possible second step of eliminating accepted names that are synonyms. Via \code{priority = "Synonym"}, it first limits candidates to those that are not synonyms, with a possible second step of eliminating names that are not accepted. When the number of matches is larger than one after these steps, a third algorithm picks the candidate with the smallest \code{taxonID}. When a \code{spec.name} is given to \code{WFO.one}, the original submitted name is inserted for the code{scientificName}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   ^
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'new_givens_path.Rd':
  ‘generate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) theme_wpa.Rd:16: Lost braces; missing escapes or markup?
    16 | you can use this font, install and load {extrafont} prior to
       |                                         ^
'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) wql-package.Rd:7: Lost braces
     7 | \title{c("\\Sexpr[results=rd,stage=build]{tools:::Rd_package_title(\"#1\")}",
       |                                          ^
checkRd: (-1) wql-package.Rd:10: Lost braces
    10 | c("\\Sexpr[results=rd,stage=build]{tools:::Rd_package_description(\"#1\")}",
       |                                   ^
checkRd: (-1) wql-package.Rd:61: Lost braces
    61 | c("\\Sexpr[results=rd,stage=build]{tools:::Rd_package_author(\"#1\")}",
       |                                   ^
checkRd: (-1) wql-package.Rd:65: Lost braces
    65 | c("\\Sexpr[results=rd,stage=build]{tools:::Rd_package_maintainer(\"#1\")}",
       |                                   ^
Found the following significant warnings:
  dataobj.c:772:23: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wrassp.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-7) 13.2.0’
checkRd: (-1) item.side.Rd:35: Lost braces
    35 |   	code{TRUE}. If any other value, the axis is not drawn.}
       |             ^
Malformed Title field: should not end in a period.
checkRd: (-1) createDemandSite.Rd:26: Lost braces
    26 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
checkRd: (-1) createDemandSite.base.Rd:26: Lost braces
    26 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
checkRd: (-1) createDemandSite.default.Rd:32: Lost braces
    32 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) predict_race.Rd:132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict_race.Rd:133: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict_race.Rd:134: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict_race.Rd:135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict_race.Rd:136: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'sample_me.Rd':
  ‘middle_name’ ‘M_rs’ ‘M_rf’ ‘M_rm’ ‘alpha’ ‘me_race’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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.
       | ^
Documented arguments not in \usage in Rd file 'Cut.off.Rd':
  ‘main’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) exploreSignatures.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:67-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateData.Rd:47: Lost braces
    47 | \bold{code{data}} \tab the generated data \cr
       |           ^
checkRd: (-1) generateData.Rd:53: Lost braces
    53 | Refer to \bold{\emph{code{\link{retrieveDataFactory}}}} and to
       |                          ^
checkRd: (-1) qualifyFunctionArguments.Rd:14: Lost braces
    14 | A emph{\code{list}} with following names
       |       ^
checkRd: (-1) qualifyFunctionArguments.Rd:26: Lost braces
    26 | \item{code{arguments}}{a \code{pairList} of argument names and values.
       |           ^
checkRd: (-1) completeManualPage.Rd:12: Lost braces
    12 | See \emph{\bold{code{\link{ProcessingContext}}}}. Only
       |                     ^
checkRd: (-1) produceAllManualPagesFromObject.Rd:14: Lost braces
    14 | See \emph{\bold{\\code{\link{ProcessingContext}}}}.}
       |                       ^
checkRd: (-1) xbrlSECdev01.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) xshow.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) xshow.Rd:20: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chemnet.Rd:111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chemnet.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:105: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xgb.txt’
GNU make is a SystemRequirements.
checkRd: (-1) XMLGetters-methods.Rd:165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:168-169: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:171: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:172: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:179-182: Lost braces in \itemize; meant \describe ?
checkRd: (-1) XMLGetters-methods.Rd:191: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) xml_to_df.Rd:144: Lost braces; missing escapes or markup?
   144 | Default {NULL} means the workbook will not be protected with a password}
       |         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rbokeh’
checkRd: (-1) read.npc.vpc.results.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) read.npc.vpc.results.Rd:19: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_
checkRd: (-1) read.npc.vpc.results.Rd:22: Escaped LaTeX specials: \_
Documented arguments not in \usage in Rd file 'xpose.create.title.Rd':
  ‘plot.text’ ‘main’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) read_nm_model.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_nm_model.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_nm_model.Rd:36-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_nm_model.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_nm_model.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'check_problem.Rd':
  ‘xpdb’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file 'XRjulia-package.Rd':
  ‘XRjulia-package’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
Argument items with no description in Rd file 'getCondition.Rd':
  ‘object’
Argument items with no description in Rd file 'screen.Rd':
  ‘fac’ ‘condition’ ‘position’
Found the following files/directories:
  ‘OPT.csv’ ‘testTecan_defaultLiquid.csv’ ‘testTecan_setLiquid.csv’
checkRd: (-1) xts.Rd:39: Lost braces
    39 |   \item{tclass}{ time class to use for the index. See code{\link{tclass}}. }
       |                                                           ^
checkRd: (-1) xwfGridsearch.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{iter}{Number of levels in the adaptive grid search. The resolution in b obtained is 2^{-1-iter}.}
       |                                                                                             ^
checkRd: (-1) cat_sim.Rd:110: Lost braces; missing escapes or markup?
   110 | \code{min} and {max} are mandatory for setting limits on the test length. User-defined
       |                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) brier_survival.Rd:21: Lost braces; missing escapes or markup?
    21 | predicting with {censored} model. This should be an unquoted column name
       |                 ^
checkRd: (-1) brier_survival_integrated.Rd:27: Lost braces; missing escapes or markup?
    27 | predicting with {censored} model. This should be an unquoted column name
       |                 ^
checkRd: (-1) roc_curve_survival.Rd:18: Lost braces; missing escapes or markup?
    18 | predicting with {censored} model. This should be an unquoted column name
       |                 ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) boot.yhat.Rd:3: Lost braces
     3 | \title{Bootstrap metrics produced from /code{calc.yhat}}
       |                                             ^
checkRd: (-1) boot.yhat.Rd:19: Lost braces
    19 |     Ouput of /code{lm}
       |                   ^
checkRd: (-1) boot.yhat.Rd:22: Lost braces
    22 |     Output of /code{calc.yhat}
       |                    ^
checkRd: (-1) booteval.yhat.rd:3: Lost braces
     3 | \title{Evaluate bootstrap metrics produced from /code{calc.yhat}}
       |                                                      ^
checkRd: (-1) booteval.yhat.rd:5: Lost braces
     5 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
checkRd: (-1) combCI.rd:26: Lost braces
    26 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
checkRd: (-1) commonality.rd:12: Lost braces
    12 |     Output from /code{aps}
       |                      ^
checkRd: (-1) dombin.rd:12: Lost braces
    12 |     Output from /code{dominance}
       |                      ^
checkRd: (-1) dominance.rd:12: Lost braces
    12 |     Output from /code{aps}
       |                      ^
checkRd: (-1) plotCI.yhat.rd:5: Lost braces
     5 |   This function plots CIs that have been produced from /code{booteval.yhat}.
       |                                                             ^
checkRd: (-1) plotCI.yhat.rd:32: Lost braces
    32 |   This function plots CIs that have been produced from /code{booteval.yhat}.   
       |                                                             ^
checkRd: (-1) plotCI.yhat.rd:35: Lost braces
    35 | This returns a plot of CIs that have been produced from /code{booteval.yhat}.
       |                                                              ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'IC.Rd':
  ‘\dots’
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) glm.cons.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{method}{the method used in fitting the model. The default method "\code{glm.fit.cons}" uses function {nnnpls} from package nnls instead of \code{lm.fit} to impose the sign of the coefficients. As in \code{glm}, the alternative method "\code{model.frame}" returns the model frame and does no fitting.}
       |                                                                                                            ^
Auto-generated content requiring editing in Rd file 'ZIBseq-package.Rd':
  \seealso: ‘~~ Optional links to other man pages, e.g. ~~ ~~ \code{\link...’
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.}
       |                            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) inside2trans.Rd:124: Lost braces
   124 | \bold{Linking number --- {Wikipedia}{,} The Free Encyclopedia}.
       |                                     ^
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:74: Escaped LaTeX specials: \_
checkRd: (-1) zid.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:182: Lost braces
   182 |   dQuote{tab-delimited text file} when you have done and close the spreadsheet
       |         ^
checkRd: (-1) in.zoom.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_ztable.Rd:75: Lost braces; missing escapes or markup?
    75 | must be NULL or contain only elements of {"h","t","b","p","!","H"}.}
       |                                          ^
checkRd: (-1) ztable_sub.Rd:78: Lost braces; missing escapes or markup?
    78 | must be NULL or contain only elements of {"h","t","b","p","!","H"}.
       |                                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
Note: found 134469 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
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    include  13.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Undeclared package ‘CCA’ in Rd xrefs
Found the following files/directories:
  ‘acceldata2.RData’
File ‘acc/libs/acc.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.
Documented arguments not in \usage in Rd file 'ADMM_EN2.Rd':
  ‘alpha’

Documented arguments not in \usage in Rd file 'ADMM_EN_SMW.Rd':
  ‘alpha’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd file 'testRmACD.Rd':
  ‘pStar’
File ‘ACDm/libs/ACDm.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
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'fitSnpNmfArray.Rd':
  ‘maxIter’ ‘acc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘hunspell’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
‘configure’: /bin/bash is not portable
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppProgress’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'd1.Rd':
  ‘The’ ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 305 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'AdaptGauss-package.Rd':
  ‘MultiModal-package’
Invalid package aliases in Rd file 'aslm-package.Rd':
  ‘aslm-package’ ‘asggm-package’
Argument items with no description in Rd file 'asggm-internal.Rd':
  ‘ansL’ ‘kNodes’ ‘spP’
Specified C++11: please drop specification unless essential
Undeclared packages ‘HI’, ‘MHadaptive’ in Rd xrefs
Unknown packages ‘HI’, ‘MHadaptive’ in Rd xrefs
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
checkRd: (-1) ada.Rd:171: 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
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'print.aTest.Rd':
  ‘how’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   3.0Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'ae_count.Rd':
  ‘patients’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  9.5Mb
  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
Undeclared package ‘future’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
Undeclared packages ‘timereg’, ‘rms’, ‘ranger’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'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
Undeclared package ‘tibble’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Zlibs.c:306:69: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
  Zlibs.c:306:73: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
  Zlibs.c:306:77: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
  Zlibs.c:306:81: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
  Zlibs.c:306:85: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
  Zlibs.c:306:89: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
  Zlibs.c:2579:70: warning: data argument not used by format string [-Wformat-extra-args]
  Zlibs.c:2818:70: warning: data argument not used by format string [-Wformat-extra-args]
  Zlibs.c:3063:70: warning: data argument not used by format string [-Wformat-extra-args]
  Zlibs.c:3301:70: warning: data argument not used by format string [-Wformat-extra-args]
See ‘/data/gannet/ripley/R/packages/tests-clang/ads.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    tutorials   5.6Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘Hmisc’ ‘WRS2’ ‘boot’ ‘car’ ‘dplyr’ ‘effects’
  ‘effsize’ ‘forcats’ ‘ggplot2’ ‘lm.beta’ ‘nlme’ ‘readr’ ‘robust’
  ‘sandwich’ ‘sjstats’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘table_AeRobiology’
Namespace in Imports field not imported from: ‘flextable’
  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
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘docstring’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Undeclared packages ‘epiR’, ‘cccrm’ in Rd xrefs
Package suggested but not available for checking: ‘rgdal’
Package which this enhances but not available for checking: ‘asreml’
Specified C++11: please drop specification unless essential
File ‘ahaz/libs/ahaz.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
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
'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
Namespaces in Imports field not imported from:
  ‘knitr’ ‘randomNames’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘multcomp’, ‘gmodels’ in Rd xrefs
Undeclared package ‘R6’ in Rd xrefs
Undeclared package ‘era’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Rsolnp’ ‘SuperLearner’ ‘future.apply’ ‘ggplot2’ ‘progressr’ ‘stats’
  ‘utils’
  All declared Imports should be used.
Invalid package aliases in Rd file 'aire.zmvm-deprecated.Rd':
  ‘aire.zmvm-deprecated-package’
Note: found 53 marked UTF-8 strings
Note: found 17 marked UTF-8 strings
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    ShinyGR   4.3Mb
    doc       3.5Mb
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 710 marked UTF-8 strings
Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
Undeclared package ‘SnowballC’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
File ‘AlgDesign/libs/AlgDesign.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) 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
Undeclared package ‘hyperSpec’ in Rd xrefs
Note: found 115 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘alphabetr/libs/alphabetr.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.
Documented arguments not in \usage in Rd file 'gs.Rd':
  ‘x’ ‘parallel’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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.
Argument items with no description in Rd file 'MLS.Rd':
  ‘MSE1’
'LazyData' is specified without a 'data' directory
Note: found 171 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metaboliteIDmapping’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'amelia.package.Rd':
  ‘amelia-package’
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘network’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Title field: should not end in a period.
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘dplyr’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'check_factors.Rd':
  ‘object’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) deshrink.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) deshrink.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) plot.mat.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) plot.wa.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) predict.prcurve.Rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'rowVars.Rd':
  \arguments: \dots: ‘~~Describe \code{\dots} here~~’
Found the following files/directories:
  ‘BH-0.05-ListOfGenes.txt’ ‘BH-0.05-VM-ListOfGenes.txt’
  ‘CompleteListOfGenes.txt’ ‘GenesOutOfAnalysis.txt’
  ‘GenesOutOfAnalysis_NotEnoughObs.txt’
  ‘GenesOutOfAnalysis_NullVar.txt’ ‘VM-CompleteListOfGenes.txt’
  ‘bonferroni-0.05-ListOfGenes.txt’
  ‘bonferroni-0.05-VM-ListOfGenes.txt’
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Note: found 237 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'crawl_interpolation.Rd':
  ‘pt.colors’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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: \_ \_
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    R  34.4Mb
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mcclust’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared packages ‘geepack’, ‘dispmod’ in Rd xrefs
Documented arguments not in \usage in Rd file 'alternate.sol3.Rd':
  ‘lambda0’

Documented arguments not in \usage in Rd file 'check.group.Rd':
  ‘k’

Documented arguments not in \usage in Rd file 'getrow3.Rd':
  ‘lambda0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: found 4 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'apci.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.bar.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.plot.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.plot.heatmap.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.plot.hexagram.Rd':
  ‘first_age’ ‘first_period’ ‘interval’ ‘first_age_isoline’
  ‘first_period_isoline’ ‘isoline_interval’ ‘line_width’ ‘line_color’
  ‘label_size’ ‘label_color’ ‘scale_units’ ‘wrap_cohort_labels’
  ‘quantile’
Argument items with no description in Rd file 'apci.plot.raw.Rd':
  ‘\dots’
Argument items with no description in Rd file 'cohortdeviation.Rd':
  ‘\dots’
Argument items with no description in Rd file 'compute_xcoordinate.Rd':
  ‘p’
Argument items with no description in Rd file 'compute_ycoordinate.Rd':
  ‘p’ ‘a’
Argument items with no description in Rd file 'maineffect.Rd':
  ‘\dots’
Argument items with no description in Rd file 'temp_model.Rd':
  ‘\dots’
Argument items with no description in Rd file 'tests.Rd':
  ‘\dots’
Namespaces in Imports field not imported from:
  ‘AER’ ‘ChainLadder’ ‘ISLR’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'apercu.Rd':
  ‘c’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: ‘bgw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘APBinary_PPV.csv’ ‘APBinary_TPF.csv’
  ‘APBinary_ap_summary(method=perturbation,B=1500).csv’
  ‘APBinary_auc_summary(method=perturbation,B=1500).csv’
  ‘APSurv_PPV.csv’ ‘APSurv_TPF.csv’
  ‘APSurv_ap_summary(method=bootstrap,B=500).csv’
  ‘APSurv_auc_summary(method=bootstrap,B=500).csv’
  ‘CompareAP_Binary_dap_summary(method=none).csv’
  ‘CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.6Mb
    doc    1.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Undeclared package ‘RCurl’ in Rd xrefs
Note: found 76 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘bannerCommenter’ ‘config’ ‘feather’ ‘here’ ‘knitr’ ‘log4r’ ‘ps’
  ‘rmarkdown’ ‘skimr’ ‘snakecase’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  r_archive.cpp:68:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/archive.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
'LazyData' is specified without a 'data' directory
Undeclared package ‘rmarkdown’ in Rd xrefs
Specified C++11: please drop specification unless essential
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Argument items with no description in Rd file 'dynamac_pkg_bounds_test.Rd':
  ‘obs’ ‘fstat’ ‘tstat’ ‘case’ ‘k’
'LazyData' is specified without a 'data' directory
Undeclared package ‘beepr’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Undeclared packages ‘survey’, ‘Matching’ in Rd xrefs
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  5.9Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.2Mb
    testScripts   1.3Mb
Documented arguments not in \usage in Rd file 'allocateFromCdf.AromaUnitTabularBinaryFile.Rd':
  ‘path’ ‘tags’ ‘footer’

Documented arguments not in \usage in Rd file 'byChipType.DChipSnpInformation.Rd':
  ‘rootPath’ ‘pattern’ ‘verbose’

Documented arguments not in \usage in Rd file 'byChipType.UgpGenomeInformation.Rd':
  ‘version’

Documented arguments not in \usage in Rd file 'calculateResidualSet.FirmaModel.Rd':
  ‘verbose’

Documented arguments not in \usage in Rd file 'findByChipType.AromaChipTypeAnnotationFile.Rd':
  ‘chipType’ ‘tags’

Documented arguments not in \usage in Rd file 'fit.SmoothMultiarrayModel.Rd':
  ‘data’

Documented arguments not in \usage in Rd file 'getCellIndices.ExonChipEffectFile.Rd':
  ‘units’

Documented arguments not in \usage in Rd file 'getImage.AffymetrixCelFile.Rd':
  ‘palette’

Documented arguments not in \usage in Rd file 'getOutputDataSet.Transform.Rd':
  ‘force’

Documented arguments not in \usage in Rd file 'getUnitTypes.AffymetrixCdfFile.Rd':
  ‘map’

Documented arguments not in \usage in Rd file 'plotMvsX.AffymetrixCelFile.Rd':
  ‘xlim’ ‘xlab’

Documented arguments not in \usage in Rd file 'process.BackgroundCorrection.Rd':
  ‘force’ ‘verbose’

Documented arguments not in \usage in Rd file 'readUnits.CnagCfhFile.Rd':
  ‘cdf’

Documented arguments not in \usage in Rd file 'setArrays.ArrayExplorer.Rd':
  ‘arrays’

Documented arguments not in \usage in Rd file 'setRestructor.AffymetrixCdfFile.Rd':
  ‘units’

Documented arguments not in \usage in Rd file 'setupExampleData.Rd':
  ‘dirs’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'fitOne.MultiSourceCopyNumberNormalization.Rd':
  ‘name’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Documented arguments not in \usage in Rd file 'fit.CopyNumberSegmentationModel.Rd':
  ‘chromosome’

Documented arguments not in \usage in Rd file 'getPath.Explorer.Rd':
  ‘create’

Documented arguments not in \usage in Rd file 'process.AromaTransform.Rd':
  ‘force’ ‘verbose’

Documented arguments not in \usage in Rd file 'process.ChromosomeExplorer.Rd':
  ‘chromosome’

Documented arguments not in \usage in Rd file 'process.Explorer.Rd':
  ‘arrays’ ‘verbose’

Documented arguments not in \usage in Rd file 'setArrays.Explorer.Rd':
  ‘arrays’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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 48.0Mb
  sub-directories of 1Mb or more:
    R      4.3Mb
    libs  43.1Mb
Undeclared package ‘readr’ in Rd xrefs
Note: found 1409 marked UTF-8 strings
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
Note: found 328 marked UTF-8 strings
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'RweaveAsciiSetup.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweaveOrg.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweavePandoc.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweaveReST.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweaveT2t.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweaveTextile.Rd':
  ‘stylepath’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ash/libs/ash.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.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
Found the following significant warnings:
  MSTOpt.cpp:21:7: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  MSTOpt.cpp:593:55: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  genetic_map_DH.cpp:191:37: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  genetic_map_DH.cpp:233:16: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  genetic_map_DH.cpp:470:22: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  genetic_map_DH.cpp:477:22: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  linkage_group_DH.cpp:123:37: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/ASMap.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
Package which this enhances but not available for checking: ‘asreml’
Documented arguments not in \usage in Rd file 'check.args_.Rd':
  ‘rename_’ ‘arg.update_’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘assertive.properties’, ‘assertive.types’ in Rd xrefs
Unknown packages ‘assertive.properties’, ‘assertive.types’ in Rd xrefs
'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
Undeclared package ‘rstudioapi’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘sets’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘asteRiskData’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following significant warnings:
  raster.c:22:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/aster.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Running examples in ‘astrochron-Ex.R’ failed
The error most likely occurred in:

> ### Name: asm
> ### Title: Average Spectral Misfit
> ### Aliases: asm
> 
> ### ** Examples
> 
> ## These frequencies are from modelA (type '?astrochron' for more information). 
> ## They are for an 8 meter window, centered at 22 meters height. Units are cycles/m . 
> freq <- c(0.1599833,0.5332776,1.5998329,2.6797201,3.2796575,3.8795948,5.5194235,6.5459830)
> freq <- data.frame(freq)
> 
> ## Rayleigh frequency in cycles/m
> rayleigh <- 0.1245274
> 
> ## Nyquist frequency in cycles/m
> nyquist <- 6.66597
> 
> ## orbital target in 1/ky. Predicted periods for 94 Ma (see Meyers et al., 2012)
> target <- c(1/405.47,1/126.98,1/96.91,1/37.66,1/22.42,1/18.33)
> 
> ## percent uncertainty in orbital target
> fper=c(0.023,0.046,0.042,0.008,0.035,0.004)
> 
> asm(freq=freq,target=target,fper=fper,rayleigh=rayleigh,nyquist=nyquist,sedmin=0.5,sedmax=3,
+     numsed=100,linLog=1,iter=100000,output=FALSE)

----- PERFORMING AVERAGE SPECTRAL MISFIT ANALYSIS -----

 *** caught segfault ***
address 0x7ffe0555c6a0, cause 'memory not mapped'

Traceback:
 1: asm1.8(freq[, 1], numfreq, target[, 1], numtarg, fper[, 1], rayleigh,     nyquist, sedmin, sedmax, numsed, linLog, ispecgen, irepl,     isetfreq, iter)
 2: asm(freq = freq, target = target, fper = fper, rayleigh = rayleigh,     nyquist = nyquist, sedmin = 0.5, sedmax = 3, numsed = 100,     linLog = 1, iter = 1e+05, output = FALSE)
An irrecoverable exception occurred. R is aborting now ...
Specified C++11: please drop specification unless essential
Undeclared package ‘iterators’ in Rd xrefs
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘lubridate’ ‘openair’ ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.rsp’
  All declared Imports should be used.
Undeclared package ‘snpar’ in Rd xrefs
Unknown package ‘snpar’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dlnm’ ‘ggplot2’ ‘mvmeta’ ‘pbs’ ‘tsModel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘gtable’ in Rd xrefs
Note: found 1 marked UTF-8 string
Note: found 54582 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘tensorflow’ in Rd xrefs
'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.
'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
Found the following significant warnings:
  RcppExports.cpp:232:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:266:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:300:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:334:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/autothresholdr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinycssloaders’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
Note: found 610 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘readxl’ ‘reshape2’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘rclipboard’ ‘rmarkdown’
  All declared Imports should be used.
'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
Namespaces in Imports field not imported from:
  ‘MixAll’ ‘dplyr’ ‘lqmm’ ‘matrixcalc’ ‘rmutil’ ‘rootSolve’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
Undeclared package ‘AzureAuth’ in Rd xrefs
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jose’ ‘openssl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httr’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Package suggested but not available for checking: ‘lixoftConnectors’
Note: found 64209 marked UTF-8 strings
Note: found 133353 marked UTF-8 strings
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'write.narrative.Rd':
  ‘trials:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared packages ‘InvariantCausalPrediction’, ‘CompareCausalNetworks’ in Rd xrefs
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 260 marked UTF-8 strings
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   3.9Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
Undeclared package ‘tidyselect’ in Rd xrefs
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'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:
    R      2.5Mb
    data   1.3Mb
    doc    1.8Mb
Undeclared package ‘akima’ in Rd xrefs
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘fdpbandsdata’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 148 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
Undeclared package ‘YaleToolkit’ in Rd xrefs
Note: found 13825 marked UTF-8 strings
File ‘Barnard/libs/Barnard.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
Namespace in Imports field not imported from: ‘mvnfast’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.4Mb
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd file 'BartMixVs-package.Rd':
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Undeclared package ‘Rraven’ in Rd xrefs
File ‘base64enc/libs/base64enc.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.
Undeclared packages ‘jsonlite’, ‘arrow’ in Rd xrefs
Package suggested but not available for checking: ‘rgdal’
Namespace in Imports field not imported from: ‘splines’
  All declared Imports should be used.
'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
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘circlize’ ‘hexbin’ ‘scales’ ‘sna’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘Rmpi’ in Rd xrefs
Namespace in Imports field not imported from: ‘vtable’
  All declared Imports should be used.
Note: found 19 marked UTF-8 strings
File ‘batman/libs/batman.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.
Note: found 490 marked UTF-8 strings
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.5Mb
GNU make is a SystemRequirements.
Invalid package aliases in Rd file 'bayesANOVA-package.Rd':
  ‘bayesANOVA-package’
'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
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
File ‘BayesComm/libs/BayesComm.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
Found the following significant warnings:
  power.c:275:30: warning: format specifies type 'double' but the argument has type 'unsigned int' [-Wformat]
  power.c:450:30: warning: format specifies type 'double' but the argument has type 'unsigned int' [-Wformat]
  power.c:750:30: warning: format specifies type 'double' but the argument has type 'unsigned int' [-Wformat]
  power.c:868:30: warning: format specifies type 'double' but the argument has type 'unsigned int' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/bayescount.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
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: \$
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   7.6Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/BayesFM.Rcheck/00install.out’ for details.
Documented arguments not in \usage in Rd file 'Q_prime.Rd':
  ‘spdean’

Documented arguments not in \usage in Rd file 'neg_kappa_fn4.Rd':
  ‘spde_mats’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘StanHeaders’ ‘astsa’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppParallel’ ‘mlbench’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Undeclared package ‘fGarch’ in Rd xrefs
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
File ‘bayesianETAS/libs/bayesianETAS.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
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    help   1.9Mb
    libs   3.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘FastGP’
  All declared Imports should be used.
Undeclared packages ‘rworldmap’, ‘snowFT’ in Rd xrefs
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   5.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   3.9Mb
Namespaces in Imports field not imported from:
  ‘HDInterval’ ‘MCMCpack’ ‘R2WinBUGS’ ‘R2jags’ ‘carData’ ‘rjags’
  All declared Imports should be used.
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: \$
Note: found 1924 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘matrixcalc’ ‘stats’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'hmmeantemp.Rd':
  ‘dat’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    ex-data   4.7Mb
Found the following significant warnings:
  mbart.cpp:406:27: warning: format specifies type 'int' but the argument has type 'ivs' (aka 'unsigned long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/BayesTree.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
checkRd: (-1) bart.Rd:271: Escaped LaTeX specials: \_
File ‘BayesTree/libs/BayesTree.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.
Note: found 385 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
Undeclared package ‘formula.tools’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Undeclared package ‘betareg’ in Rd xrefs
File ‘BCBCSF/libs/BCBCSF.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.
Found the following files/directories:
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData’
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   3.3Mb
Found the following files/directories:
  ‘fabiabreast.txt’
checkRd: (-1) tlsce.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:93: Escaped LaTeX specials: \_
S3 methods shown with full name in Rd file 'export.bce.Rd':
  ‘export.bce’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘coda’ ‘knitr’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ./Params.h:122:76: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  ./Graph.h:187:27: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  Cbcpgraph.cpp:58:66: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
See ‘/data/gannet/ripley/R/packages/tests-clang/bcp.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 72 marked UTF-8 strings
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 2666 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘dump.txt’
Argument items with no description in Rd file 'bdw.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plot.bdw.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.bdw.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
GNU make is a SystemRequirements.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘beast_plot_toy.pdf’
Note: found 107 marked UTF-8 strings
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘forecast’
  All declared Imports should be used.
'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.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘BenfordTests/libs/BenfordTests.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.
Undeclared package ‘tibble’ in Rd xrefs
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Found the following significant warnings:
  RcppExports.cpp:45:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:85:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:124:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:158:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:203:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:248:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:292:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/BeSS.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Namespace in Imports field not imported from: ‘BiDAG’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘ggplot2’ ‘readxl’ ‘rlist’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 42 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘betategarch/libs/betategarch.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.
Malformed Title field: should not end in a period.
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'print_summary_gibbs_psd_help.Rd':
  ‘flag=T:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 379 marked UTF-8 strings
Note: found 1227 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  sampler_multitrait.c:579:45: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
  sampler_multitrait.c:583:72: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
  sampler_multitrait.c:583:63: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
See ‘/data/gannet/ripley/R/packages/tests-clang/BGLR.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
Found the following significant warnings:
  RcppExports.cpp:58:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/BGVAR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
Note: found 582 marked UTF-8 strings
GNU make is a SystemRequirements.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/bgw.Rcheck/00install.out’ for details.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Undeclared package ‘conf.design’ in Rd xrefs
Specified C++11: please drop specification unless essential
installed size is 155.7Mb
  sub-directories of 1Mb or more:
    include  155.6Mb
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'h.pr.u.Rd':
  ‘z’ ‘ih’ ‘mu’ ‘sigma’ ‘pk’ ‘K’ ‘H’ ‘n’
Argument items with no description in Rd file 'hatpai.u.Rd':
  ‘z’ ‘hk1’ ‘hk0’ ‘ph1’ ‘ph0’ ‘sigma1’ ‘sigma0’ ‘mu1’ ‘mu0’ ‘pai’ ‘H’
  ‘n’
Argument items with no description in Rd file 'ind.u.Rd':
  ‘pr’
Argument items with no description in Rd file 'lambda.u.Rd':
  ‘nu’
Argument items with no description in Rd file 'mu.k.u.Rd':
  ‘k’ ‘ik’ ‘z’ ‘sigma’ ‘mu0’
Argument items with no description in Rd file 'nu.u.Rd':
  ‘ind’ ‘tau’ ‘H’
Argument items with no description in Rd file 'pai.u.Rd':
  ‘b’ ‘a.pai’ ‘b.pai’
Argument items with no description in Rd file 'sig.k.u.Rd':
  ‘k’ ‘ik’ ‘z’ ‘mu0’ ‘a0’ ‘b0’
Argument items with no description in Rd file 'z.pr.u.Rd':
  ‘z’ ‘hk’ ‘mu’ ‘sigma’ ‘ph’ ‘H’ ‘n’
File ‘BiasedUrn/libs/BiasedUrn.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
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 99 marked UTF-8 strings
Note: found 1904 marked UTF-8 strings
Note: found 573 marked UTF-8 strings
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘DAAG’ ‘datasets’ ‘expm’ ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nycflights13’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RBGL’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘lavaan.survey’
Unknown package ‘lavaan.survey’ in Rd xrefs
Found the following significant warnings:
  bigalgebra.cpp:51:21: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/bigalgebra.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Package suggested but not available for checking: ‘ffbase’
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Invalid package aliases in Rd file 'package_bigdist.Rd':
  ‘package_bigdist-package’
Note: found 940 marked Latin-1 strings
Specified C++11: please drop specification unless essential
Found the following calls to data() loading into the global environment:
File ‘biglm/R/bigglm.R’:
  data(reset = TRUE)
  data(reset = FALSE)
See section ‘Good practice’ in ‘?data’.
File ‘biglm/libs/biglm.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++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
Found the following significant warnings:
  deepcopy.cpp:115:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  bigmemory.cpp:898:13: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/bigmemory.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Undeclared package ‘bigrquery’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  RcppExports.cpp:39:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:70:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:101:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/bigReg.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
File ‘bigReg/libs/bigReg.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.
Found the following files/directories:
  ‘outputs’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 660 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
'LazyData' is specified without a 'data' directory
Undeclared packages ‘tint’, ‘pinp’, ‘linl’ in Rd xrefs
Found the following files/directories:
  ‘ccf_ccf_ID31_ID32_res.jpg’ ‘ccf_ccf_ID31_ID32_res.pdf’
  ‘output_ENSO_NHSST.tmp’ ‘plot_plot_ts_RAW_BIN_enso_sst.pdf’
  ‘plot_plot_ts_RAW_BIN_enso_sst01.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst02.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst03.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst04.png’ ‘plot_ts_ACER_ABRUPT.pdf’
  ‘plot_ts_ACER_ABRUPT01.png’ ‘plot_ts_ACER_ABRUPT02.png’
  ‘plot_ts_ACER_ABRUPT03.png’ ‘plot_ts_ACER_ABRUPT04.png’
  ‘salida_ACER_ABRUPT.tmp’ ‘scaterplot_scatterplot_ENSO_SST.jpg’
  ‘scaterplot_scatterplot_ENSO_SST.pdf’
Found the following significant warnings:
  RcppExports.cpp:40:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:73:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:106:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:139:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:172:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:205:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:238:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:271:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:304:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:337:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:370:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:403:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/bindrcpp.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘genalg’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘binom/libs/binom.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: ‘gtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
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
S3 methods shown with full name in Rd file 'select.cfs.Rd':
  ‘select.cfs’

S3 methods shown with full name in Rd file 'select.fast.filter.Rd':
  ‘select.fast.filter’

S3 methods shown with full name in Rd file 'select.forward.Corr.Rd':
  ‘select.forward.Corr’

S3 methods shown with full name in Rd file 'select.forward.wrapper.Rd':
  ‘select.forward.wrapper’

S3 methods shown with full name in Rd file 'select.inf.chi2.Rd':
  ‘select.inf.chi2’

S3 methods shown with full name in Rd file 'select.inf.gain.Rd':
  ‘select.inf.gain’

S3 methods shown with full name in Rd file 'select.inf.symm.Rd':
  ‘select.inf.symm’

S3 methods shown with full name in Rd file 'select.process.Rd':
  ‘select.process’

S3 methods shown with full name in Rd file 'select.relief.Rd':
  ‘select.relief’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘seqinr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
Documented arguments not in \usage in Rd file 'predict2.em.Rd':
  ‘na.rm’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘bioPN/libs/bioPN.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.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.0Mb
Undeclared package ‘vegan’ in Rd xrefs
Invalid package aliases in Rd file 'bios2cor-package.Rd':
  ‘bios2cor-package’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 46 marked UTF-8 strings
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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
Undeclared package ‘RColorBrewer’ in Rd xrefs
Package suggested but not available for checking: ‘RQuantLib’
Note: found 516 marked UTF-8 strings
Argument items with no description in Rd file 'ONA_compiled.Rd':
  ‘ATN’
Namespaces in Imports field not imported from:
  ‘R6’ ‘knitr’
  All declared Imports should be used.
Found the following significant warnings:
  RcppExports.cpp:125:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:159:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/blatent.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘digest’ ‘ergm’ ‘foreign’ ‘gWidgets2’ ‘gWidgets2tcltk’ ‘haven’
  ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
Argument items with no description in Rd file 'export.dyadic.Rd':
  ‘blauObj’
Package suggested but not available for checking: ‘cmdstanr’
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R          1.2Mb
    libs       7.3Mb
    testdata   1.4Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘np’ in Rd xrefs
File ‘blockTools/libs/blockTools.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: ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
Specified C++11: please drop specification unless essential
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
GNU make is a SystemRequirements.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'id2rownum.Rd':
  ‘ids’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘fastDummies’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
Note: found 21550 marked UTF-8 strings
Package suggested but not available for checking: ‘sangerseqR’
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    include  10.5Mb
    lib      36.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘HSAUR3’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘psych’ in Rd xrefs
File ‘bootruin/libs/bootruin.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.
Documented arguments not in \usage in Rd file 'check_inputs.Rd':
  ‘h_rs’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
Documented arguments not in \usage in Rd file 'InternalFunctions.Rd':
  ‘metric’ ‘matrix’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'info.Rd':
  ‘mod_spec’ ‘pkg_spec’

Documented arguments not in \usage in Rd file 'path.Rd':
  ‘args’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared packages ‘data.table’, ‘readxl’, ‘openxlsx’ in Rd xrefs
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'b_samp.Rd':
  ‘Y’

Documented arguments not in \usage in Rd file 'betaBlock.Rd':
  ‘Y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Documented arguments not in \usage in Rd file 'utils.Rd':
  ‘max.len’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘Branching/libs/Branching.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: ‘dplyr’
  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
Undeclared package ‘generics’ in Rd xrefs
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'availability.int.Rd':
  ‘v.set’ ‘dir.set’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'subset.int.Rd':
  ‘subset.int’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 87 marked UTF-8 strings
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
Found the following significant warnings:
  read_file.c:29:43: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_file_raw.c:29:43: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_lines.c:67:43: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/brio.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘cmdstanr’
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R     3.0Mb
    doc   3.6Mb
Package suggested but not available for checking: ‘glmmADMB’
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'table.Rd':
  ‘headTitles’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Undeclared package ‘data.table’ in Rd xrefs
Undeclared package ‘weibullness’ in Rd xrefs
Argument items with no description in Rd file 'plot.bshazard.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.bshazard.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.bshazard.Rd':
  ‘\dots’
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    fonts   3.7Mb
    lib     5.4Mb
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘grDevices’ ‘graphics’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   2.6Mb
Namespaces in Imports field not imported from:
  ‘mvtnorm’ ‘ssmn’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  bsts.cc:101:24: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  dirm.cc:91:24: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/bsts.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘RSiena’
Note: found 89 marked UTF-8 strings
Package suggested but not available for checking: ‘gvcm.cat’
Specified C++11: please drop specification unless essential
Unknown package ‘gvcm.cat’ in Rd xrefs
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘mitools’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
Undeclared package ‘googledrive’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘magrittr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'count.Rd':
  ‘.data’

Documented arguments not in \usage in Rd file 'unite.Rd':
  ‘.data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared packages ‘Hmisc’, ‘gtools’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'calcIntegralSurv2_cpp.Rd':
  ‘dsurvival’

Documented arguments not in \usage in Rd file 'dot-calcIntegralCif_cpp.Rd':
  ‘cif’ ‘CIF_t’

Documented arguments not in \usage in Rd file 'validFCTs.Rd':
  ‘super.classes’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘bvarsv/libs/bvarsv.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.
Found the following significant warnings:
  RcppExports.cpp:157:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:279:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:317:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:355:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/bvartools.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Undeclared packages ‘quadprog’, ‘nnls’ in Rd xrefs
File ‘bvls/libs/bvls.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
'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.
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
Note: found 179 marked UTF-8 strings
'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
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
Note: found 58 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'get_result.Rd':
  ‘out’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘CAMAN/libs/CAMAN.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
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rgdal', 'tesseract'

Requires orphaned package: ‘overlap’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc        2.2Mb
    pictures   4.2Mb
Undeclared package ‘plotrix’ in Rd xrefs
Note: found 287 marked UTF-8 strings
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Note: found 2992 marked UTF-8 strings
Note: found 23 marked UTF-8 strings
Argument items with no description in Rd file 'makeEventHistory.Rd':
  ‘type’
Argument items with no description in Rd file 'plotSeqCount.Rd':
  ‘segColors’
Undeclared packages ‘yacca’, ‘CCA’ in Rd xrefs
Found the following files/directories:
  ‘MDA231_tree.pdf’
'LazyData' is specified without a 'data' directory
Note: found 59 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘htmltools’ ‘shinydashboard’
  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:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
Note: found 1 marked UTF-8 string
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘methods’ ‘readr’ ‘recipes’ ‘sf’ ‘stringr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Undeclared package ‘plotrix’ in Rd xrefs
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    www  12.3Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'EcoLinkPredict.Rd':
  ‘EcoLinkPredict-package’
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       2.8Mb
    extdata   1.9Mb
Documented arguments not in \usage in Rd file 'validate_cover_cats.Rd':
  ‘cats_target’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘broom’ ‘epitools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    doc  37.7Mb
Documented arguments not in \usage in Rd file 'add_catmaply_slider.Rd':
  ‘text_font_color’ ‘categorical_col’

Documented arguments not in \usage in Rd file 'add_catmaply_traces.Rd':
  ‘categorical_col’

Documented arguments not in \usage in Rd file 'catmaply_annotations.Rd':
  ‘fig’ ‘text_font_color’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
Undeclared packages ‘pixmap’, ‘XML’, ‘exactRankTests’, ‘coin’, ‘ROCR’, ‘Epi’, ‘verification’, ‘Hmisc’, ‘gtools’, ‘magic’, ‘zoo’ in Rd xrefs
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘epitools’ ‘forcats’ ‘purrr’
  All declared Imports should be used.
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
Undeclared packages ‘extraDistr’, ‘mvtnorm’ in Rd xrefs
Note: found 32 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘CBPS’ ‘spelling’
  All declared Imports should be used.
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
Undeclared package ‘graph’ in Rd xrefs
GNU make is a SystemRequirements.
Note: found 1 marked UTF-8 string
Undeclared package ‘sitmo’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
GNU make is a SystemRequirements.
Found the following significant warnings:
  RPP.cpp:23:14: warning: 'operator<<' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  RPP.cpp:24:14: warning: 'operator<<' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/cccp.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Namespace in Imports field not imported from: ‘GeneNet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hotcold.csv’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Packages which this enhances but not available for checking:
  'CirceR', 'Capr'
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Found the following significant warnings:
  cec_r.cpp:65:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  cec_r.cpp:75:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  cec_r.cpp:123:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  cec_r.cpp:133:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  cec_r.cpp:160:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  cec_r.cpp:167:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/CEC.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'buildModel.Rd':
  ‘x’ ‘y’

Documented arguments not in \usage in Rd file 'modelKrigingInternalPredictor.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'selfAdapt.Rd':
  ‘nvaleus’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
Documented arguments not in \usage in Rd file 'evaluate_rule.Rd':
  ‘class’

Documented arguments not in \usage in Rd file 'tree_leaf_nodes.Rd':
  ‘classes.’ ‘invert.’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'CensMFM-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Documented arguments not in \usage in Rd file 'blackboost_train.Rd':
  ‘x’ ‘y’

Documented arguments not in \usage in Rd file 'survival_prob_mboost.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'centralplot.Rd':
  ‘alpha’
'LazyData' is specified without a 'data' directory
Note: found 104 marked UTF-8 strings
Undeclared package ‘vegan’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘base’ ‘stats’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘batchtools’ ‘data.table’ ‘dplyr’ ‘ggplot2’ ‘htmltools’
  ‘jsonlite’ ‘magrittr’ ‘methods’ ‘plotly’ ‘reshape’ ‘rlang’ ‘shiny’
  ‘shinyWidgets’ ‘shinyjqui’ ‘shinyjs’ ‘shinymaterial’ ‘sortable’ ‘ssh’
  ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
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
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'create_epa.Rd':
  ‘clean_pbp_dat’ ‘df’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 38.5Mb
  sub-directories of 1Mb or more:
    include  38.3Mb
Malformed Title field: should not end in a period.
File ‘cgAUC/libs/cgAUC.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
S3 methods shown with full name in Rd file 'select.cglasso.Rd':
  ‘select.cglasso’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Undeclared packages ‘bigBits’, ‘dplyr’, ‘matrixStats’, ‘filesstrings’, ‘pracma’, ‘sf’ in Rd xrefs
Objects in \usage without \alias in Rd file 'influence-methods.Rd':
  ‘influence’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file 'jumpointsVar-package.Rd':
  ‘jumpointsVar-package’
Objects in \usage without \alias in Rd file 'jumpointsVar-internal.Rd':
  ‘seg.lm.fit0.gamma’ ‘max.rss’ ‘print.jumpointsVar’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'jumpointsVar-internal.Rd':
  ‘max.rss’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘bench’ ‘ggplot2’
  All declared Imports should be used.
Invalid package aliases in Rd file 'ChangePointAnalyzer-package.Rd':
  ‘ChangePointAnalyzer-package’
Auto-generated content requiring editing in Rd file 'ChangePointAnalyzer-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Documented arguments not in \usage in Rd file 'multiplierDSeqfun.Rd':
  ‘MC’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘AER’ ‘graphics’ ‘lmtest’
  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
Package suggested but not available for checking: ‘darts’
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Note: found 200 marked UTF-8 strings
Undeclared package ‘mvoutlier’ in Rd xrefs
Documented arguments not in \usage in Rd file 'dot-chkArgs.Rd':
  ‘mode.’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘countreg’
Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown'
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Note: found 32 marked UTF-8 strings
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Note: found 8119 marked UTF-8 strings
Invalid package aliases in Rd file 'ChIPtest-package.Rd':
  ‘ChIPtest_1.0-package’
File ‘ChIPtest/libs/ChIPtest.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
Package suggested but not available for checking: ‘cmdstanr’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘cmdstanr’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.1Mb
    libs      1.9Mb
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
Objects in \usage without \alias in Rd file 'choplump-internal.Rd':
  ‘chooseMatrix’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘entab’
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘prettydoc’ ‘rmdformats’ ‘skimr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
Documented arguments not in \usage in Rd file 'SearchEmptyClusters.Rd':
  ‘oldcluster’ ‘SSminvec’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘R6’
  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
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 28982 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘circlize’ ‘utils’
  All declared Imports should be used.
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.3Mb
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘networkD3’
  All declared Imports should be used.
'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
Note: found 29 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
    help   1.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Undeclared package ‘reshape’ in Rd xrefs
Note: found 9 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
'LazyData' is specified without a 'data' directory
Undeclared packages ‘bslib’, ‘shiny’ in Rd xrefs
'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
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ClickClust/libs/ClickClust.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.
Note: found 1 marked UTF-8 string
Note: found 27934 marked UTF-8 strings
Note: found 10332 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 8737 marked UTF-8 strings
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Undeclared package ‘s2dv’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Found the following significant warnings:
  progress.c:98:37: warning: data argument not used by format string [-Wformat-extra-args]
See ‘/data/gannet/ripley/R/packages/tests-clang/cli.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
File ‘clogitboost/libs/clogitboost.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 ‘clogitL1/libs/clogitL1.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.
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'clpm-internal.Rd':
  ‘lpm.newton2’ ‘lpm.fit’ ‘lpm.newton’ ‘L_lambda’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘mlbench’, ‘fpc’ in Rd xrefs
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'auxiliary_functions.Rd':
  ‘edelist’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Objects in \usage without \alias in Rd file 'clustEff-internal.Rd':
  ‘.get_ave_sil_width’ ‘.get_withinSS’ ‘print.clustEff’
  ‘print.summary.clustEff’ ‘print.fpcac’ ‘print.summary.fpcac’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘clusterhap_reports’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'calculate_connectivity.Rd':
  ‘datdf’

Documented arguments not in \usage in Rd file 'dunn_metric.Rd':
  ‘distance’ ‘method’

Documented arguments not in \usage in Rd file 'evaluate_all_column_dataset.Rd':
  ‘data’

Documented arguments not in \usage in Rd file 'information_external.Rd':
  ‘info’

Documented arguments not in \usage in Rd file 'information_internal.Rd':
  ‘info’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘clustering.sc.dp/libs/clustering.sc.dp.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: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ClusterStability/libs/ClusterStability.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:
  ‘sp’ ‘spdep’
  All declared Imports should be used.
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Note: found 5626 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘datasets’ ‘dplyr’ ‘klaR’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘clv/libs/clv.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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MPV’
  All declared Imports should be used.
'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: ‘MASS’
  All declared Imports should be used.
Note: found 4622 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:22: Escaped LaTeX specials: \#
File ‘cmprsk/libs/cmprsk.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:
  ‘FNN’ ‘R.utils’ ‘SearchTrees’ ‘colorspace’ ‘colourpicker’
  ‘data.table’ ‘maps’ ‘ncdf4’ ‘raster’ ‘shinyFiles’ ‘shinyWidgets’
  ‘shinyjs’ ‘shinythemes’ ‘tcltk’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tobit1’
'LazyData' is specified without a 'data' directory
Undeclared package ‘wavethresh’ in Rd xrefs
Specified C++11: please drop specification unless essential
'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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
Namespace in Imports field not imported from: 'Hmisc'
  All declared Imports should be used.
Package suggested but not available for checking: ‘PopGenome’
Documented arguments not in \usage in Rd file 'feat_sample.Rd':
  ‘locus_group’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'get_superior.Rd':
  ‘stirng’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘disttree’
Documented arguments not in \usage in Rd file 'lb_calculation.Rd':
  ‘qu.param’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) drqssbc.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) qbsks.Rd:81: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 14729 marked UTF-8 strings
Package which this enhances but not available for checking: ‘rkward’
Undeclared package ‘pls’ in Rd xrefs
Documented arguments not in \usage in Rd file 'cocorresp-internal.Rd':
  ‘Y’ ‘eps’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package which this enhances but not available for checking: ‘rkward’
Note: found 27 marked UTF-8 strings
Package suggested but not available for checking: ‘userfriendlyscience’
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘rlang’ ‘tidyselect’ ‘vctrs’
  All declared Imports should be used.
Note: found 65 marked UTF-8 strings
Note: found 30244 marked UTF-8 strings
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
Note: found 6 marked UTF-8 strings
Package suggested but not available for checking: ‘bvpSolve’
'LazyData' is specified without a 'data' directory
File ‘coenoflex/libs/coenoflex.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: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   2.2Mb
Note: found 4186 marked UTF-8 strings
Note: found 89 marked Latin-1 strings
  Note: found 1203 marked UTF-8 strings
File ‘collUtils/libs/collUtils.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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘qpdf’
  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
'LazyData' is specified without a 'data' directory
Note: found 742 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   2.1Mb
Note: found 2 marked UTF-8 strings
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.
Namespaces in Imports field not imported from:
  ‘chi’ ‘dplyr’ ‘spatstat.utils’ ‘utils’
  All declared Imports should be used.
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
Argument items with no description in Rd file 'summary.CommunityClimateInput.Rd':
  ‘object’ ‘\dots’
Argument items with no description in Rd file 'summary.CommunityClimateStatistics.Rd':
  ‘object’ ‘\dots’
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
Objects in \usage without \alias in Rd file 'comf-internal.Rd':
  ‘calcet’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘GGally’ ‘RColorBrewer’ ‘abind’ ‘diagram’ ‘ggplot2’ ‘grid’ ‘gtable’
  ‘igraph’ ‘magrittr’ ‘plyr’ ‘purrr’ ‘reshape2’ ‘scales’ ‘useful’
  All declared Imports should be used.
Found the following significant warnings:
  RcppExports.cpp:59:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:110:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:159:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/Compack.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘CAM’
File ‘compareC/libs/compareC.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.
Documented arguments not in \usage in Rd file 'CopulaSelection.Rd':
  ‘rhoType’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
Rd files without \alias:
  ‘CompoundEvents-package.Rd’
'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
File ‘ConConPiWiFun/libs/ConConPiWiFun.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.
Note: found 92 marked UTF-8 strings
Undeclared packages ‘DescTools’, ‘epiR’ in Rd xrefs
Auto-generated content requiring editing in Rd file 'concordancer-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kernlab’ ‘purrr’ ‘survminer’ ‘tidyverse’
  All declared Imports should be used.
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Undeclared package ‘mvtnorm’ in Rd xrefs
'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 export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  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: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘base’ ‘lwgeom’ ‘s2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘dplyr’ ‘foreign’ ‘lavaan’ ‘openxlsx’ ‘purrr’ ‘semTools’
  ‘shinyWidgets’ ‘stringr’ ‘summarytools’ ‘waiter’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.9Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'postProcessSys.Rd':
  ‘myFile’

Documented arguments not in \usage in Rd file 'theta_ll.Rd':
  ‘params’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘scales’ ‘sna’
  All declared Imports should be used.
Note: found 244 marked UTF-8 strings
Undeclared package ‘ggplot2’ in Rd xrefs
File ‘ConsReg/libs/ConsReg.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.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
File ‘contoureR/libs/contoureR.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
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'print_table.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 1 marked UTF-8 string
'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 significant warnings:
  RcppExports.cpp:47:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:84:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:120:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:157:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/cooltools.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Invalid package aliases in Rd file 'coopProductGame-package.Rd':
  ‘coopProducGame-package’
Note: found 144 marked UTF-8 strings
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.6Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'ft.Rd':
  ‘theta’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘cord/libs/cord.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
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘re2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
Note: found 1187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 438 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘xcms’
Note: found 2 marked Latin-1 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
Note: found 59 marked UTF-8 strings
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘xaringan’, ‘beepr’ in Rd xrefs
'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:
    R      1.2Mb
    data   1.1Mb
    doc    1.3Mb
    help   2.0Mb
Note: found 9044 marked UTF-8 strings
Note: found 140280 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
File ‘covBM/libs/covBM.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
Found the following files/directories:
  ‘covfefe_inauguration.txt’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.7Mb
Note: found 1934235 marked UTF-8 strings
Note: found 2385 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mapview’ ‘plotly’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
Note: found 213180 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘gsl’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘CoxPlus/libs/CoxPlus.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
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘BEST’
Found the following significant warnings:
  cpglmm.c:273:18: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  cpglmm.c:273:28: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  cpglmm.c:1096:18: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  cpglmm.c:1096:28: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/cplm.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
File ‘cpm/libs/cpm.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++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
File ‘cqrReg/libs/cqrReg.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
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
File ‘credule/libs/credule.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.
Note: found 37 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer3’
Namespaces in Imports field not imported from:
  ‘DT’ ‘gbm’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
Packages suggested but not available for checking: 'conos', 'pagoda2'
Documented arguments not in \usage in Rd file 'pinvGamma.Rd':
  ‘logical;’

Documented arguments not in \usage in Rd file 'qinvGamma.Rd':
  ‘logical;’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
‘cleanup’: /bin/bash is not portable
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
Undeclared package ‘R2jags’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘crrSC/libs/crrSC.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.
Note: found 500 marked UTF-8 strings
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘geosphere’ ‘mapdata’ ‘maps’ ‘marmap’ ‘shinydashboard’
  ‘shinyjs’ ‘stringr’ ‘swfscDAS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘copula’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgeos’
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘Rdpack’
  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:
  ‘extrafont’ ‘future’
  All declared Imports should be used.
Note: found 282 marked UTF-8 strings
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    1.6Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Note: found 3031 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'tool.Rd':
  ‘seq’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    1.4Mb
    libs   2.1Mb
Found the following significant warnings:
  int64.c:187:92: warning: format specifies type 'long long' but the argument has type 'double' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/csvread.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.
'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 significant warnings:
  RcppExports.cpp:38:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:71:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/ctmcd.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'ctqr-internal.Rd':
  ‘findagoodestimator’ ‘safe.pch’ ‘quickpred’ ‘check.in.ctqr’ ‘start’
  ‘ee.u’ ‘ee.cens’ ‘ee.cens.trunc’ ‘ee.icens’ ‘qr.gs’ ‘nobs.ctqr’
  ‘vcov.ctqr’ ‘coef.ctqr’ ‘print.ctqr’ ‘summary.ctqr’
  ‘print.summary.ctqr’ ‘firstep.ct’ ‘firstep.ic’ ‘asy.qr.ct’
  ‘asy.qr.ic’ ‘safesolve’ ‘regularize_corr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'ctqr-internal.Rd':
  ‘qr.gs’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
Note: found 1350 marked UTF-8 strings
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.7Mb
    libs  11.5Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘par-7269706c6579’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Hello.csv’
'LazyData' is specified without a 'data' directory
Undeclared package ‘caret’ in Rd xrefs
Documented arguments not in \usage in Rd file 'chi2cub2cov.Rd':
  ‘covar’

Documented arguments not in \usage in Rd file 'cubpq.Rd':
  ‘summary’

Documented arguments not in \usage in Rd file 'cubshe.Rd':
  ‘makeplot’ ‘summary’

Documented arguments not in \usage in Rd file 'kkk.Rd':
  ‘Vector’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  handle.c:115:20: warning: field precision should have type 'int', but argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  utils.c:42:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  utils.c:78:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  utils.c:87:29: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/curl.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 459 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
Specified C++11: please drop specification unless essential
'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: \_ \_ \_
Documented arguments not in \usage in Rd file 'cvRiskPlot.Rd':
  ‘estimator’

Documented arguments not in \usage in Rd file 'matrixMetrics.Rd':
  ‘estimator’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package which this enhances but not available for checking: ‘RGtk2’
Documented arguments not in \usage in Rd file 'compute_stat.Rd':
  ‘K_0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    doc    1.2Mb
    help   1.1Mb
File ‘cycleRtools/libs/cycleRtools.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.
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    docs          1.0Mb
    extdata       1.4Mb
    htmlwidgets   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    img   4.4Mb
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 469 marked UTF-8 strings
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'tree.filter.Rd':
  ‘nodeList’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 109157 marked UTF-8 strings
Note: found 4 marked Latin-1 strings
  Note: found 21 marked UTF-8 strings
Note: found 2020 marked UTF-8 strings
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 212 marked Latin-1 strings
  Note: found 12719 marked UTF-8 strings
File ‘DALY/libs/DALY.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.
Documented arguments not in \usage in Rd file 'mm_run_reg.Rd':
  ‘all_params’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
Invalid package aliases in Rd file 'dap-package.Rd':
  ‘dap-package’
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
Undeclared package ‘DRquality’ in Rd xrefs
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'plotDataExplorer.single.Rd':
  ‘obj’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘my new data set.rds’
Namespace in Imports field not imported from: ‘lattice’
  All declared Imports should be used.
Note: found 72720 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Datastream DWE - now decommissioned by Refinitiv
    CRAN
Documented arguments not in \usage in Rd file 'dotgetJSONValue.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 8 marked Latin-1 strings
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
Undeclared package ‘tidyselect’ in Rd xrefs
Undeclared package ‘FCPS’ in Rd xrefs
Undeclared package ‘performance’ in Rd xrefs
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 2596 marked UTF-8 strings
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 54339 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘sfsmisc’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tidyverse’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘withr’ in Rd xrefs
Package suggested but not available for checking: ‘dblog’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
S3 methods shown with full name in Rd file 'dbglm-internal.Rd':
  ‘dbglm.iteration’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘html5’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘lubridate’ ‘tseries’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'a_dcc_mat_est.Rd':
  ‘param’

Documented arguments not in \usage in Rd file 'dcc_mat_est.Rd':
  ‘param’

Documented arguments not in \usage in Rd file 'deco_mat_est.Rd':
  ‘param’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 122 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 38 marked UTF-8 strings
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Undeclared package ‘fda.usc’ in Rd xrefs
Found the following significant warnings:
  difeq.c:269:14: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  dopri.c:333:16: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  r_difeq.c:215:14: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  r_difeq.c:224:16: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  r_dopri.c:93:64: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  util.c:36:62: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/dde.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    sample_data   3.1Mb
Namespace in Imports field not imported from: ‘shinydisconnect’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'DDPNA-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
Argument items with no description in Rd file 'DEP_Mod_net_plot.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
Note: found 53 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'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
Undeclared package ‘future’ in Rd xrefs
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
Note: found 1 marked Latin-1 string
  Note: found 46826 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'getTriContextFraction.Rd':
  ‘trimer.counts.ref’

Documented arguments not in \usage in Rd file 'norm.it.Rd':
  ‘trimer.counts’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 7 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
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'degreenet-internal.Rd':
  ‘range’ ‘lims’
Objects in \usage without \alias in Rd file 'degreenet-internal.Rd':
  ‘bootstrapyule’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Undeclared packages ‘e1071’, ‘nloptr’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘knitr’ ‘shinyBS’ ‘shinyMatrix’
  All declared Imports should be used.
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
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
Found the following files/directories:
  ‘smd_table.docx’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Documented arguments not in \usage in Rd file 'boot_f_cor.Rd':
  ‘fun’

Documented arguments not in \usage in Rd file 'boot_f_pcor.Rd':
  ‘fun’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
Note: found 3 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: found 2534 marked UTF-8 strings
Rd files without \alias:
  ‘densityClust-package.Rd’
Undeclared package ‘DEoptim’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    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’
Specified C++11: please drop specification unless essential
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘FactoMineR’, ‘vcd’ in Rd xrefs
Note: found 5764 marked UTF-8 strings
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’
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘htmlwidgets’ in Rd xrefs
Package suggested but not available for checking: ‘RDCOMClient’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.6Mb
Undeclared packages ‘ineq’, ‘randtests’, ‘Hmisc’, ‘plotrix’, ‘caret’, ‘pcaPP’, ‘polycor’, ‘lmtest’, ‘car’, ‘gmp’, ‘vcdExtra’, ‘chron’, ‘coin’, ‘caTools’, ‘forecast’, ‘sfsmisc’, ‘vcd’, ‘areaplot’, ‘corrgram’, ‘UsingR’, ‘memisc’, ‘gtools’, ‘BSDA’, ‘prettyR’ in Rd xrefs
Undeclared package ‘RcppArmadillo’ in Rd xrefs
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
Note: found 47 marked UTF-8 strings
'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          1.8Mb
    htmlwidgets   3.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Documented arguments not in \usage in Rd file 'encode_unit.Rd':
  ‘original’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 8014 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘purrr’
  All declared Imports should be used.
Undeclared package ‘tibble’ in Rd xrefs
'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
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
File ‘diffIRT/libs/diffIRT.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
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'Nortonbass_startvalgen.Rd':
  ‘param’ ‘startvalgen’

Documented arguments not in \usage in Rd file 'seqdiffusion.Rd':
  ‘w’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘gurobi’
Note: found 15 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘CVST’ in Rd xrefs
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘gamlss’, ‘flexsurv’ in Rd xrefs
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘discreteMTP’
Unknown package ‘discreteMTP’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'RV.Rd':
  ‘RV-package’
'LazyData' is specified without a 'data' directory
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: \&
Undeclared package ‘Hmisc’ in Rd xrefs
Note: found 270 marked UTF-8 strings
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
Note: found 106 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
'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: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘proxy’
  All declared Imports should be used.
Undeclared package ‘robustbase’ in Rd xrefs
Documented arguments not in \usage in Rd file 'internals.Rd':
  ‘namestoGather’ ‘namestoGatherNS’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘RobAStBase’ in Rd xrefs
Documented arguments not in \usage in Rd file 'internalmleHelpers.Rd':
  ‘validity.check’

Objects in \usage without \alias in Rd file 'internals.Rd':
  ‘.csimpsum’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Assignments in \usage in Rd file 'internalGenerics.Rd':
  x <- samplesize(object, value)

Documented arguments not in \usage in Rd file 'internals.Rd':
  ‘DClass’
Objects in \usage without \alias in Rd file 'internals.Rd':
  ‘.consolidategaps’ ‘.List’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘distrTEst’ in Rd xrefs
Undeclared package ‘distr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'diveMove-internal.Rd':
  ‘.diveMatches’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘truncnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggmulti’ ‘loon’ ‘loon.data’ ‘loon.ggplot’ ‘loon.shiny’ ‘loon.tourr’
  ‘stats’ ‘zenplots’
  All declared Imports should be used.
Found the following significant warnings:
  GslOdeBase.cpp:48:7: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  GslOdeBase.cpp:48:15: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  GslOdeBase.cpp:103:7: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  GslOdeBase.cpp:103:15: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  TimeMachine.cpp:39:50: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  TimeMachine.cpp:39:57: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/diversitree.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used Fortran compiler: ‘flang-new version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
Package suggested but not available for checking: ‘BOLTSSIRR’
Package suggested but not available for checking: ‘rgdal’
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plotly’ ‘pryr’ ‘rpart’
  All declared Imports should be used.
Undeclared package ‘palaeoverse’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘dkDNA/libs/dkDNA.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
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include  16.3Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:20: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:26: Escaped LaTeX specials: \&
Invalid package aliases in Rd file 'dmaiIntro.Rd':
  ‘dmaiIntro-package’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'dml_bagging.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_boosting.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_ensemble_lm.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_ensemble_rf.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_neural_network.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_random_forest.Rd':
  ‘y,x,d,data,sed’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
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++11: please drop specification unless essential
Invalid package aliases in Rd file 'dnapath2-package.Rd':
  ‘dnapath2-package’
Auto-generated content requiring editing in Rd file 'dnapath2-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Note: found 175 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
S3 methods shown with full name in Rd file 'add.joint.mean.many.Rd':
  ‘all.cond.mean.PO’ ‘all.cond.mean2.PO’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd file 'derivType.Rd':
  ‘L’ ‘mu’ ‘eps’
Argument items with no description in Rd file 'getNewParams.SC.Rd':
  ‘n.fft’
Argument items with no description in Rd file 'graph.CTMC.Rd':
  ‘\dots’
Argument items with no description in Rd file 'num.deriv.Rd':
  ‘\dots’
Argument items with no description in Rd file 'power.coef.one.Rd':
  ‘\dots’
Documented arguments not in \usage in Rd file 'concDict.Rd':
  ‘text’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Note: found 9796 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'check_results.Rd':
  ‘error_on_failure’ ‘error_on_warning’

Documented arguments not in \usage in Rd file 'function_get_comments.Rd':
  ‘thresholds’

Documented arguments not in \usage in Rd file 'vignette_results_display.Rd':
  ‘vignette_results’ ‘error_on_failure’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   1.0Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    data      1.9Mb
    extdata   2.3Mb
Undeclared package ‘molaR’ in Rd xrefs
Note: found 100 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New features
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘DT’ ‘DoseFinding’ ‘Rsolnp’ ‘ggplot2’ ‘kableExtra’ ‘knitr’
  ‘latticeExtra’ ‘purrr’ ‘readxl’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  ‘stringr’ ‘utils’
  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.
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
Note: found 2 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Undeclared package ‘broomExtra’ in Rd xrefs
Unknown package ‘broomExtra’ in Rd xrefs
'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  5.3Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.1Mb
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘ggplot2’ ‘nloptr’
  All declared Imports should be used.
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Undeclared package ‘RcppEigen’ in Rd xrefs
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'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: \&
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
Undeclared package ‘SimMultiCorrData’ in Rd xrefs
'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: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: \&
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
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   3.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   2.3Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘data.table’ in Rd xrefs
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rJava’ ‘tools’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Undeclared package ‘EvalEst’ in Rd xrefs
Documented arguments not in \usage in Rd file 'forecastCovCompiled.Rd':
  ‘obj’ ‘zero’ ‘trend’ ‘estimation.sample’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘dse/libs/dse.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.
Note: found 149 marked UTF-8 strings
Note: found 4891 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘dsBaseClient’
'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.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘dstat’, ‘sensitivity2x2xk’ in Rd xrefs
Note: found 1 marked Latin-1 string
'LazyData' is specified without a 'data' directory
Note: found 281 marked UTF-8 strings
'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
Undeclared package ‘vctrs’ in Rd xrefs
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.0Mb
GNU make is a SystemRequirements.
Objects in \usage without \alias in Rd file 'd.spls.norm1.Rd':
  ‘d.spls.norm2’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘dualtrees/libs/dualtrees.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:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 39.2Mb
  sub-directories of 1Mb or more:
    libs  38.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2854 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Undeclared package ‘rdwd’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GenEst’ ‘expint’ ‘numDeriv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘quadprog’ in Rd xrefs
Undeclared package ‘stringdist’ in Rd xrefs
Package suggested but not available for checking: ‘rgdal’
Package suggested but not available for checking: ‘cmdstanr’
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    R      3.3Mb
    data   8.3Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘NatureSounds’ ‘av’ ‘magrittr’ ‘stats’
  All declared Imports should be used.
Undeclared package ‘warbleR’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'dynConfiR-package.Rd':
  ‘dynWEV-package’
Package suggested but not available for checking: ‘lle’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Undeclared package ‘CausalImpact’ in Rd xrefs
'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: \&
File ‘dynpred/libs/dynpred.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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.4Mb
Note: found 9 marked UTF-8 strings
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Undeclared package ‘leaps’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 10 marked UTF-8 strings
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘example_table1.csv’ ‘example_table1.txt’ ‘example_table2.csv’
  ‘example_table2.txt’ ‘example_table3.csv’ ‘example_table3.txt’
  ‘table1.csv’ ‘table2.csv’ ‘table2.txt’ ‘table3.txt’ ‘table4.txt’
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘stringi’
  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: ‘rprojroot’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
Namespace in Imports field not imported from: ‘qcr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Found the following significant warnings:
  RcppExports.cpp:41:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:75:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:112:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:147:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:177:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/ECctmc.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'e.cluster.decision.Rd':
  ‘reg_data’ ‘log.lambda’
Argument items with no description in Rd file 'e.cluster.dendrogram.Rd':
  ‘echelon.obj’ ‘n.sim’ ‘cluster.legend.pos’ ‘cluster_reg’ ‘p_rank’
  ‘para’
Argument items with no description in Rd file 'e.cluster.map.Rd':
  ‘x’ ‘c_separates’ ‘locs’ ‘coo’ ‘rin’ ‘p_rank’ ‘cluster_reg’ ‘n.sim’
  ‘cluster.type’
Argument items with no description in Rd file 'e.dendrogram.Rd':
  ‘peaks’ ‘locs’ ‘x’ ‘separates’ ‘c_separates’ ‘number’ ‘parents’
  ‘pare_locs’ ‘progeny’ ‘symbols’ ‘col.symbols’ ‘cex.symbols’ ‘lwd’
  ‘col’ ‘ens’ ‘adj.ens’ ‘col.ens’ ‘cex.ens’ ‘limb’
Argument items with no description in Rd file 'e.dendrogram.axis.Rd':
  ‘main’ ‘ylab’ ‘yaxes’ ‘ylim’ ‘xaxes’ ‘xdper’ ‘dmai’ ‘peaks’ ‘x’
Argument items with no description in Rd file 'e.main.Rd':
  ‘x’ ‘rin’ ‘T’
Argument items with no description in Rd file 'e.monte.bin.Rd':
  ‘rin’ ‘cas’ ‘pop’ ‘n.sim’ ‘K’ ‘cluster.type’
Argument items with no description in Rd file 'e.monte.poi.Rd':
  ‘rin’ ‘cas’ ‘pop’ ‘ex’ ‘n.sim’ ‘K’ ‘cluster.type’
Argument items with no description in Rd file 'e.profile.Rd':
  ‘peaks’ ‘parents’ ‘separates’
Argument items with no description in Rd file 'e.scan.Rd':
  ‘x’ ‘locs’ ‘peaks’ ‘c_separates’ ‘parents’ ‘K’
Argument items with no description in Rd file 'e.scan.pop.Rd':
  ‘x’ ‘locs’ ‘peaks’ ‘c_separates’ ‘parents’ ‘K’ ‘pop’
Argument items with no description in Rd file 'nlimb.Rd':
  ‘x’ ‘k2’
'LazyData' is specified without a 'data' directory
Note: found 1281 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 42 marked UTF-8 strings
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  RcppExports.cpp:40:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:74:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:108:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/eddington.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Undeclared package ‘magrittr’ in Rd xrefs
'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
Note: found 22 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared packages ‘tidyr’, ‘scales’ in Rd xrefs
Note: found 6 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘htmlwidgets’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘tibble’
  All declared Imports should be used.
Note: found 74 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'fcf.env.Rd':
  ‘vars’

Documented arguments not in \usage in Rd file 'getlevels.Rd':
  ‘editarray’

Documented arguments not in \usage in Rd file 'parseCatEdit.Rd':
  ‘e’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Undeclared package ‘ndl’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘T2EQ’ in Rd xrefs
Note: found 136358 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘PCovR’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Package suggested but not available for checking: ‘lavaan.survey’
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘carData’ in Rd xrefs
Undeclared packages ‘carData’, ‘faraway’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 24 marked UTF-8 strings
Found the following files/directories:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Package suggested but not available for checking: ‘eggCountsExtra’
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'rotate_to_equilibrium.Rd':
  ‘xy_may’

Documented arguments not in \usage in Rd file 'wide.dyads.to.edgelist.Rd':
  ‘fist.var’

Documented arguments not in \usage in Rd file 'wide.to.long.Rd':
  ‘last.col’ ‘ego.vars’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 7 marked UTF-8 strings
Invalid package aliases in Rd file 'HOF-package.Rd':
  ‘HOF-package’
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Undeclared package ‘eRm’ in Rd xrefs
Documented arguments not in \usage in Rd file 'colBoxplot4.Rd':
  ‘id’

Documented arguments not in \usage in Rd file 'elaborator_server.Rd':
  ‘id’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
'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: \_
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'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
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘EloRating’ in Rd xrefs
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
GNU make is a SystemRequirements.
File ‘elsa/libs/elsa.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.
Undeclared package ‘textrecipes’ in Rd xrefs
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Note: found 155 marked UTF-8 strings
Note: found 50 marked Latin-1 strings
License stub is invalid DCF.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Found the following significant warnings:
  ./bitstring.h:28:59: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/emoa.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
File ‘emoa/libs/emoa.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.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.5Mb
Note: found 16919 marked UTF-8 strings
Undeclared packages ‘Kendall’, ‘geoR’ in Rd xrefs
Found the following significant warnings:
  RcppExports.cpp:42:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:77:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:112:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:147:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/empichar.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
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 23639 marked Latin-1 strings
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘enc-package.Rd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Found the following files/directories:
  ‘file.path(temp_dir, gp2.csv)’
Note: found 2 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘DECIPHER’ ‘ggplot2’ ‘reshape2’ ‘usethis’
  All declared Imports should be used.
File ‘EntropyEstimation/libs/EntropyEstimation.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
Packages suggested but not available for checking: 'xcms', 'MSnbase'
Package suggested but not available for checking: ‘RStoolbox’
Documented arguments not in \usage in Rd file 'div_plot.Rd':
  ‘plot_cols’

Documented arguments not in \usage in Rd file 'seq_plot.Rd':
  ‘plot_cols’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Auto-generated content requiring editing in Rd file 'EnviroPRA-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.6Mb
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
Found export directives that require package ‘methods’:
  ‘exportClasses’ ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 1 marked Latin-1 string
  Note: found 1508 marked UTF-8 strings
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    help   2.5Mb
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tinytest’
  All declared Imports should be used.
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘epidict’
Documented arguments not in \usage in Rd file 'dots_to_charlist.Rd':
  ‘call’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    help   2.1Mb
    libs   8.0Mb
GNU make is a SystemRequirements.
S3 methods shown with full name in Rd file 'addDrug.Lexis.Rd':
  ‘addDrug.Lexis’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘episcan_1geno_cc.txt’ ‘episcan_1geno_quant.txt’
  ‘episcan_2geno_cc.txt’ ‘episcan_2geno_quant.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taskscheduleR’

Imports includes 34 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘knitr’ ‘plyr’ ‘tidyverse’ ‘xml2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xts’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 15 marked UTF-8 strings
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Undeclared package ‘OpenMx’ in Rd xrefs
Invalid package aliases in Rd file 'equateMultiple-package.Rd':
  ‘EquateMultiple-package’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
File ‘equivalence/libs/equivalence.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:
  ‘cubature’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gcspikelite’
Running examples in ‘erah-Ex.R’ failed
The error most likely occurred in:

> ### Name: createInstrumentalTable
> ### Title: Create Instrumental Table
> ### Aliases: createInstrumentalTable
> 
> ### ** Examples
> 
> library(gcspikelite)
Error in library(gcspikelite) : there is no package called ‘gcspikelite’
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(erah)
  
  
        _____        _
       |  __ \      | |        eRah R package:
    ___| |__) | __ _| |__   	 ----------------
   / _ \  _   // _` |  _ \     Untargeted GC-MS metabolomics profiling
  |  __/ |  \ \ (_| | | | |
   \___|_|   \_\__,_|_| |_|    Version 2.0.0
  
   - Type 'citation('erah')' for citing this R package in publications.
   - Type 'vignette('eRahManual', package='erah')' for a tutorial on eRah's usage.
   - For bugs, problems and issues, please do not hesitate in contacting xavier.domingoa@eurecat.org or opening an issue on the Github repository (https://github.com/xdomingoal/erah-devel/issues).
  > 
  > test_check("erah")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-newExp.R:4:1'): (code run outside of `test_that()`) ────────────
  <packageNotFoundError/error/condition>
  Error in `library(gcspikelite)`: there is no package called 'gcspikelite'
  Backtrace:
      ▆
   1. └─base::library(gcspikelite) at test-newExp.R:4:1
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Undeclared package ‘margins’ in Rd xrefs
Documented arguments not in \usage in Rd file 'subnetwork_templates.Rd':
  ‘nams.vattr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  ./changestats.h:27:9: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  wtedgetree.c:288:28: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/ergm.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   1.7Mb
Documented arguments not in \usage in Rd file 'call.ErgmTerm.Rd':
  ‘A’

Objects in \usage without \alias in Rd file 'ergm-defunct.Rd':
  ‘sociality’

Documented arguments not in \usage in Rd file 'ergm-deprecated.Rd':
  ‘fname’ ‘varnames’ ‘vartypes’ ‘defaultvalues’ ‘required’
  ‘nw.bipartiteflag’ ‘requirement’ ‘extramessage’ ‘nw.directedflag’ ‘m’
  ‘response’ ‘new’ ‘from.new’ ‘model’ ‘proposal’ ‘eta0’ ‘control’
  ‘verbose’ ‘update.nws’ ‘Clist’ ‘prev.run’ ‘burnin’ ‘samplesize’
  ‘interval’ ‘maxedges’ ‘attrname’ ‘label’ ‘coord’ ‘jitter’ ‘thresh’
  ‘usearrows’ ‘mode’ ‘displayisolates’ ‘interactive’ ‘xlab’ ‘ylab’
  ‘xlim’ ‘ylim’ ‘pad’ ‘label.pad’ ‘displaylabels’ ‘boxed.labels’
  ‘label.pos’ ‘label.bg’ ‘vertex.sides’ ‘vertex.rot’ ‘arrowhead.cex’
  ‘label.cex’ ‘loop.cex’ ‘vertex.cex’ ‘edge.col’ ‘label.col’
  ‘vertex.col’ ‘label.border’ ‘vertex.border’ ‘edge.lty’ ‘label.lty’
  ‘vertex.lty’ ‘edge.lwd’ ‘label.lwd’ ‘edge.len’ ‘edge.curve’
  ‘edge.steps’ ‘loop.steps’ ‘object.scale’ ‘uselen’ ‘usecurve’
  ‘suppress.axes’ ‘vertices.last’ ‘layout.par’ ‘cex.main’ ‘cex.sub’
  ‘seed’ ‘latent.control’ ‘colornames’ ‘latent’ ‘preserve.eattr’

Documented arguments not in \usage in Rd file 'ergm_state.Rd':
  ‘nw’

Documented arguments not in \usage in Rd file 'nodal_attributes-API.Rd':
  ‘l’

Documented arguments not in \usage in Rd file 'summary.ergm_model.Rd':
  ‘response’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
S3 methods shown with full name in Rd file 'summary.error_interval.Rd':
  ‘summary.error_interval’

S3 methods shown with full name in Rd file 'summary.measure.Rd':
  ‘summary.measure’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Invalid package aliases in Rd file 'esaBcv_package.Rd':
  ‘esaBcv_package-package’
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc  13.1Mb
Undeclared package ‘metafor’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 3 marked UTF-8 strings
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'ETAS-internal.Rd':
  ‘Smooth.catalog’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Documented arguments not in \usage in Rd file 'poly_clip.Rd':
  ‘x’ ‘y’

Documented arguments not in \usage in Rd file 'setup_gpar.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'setup_grobs.Rd':
  ‘centers’

Documented arguments not in \usage in Rd file 'update_list.Rd':
  ‘x’ ‘val’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 1350 marked UTF-8 strings
Note: found 1054 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘forcats’ ‘rqPen’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘curl’ ‘scales’ ‘stringr’
  All declared Imports should be used.
Undeclared package ‘R6’ in Rd xrefs
Documented arguments not in \usage in Rd file 'doHttrRequest.Rd':
  ‘params’ ‘customConfig’

Documented arguments not in \usage in Rd file 'errorMessage.Rd':
  ‘test_me’

Documented arguments not in \usage in Rd file 'isError.Rd':
  ‘test_me’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
Undeclared packages ‘ks’, ‘evd’, ‘ismev’, ‘mixtools’, ‘evir’, ‘smoothtail’ in Rd xrefs
Found the following files/directories:
  ‘sample .nwk’
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.6Mb
    extdata   2.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'borrOrderingInternal.Rd':
  ‘n.cntrl’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘ExactData’
checkRd: (-1) exams2sakai.Rd:152: Escaped LaTeX specials: \&
Undeclared package ‘tth’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 342 marked UTF-8 strings
Undeclared package ‘iptools’ in Rd xrefs
Unknown package ‘iptools’ in Rd xrefs
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
File ‘exif/libs/exif.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
Found the following significant warnings:
  error.c:45:38: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/ExomeDepth.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
Undeclared packages ‘tseriesChaos’, ‘rSFA’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
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: \&
Undeclared package ‘quantreg’ in Rd xrefs
Argument items with no description in Rd file 'plot.expectreg.Rd':
  ‘\dots’
Argument items with no description in Rd file 'update.expectreg.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.7Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc      3.5Mb
    images   1.1Mb
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
Argument items with no description in Rd file 'fbvpot.Rd':
  ‘cutoff’
checkRd: (-1) outlierPlot.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) outlierPlot.Rd:32: Escaped LaTeX specials: \$
Documented arguments not in \usage in Rd file 'getQQLimit.Rd':
  ‘N’ ‘rho’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘extremis/libs/extremis.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.
Package suggested but not available for checking: ‘exuberdata’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Namespace in Imports field not imported from: ‘rlang’
  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
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'complete.log.likelihood_Sj.Rd':
  ‘z’
Auto-generated content requiring editing in Rd file 'getStuffForDIC.Rd':
  \details: ‘If necessary, more details than the description above’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘strucchange’ in Rd xrefs
Undeclared package ‘pyinit’ in Rd xrefs
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    minor changes
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'procrustes_switching.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'rsp_exact.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'rsp_full_sa.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'rsp_partial_sa.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'weighted_procrustes_switching.Rd':
  \details: ‘If necessary, more details than the description above.’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘caTools’ ‘httr’ ‘jsonlite’ ‘rlang’
  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.
Namespaces in Imports field not imported from:
  ‘base’ ‘data.table’
  All declared Imports should be used.
Note: found 55 marked UTF-8 strings
File ‘falcon/libs/falcon.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.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    doc    1.0Mb
    help   1.2Mb
Documented arguments not in \usage in Rd file 'dot-get_default_sign_size.Rd':
  ‘outcome_type’

Documented arguments not in \usage in Rd file 'dot-get_iteration_data.Rd':
  ‘file_dir’

Documented arguments not in \usage in Rd file 'extract_model_vimp.Rd':
  ‘feature_similarity_table’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ezprof.c:55:30: warning: format specifies type 'double' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat]
  ezprof.c:57:30: warning: format specifies type 'double' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/fanc.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'cache.Rd':
  ‘data’ ‘reset’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 179 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Undeclared package ‘RWeka’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1430 marked UTF-8 strings
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘FastBandChol/libs/FastBandChol.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.
Found the following significant warnings:
  fastcluster_R.cpp:702:17: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  fastcluster_R.cpp:889:17: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/fastcluster.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
File ‘fastcmh/libs/fastcmh.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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Documented arguments not in \usage in Rd file 'kkk.Rd':
  ‘Vector’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
File ‘fastdigest/libs/fastdigest.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.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'Get_C_R_K_Q.Rd':
  ‘have_noise’

Documented arguments not in \usage in Rd file 'Sample_KF_post.Rd':
  ‘C0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
File ‘FastGP/libs/FastGP.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
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘coxKM’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
'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
Undeclared packages ‘ICSNP’, ‘ICS’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
Rd files without \alias:
  ‘FastPCS-package.Rd’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
Invalid package aliases in Rd file 'FastRCS-package.Rd':
  ‘FastPCS-package’
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
File ‘FastRWeb/libs/null.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
Undeclared package ‘earth’ in Rd xrefs
Documented arguments not in \usage in Rd file 'bin.Rd':
  ‘Integer’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘NNLM’
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘collapse’ ‘data.table’ ‘kit’ ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Undeclared package ‘magrittr’ in Rd xrefs
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.Rprofile’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    1.5Mb
    help   2.1Mb
Unexported object imported by a ':::' call: ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  Density_Estimation/Source/../../Skeletons/Include/../../Density_Estimation/Include/Data_Problem_imp.h:174:66: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  FPCA/Source/Mixed_FE_FPCA.cpp:290:237: warning: format specifies type 'int' but the argument has type 'value_type' (aka 'double') [-Wformat]
  Inference/Source/Inference_Data.cpp:221:19: warning: format specifies type 'int' but the argument has type 'const_reference' (aka '__bit_const_reference<vector<bool, allocator<bool>>>') [-Wformat]
  Inference/Source/Inference_Data.cpp:271:27: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  C_Libraries/triangle.c:1426:35: warning: data argument not used by format string [-Wformat-extra-args]
See ‘/data/gannet/ripley/R/packages/tests-clang/fdaPDE.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘FastGP’ ‘MASS’ ‘fdapace’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
Argument items with no description in Rd file 'getbasispenalty.Rd':
  ‘Lfdobj’
Note: found 76 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 3 marked Latin-1 strings
  Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘data.table’ ‘ggplot2’ ‘randomcoloR’ ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘FD/libs/FD.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.
Found the following files/directories:
  ‘vert.txt’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘treesAll.txt’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘e1071’ ‘lattice’ ‘randomForest’ ‘tibble’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 20 marked UTF-8 strings
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: \#
File ‘fechner/libs/fechner.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
Namespace in Imports field not imported from: ‘panelView’
  All declared Imports should be used.
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
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 43825 marked UTF-8 strings
Note: found 134 marked UTF-8 strings
checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  r_ff.c:472:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  r_ff.c:642:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/ff.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
Documented arguments not in \usage in Rd file 'checkStream.Rd':
  ‘skipChecks’

Documented arguments not in \usage in Rd file 'cpp_detectCUSUMMeanSinglePrechange.Rd':
  ‘BL’

Documented arguments not in \usage in Rd file 'cpp_detectEWMAMeanSinglePrechange.Rd':
  ‘BL’

Documented arguments not in \usage in Rd file 'makeStreamMeanChangeR.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'update_Omega.Rd':
  ‘m_new’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  fftw.c:112:40: warning: format specifies type 'unsigned int' but the argument has type 'fftw_complex *' (aka 'double (*)[2]') [-Wformat]
  fftw.c:113:40: warning: format specifies type 'unsigned int' but the argument has type 'fftw_complex *' (aka 'double (*)[2]') [-Wformat]
  fftw.c:114:40: warning: format specifies type 'unsigned int' but the argument has type 'fftw_plan' (aka 'struct fftw_plan_s *') [-Wformat]
  fftw.c:115:40: warning: format specifies type 'unsigned int' but the argument has type 'fftw_plan' (aka 'struct fftw_plan_s *') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/fftw.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'recode_subquad.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    extdata   2.8Mb
Undeclared packages ‘MLEcens’, ‘Icens’ in Rd xrefs
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
Package suggested but not available for checking: ‘MicrobeDS’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    3.0Mb
    help   1.1Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R         4.6Mb
    doc       2.1Mb
    extdata   2.1Mb
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'filename.Rd':
  ‘filename-package’
'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
Namespaces in Imports field not imported from:
  ‘rclipboard’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Namespace in Imports field not imported from: ‘tidyselect’
  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: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 222 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘FinePop’ in Rd xrefs
Package suggested but not available for checking: ‘diveRsity’
Unknown package ‘diveRsity’ in Rd xrefs
Found the following files/directories:
  ‘AH_genepop.txt’ ‘AH_popname.txt’ ‘JSM_MS_freq.txt’
  ‘JSM_MS_genepop.txt’ ‘JSM_genepop_clipped_both.txt’
  ‘JSM_genepop_clipped_maf.txt’ ‘JSM_genepop_clipped_name.txt’
  ‘JSM_mtDNA_freq.txt’ ‘JSM_popname.txt’ ‘result_DJ.csv’
  ‘result_EBDJ.csv’ ‘result_EBFST.csv’ ‘result_EBFST_mtDNA.csv’
  ‘result_EBGstH.csv’ ‘result_GstH.csv’ ‘result_GstN.csv’
  ‘result_GstNC.csv’ ‘result_thetaWCpair.csv’
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Found the following significant warnings:
  finite_moment_test.cpp:300:27: warning: 'operator<<' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  finite_moment_test.cpp:412:19: warning: 'operator<<' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/finity.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
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.
Note: found 7 marked UTF-8 strings
Specified C++11: please drop specification unless essential
File ‘fishMod/libs/fishMod.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:
  ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Documented arguments not in \usage in Rd file 'plot_data_type.Rd':
  ‘client_id’ ‘client_secret’ ‘refresh_token’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘conicfit’ in Rd xrefs
Undeclared package ‘ks’ in Rd xrefs
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Undeclared package ‘extraDistr’ in Rd xrefs
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'nCDunnett', 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
Note: found 584 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
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.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
File ‘flashClust/libs/flashClust.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
checkRd: (-1) cclust.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) randIndex.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:28: Escaped LaTeX specials: \&
Undeclared package ‘mixture’ in Rd xrefs
'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:
  ‘FPCEnv’
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc   9.1Mb
Undeclared package ‘flip’ in Rd xrefs
File ‘flock/libs/flock.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.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
Packages suggested but not available for checking: 'gpls', 'vbmp'
Undeclared package ‘Kendall’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  FLSAGeneral.cc:248:95: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  FLSAGeneral.cc:248:113: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  FLSAGeneral.cc:280:81: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  FLSAGeneral.cc:369:83: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  FLSAGeneral.cc:369:103: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  MaxFlowGraph.cc:560:48: warning: format specifies type 'int' but the argument has type 'decltype(__x.base() - __y.base())' (aka 'long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/flsa.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Undeclared package ‘HMR’ in Rd xrefs
Found the following files/directories:
  ‘flux.CH4.txt’
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'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
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'hl.factor.number.Rd':
  ‘w’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  ANN.cpp:173:31: warning: data argument not used by format string [-Wformat-extra-args]
  ANN.cpp:181:34: warning: data argument not used by format string [-Wformat-extra-args]
  KNN_cover_tree.cpp:103:50: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  KNN_cover_tree.cpp:156:48: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  KNN_cover_tree.cpp:221:52: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/FNN.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
Undeclared package ‘XICOR’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 446 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
  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.
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 234 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘ForecastCombinations’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘decomposedPSF’
  All declared Imports should be used.
'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:
    Previous versions (not tagged nor released)
Namespaces in Imports field not imported from:
  ‘blockCV’ ‘patchwork’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgKitten’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tibble’ ‘viridis’
  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’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 31 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  RcppExports.cpp:47:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:87:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:127:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:167:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:207:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:247:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:287:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:327:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/fourierin.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘LaplacesDemon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
File ‘fpow/libs/fpow.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: ‘psych’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RandomFields’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘fractional/libs/fractional.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
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    help   2.3Mb
    libs   9.8Mb
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'assert.surface.Rd':
  ‘surf’

Documented arguments not in \usage in Rd file 'check.dtype.for.data.Rd':
  ‘silent’

Documented arguments not in \usage in Rd file 'fread3.Rd':
  ‘filehandle:’

Documented arguments not in \usage in Rd file 'fwrite3.Rd':
  ‘filehandle:’ ‘data:’

Documented arguments not in \usage in Rd file 'polygon.soup.to.indexed.mesh.Rd':
  ‘face_vertex_coords’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'freqdom.transpose.Rd':
  ‘S’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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  5.8Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Note: found 50 marked UTF-8 strings
Package suggested but not available for checking: ‘dggrids’
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    1.8Mb
    libs   1.6Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘chillR’ in Rd xrefs
Documented arguments not in \usage in Rd file 'draw.colorbar.Rd':
  ‘coloredmesh’

Documented arguments not in \usage in Rd file 'extend_neighbors.Rd':
  ‘min_dotp_threshold’

Documented arguments not in \usage in Rd file 'surf.sphere.spatialfilter.Rd':
  ‘gaussian_weight’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
Argument items with no description in Rd file 'fsdam.Rd':
  ‘verbose’ ‘which’
Argument items with no description in Rd file 'plot.classes.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.fsim.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.lm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.sfpl.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.sfplsim.FASSMR.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.summary.mfplsim.Rd':
  ‘\dots’
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’ ‘neuralnet’ ‘rpart’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'imp_small_gaps_WMA.Rd':
  ‘Data’ ‘univariate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 39 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
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
Note: found 7921 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Objects in \usage without \alias in Rd file 'funData-constructor.Rd':
  ‘funData’

Objects in \usage without \alias in Rd file 'irregFunData-constructor.Rd':
  ‘irregFunData’

Objects in \usage without \alias in Rd file 'multiFunData-constructor.Rd':
  ‘multiFunData’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'plot.funData.Rd':
  ‘plot.funData’

S3 methods shown with full name in Rd file 'plot.irregFunData.Rd':
  ‘plot.irregFunData’

S3 methods shown with full name in Rd file 'plot.multiFunData.Rd':
  ‘plot.multiFunData’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 120 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 36 marked UTF-8 strings
Documented arguments not in \usage in Rd file 'build_limits_lookup.Rd':
  ‘min_preds’ ‘max_preds’ ‘min_ratio’ ‘max_ratio’ ‘draw_unadjusted’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘completeTrial_byArm_eventPriorRateC3=0.001_eventPriorRateT1=0_eventPriorRateT2=0_eventPriorWt=0.5.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.2.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.4.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.6.RData’
  ‘completeTrial_pooled_eventPriorRate=0.001_eventPriorWt=0.5.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.2.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.4.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.6.RData’
  ‘rcdf_byArm_arm=T1_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03.pdf’
  ‘rcdf_pooled_eventPriorRate=0.06.pdf’
Documented arguments not in \usage in Rd file 'loggedOutput.Rd':
  ‘future’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  RcppExports.cpp:37:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:70:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:102:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/futureheatwaves.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
File ‘futureheatwaves/libs/futureheatwaves.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.
Documented arguments not in \usage in Rd file 'mandelbrot.Rd':
  ‘Z’ ‘xmid’ ‘ymid’ ‘side’ ‘resolution’ ‘maxIter’ ‘tau’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   4.3Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
Invalid package aliases in Rd file 'GAabbreviate-internal.Rd':
  ‘GAabbreviation-package’
Undeclared package ‘mfdb’ in Rd xrefs
File ‘gafit/libs/gafit.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:
  ‘gargle’ ‘getProxy’ ‘rappsflyer’ ‘rfacebookstat’ ‘rgoogleads’
  ‘rmytarget’ ‘rvkstat’ ‘ryandexdirect’ ‘rym’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘webshot’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'splitQTL_comment.Rd':
  ‘output_qtls’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LGAclaims.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:36: Escaped LaTeX specials: \_
Undeclared package ‘gamlss’ in Rd xrefs
Undeclared packages ‘gamlss.dist’, ‘gamlss.add’ in Rd xrefs
Invalid package aliases in Rd file 'gamlss.mx.package.Rd':
  ‘gamlss.mix-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
Documented arguments not in \usage in Rd file 'as.gapdata.Rd':
  ‘labels_df’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    7.9Mb
    libs   2.2Mb
Undeclared package ‘car’ in Rd xrefs
Specified C++14: please drop specification unless essential
installed size is 45.5Mb
  sub-directories of 1Mb or more:
    doc  44.3Mb
':::' call which should be '::': ‘graphics:::grid’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Logger.cpp:29:14: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
  Logger.cpp:39:15: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
  Logger.cpp:50:20: warning: format specifies type 'char *' but the argument has type 'int *' [-Wformat]
  Logger.cpp:62:20: warning: format specifies type 'char *' but the argument has type 'int *' [-Wformat]
  Logger.cpp:87:14: warning: field precision should have type 'int', but argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  Logger.cpp:96:14: warning: field precision should have type 'int', but argument has type 'size_type' (aka 'unsigned long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/gaselect.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      1.8Mb
Documented arguments not in \usage in Rd file 'lrr_plot.Rd':
  ‘plot_cols’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared packages ‘fortunes’, ‘rmsfact’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘checkdata.csv’ ‘gbmforest.sas’
Found the following significant warnings:
  node_categorical.cpp:42:23: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  node_categorical.cpp:45:22: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  node_categorical.cpp:52:27: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  node_categorical.cpp:55:22: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  node_continuous.cpp:38:12: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  node_continuous.cpp:44:12: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/gbm.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘gbp/libs/gbp.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) 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: \&
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_argument_names’ ‘tools:::RdTags’ ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'align_peaks.Rd':
  ‘gc_peak_df’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘gputools’
Package suggested but not available for checking: ‘paleofire’
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘gcmr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘GCPM/libs/GCPM.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
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    libs     3.5Mb
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  RcppExports.cpp:108:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:147:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:182:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:221:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:261:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:301:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:340:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:374:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:408:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/gdtools.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
Undeclared packages ‘palmerpenguins’, ‘readxl’ in Rd xrefs
File ‘GEEaSPU/libs/GEEaSPU.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.
Objects in \usage without \alias in Rd file 'geepack-internal.Rd':
  ‘genZcor’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
File ‘gelnet/libs/gelnet.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.
Auto-generated content requiring editing in Rd file 'gemlog-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
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
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘pracma’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Package required but not available: ‘ggseqlogo’

Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid package aliases in Rd file 'GenBinom-package.Rd':
  ‘GenbinomApps-package’
Undeclared package ‘poibin’ in Rd xrefs
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘genderdata’
Undeclared package ‘mmap’ in Rd xrefs
Documented arguments not in \usage in Rd file 'CirDisp.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'CirKurt.Rd':
  ‘x’ ‘na.rm’

Documented arguments not in \usage in Rd file 'CirSD.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'CirSkew.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'CirVar.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'MeanDir.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'impact.Rd':
  ‘na.rm’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'expand.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'grapes-bq-grapes.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'grapes-bt-grapes.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'stftcalc.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘R.utils’ ‘markdown’
  All declared Imports should be used.
Package suggested but not available for checking: ‘maptools’
Package suggested but not available for checking: ‘rrvgo’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'generalizedwendland-internal.Rd':
  ‘numint.abstol (default: 1e-3)’ ‘numint.reltol (default: 1e-3)’
  ‘numint.qag_key (default: 0)’ ‘numint.subintervals (default: 0)’
  ‘interp.method (default: 'none')’ ‘interp.num_support (default: 0)’
  ‘cov.reparameterize (default: TRUE)’ ‘cov.eps (default:
  .Machine$double.eps^0.5)’ ‘cov.d_value (default: 2)’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘GGEBiplots’ ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’
  ‘reshape2’
  All declared Imports should be used.
Undeclared package ‘bootstrap’ in Rd xrefs
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'GenlibR-package.Rd':
  ‘GenlibR-package’
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  Engine.cpp:297:64: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  Engine.cpp:321:50: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/GenSA.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
File ‘GenSA/libs/GenSA.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.
Found the following significant warnings:
  set_ops.c:133:41: warning: data argument not used by format string [-Wformat-extra-args]
See ‘/data/gannet/ripley/R/packages/tests-clang/genscore.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 144 marked UTF-8 strings
Note: found 58 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
Note: found 80 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘RiemBase’ in Rd xrefs
Note: found 646 marked UTF-8 strings
Note: found 87001 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  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
Documented arguments not in \usage in Rd file 'variables_query-method.Rd':
  ‘variables’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘geomarocdata’
'LazyData' is specified without a 'data' directory
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    R         9.5Mb
    extdata   2.6Mb
    help      2.6Mb
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
Found the following significant warnings:
  geoR.c:595:59: warning: format specifies type 'long' but the argument has type 'int' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/geoR.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Undeclared package ‘car’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
Undeclared package ‘loo’ in Rd xrefs
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘RandomFields’
Unknown package ‘RandomFields’ in Rd xrefs
Note: found 4 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
Found the following calls to data() loading into the global environment:
File ‘geotools/R/zzz.R’:
  data(fr_geo_rad)
See section ‘Good practice’ in ‘?data’.
Note: found 64 marked Latin-1 strings
  Note: found 25 marked UTF-8 strings
Package suggested but not available for checking: ‘rgdal’
Namespaces in Imports field not imported from:
  ‘DT’ ‘GWmodel’ ‘beepr’ ‘cartography’ ‘dplyr’ ‘raster’ ‘readxl’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinybusy’ ‘shinyjs’ ‘sp’
  ‘spdep’
  All declared Imports should be used.
'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 significant warnings:
  hostname2ip.c:84:116: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/getip.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Namespaces in Imports field not imported from:
  ‘pipeR’ ‘rlang’
  All declared Imports should be used.
Package suggested but not available for checking: ‘argon2’
Found the following significant warnings:
  readline_masked.c:59:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/getPass.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Package suggested but not available for checking: ‘RGtk2’
Namespaces in Imports field not imported from:
  ‘googlesheets4’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'attract_by_distance.Rd':
  ‘prop_start’ ‘prop_end’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'labels.rpart.Rd':
  ‘pretty:’

Documented arguments not in \usage in Rd file 'rpart_labels.Rd':
  ‘model’ ‘...’

Documented arguments not in \usage in Rd file 'rpart_segments.Rd':
  ‘model’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘gge’ in Rd xrefs
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘utils’
  All declared Imports should be used.
Found the following assignments to the global environment:
File ‘ggExtra/R/ggMarginalGadget.R’:
  assign(plotname, eval(parse(text = origPlot)), envir = .GlobalEnv)
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'interpolateDataFrame.Rd':
  ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared packages ‘akima’, ‘ggforce’ in Rd xrefs
'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
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘gtable’
  All declared Imports should be used.
Undeclared package ‘rlang’ in Rd xrefs
Specified C++11: please drop specification unless essential
Undeclared package ‘rlang’ in Rd xrefs
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Found the following significant warnings:
  dsvg_dev.cpp:154:25: warning: format specifies type 'wchar_t *' but the argument has type 'const char *' [-Wformat]
  dsvg_dev.cpp:198:25: warning: format specifies type 'wchar_t *' but the argument has type 'const char *' [-Wformat]
  dsvg_dev.cpp:209:25: warning: format specifies type 'wchar_t *' but the argument has type 'const char *' [-Wformat]
  dsvg_dev.cpp:214:25: warning: format specifies type 'wchar_t *' but the argument has type 'const char *' [-Wformat]
  dsvg_dev.cpp:220:25: warning: format specifies type 'wchar_t *' but the argument has type 'const char *' [-Wformat]
  dsvg_dev.cpp:226:25: warning: format specifies type 'wchar_t *' but the argument has type 'const char *' [-Wformat]
  dsvg_dev.cpp:232:25: warning: format specifies type 'wchar_t *' but the argument has type 'const char *' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/ggiraph.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mathjaxr’
  All declared Imports should be used.
checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rdpack’
  All declared Imports should be used.
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.
Package required but not available: ‘ggseqlogo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘graph’
  All declared Imports should be used.
Argument items with no description in Rd file 'isADMG.Rd':
  ‘amat’
Argument items with no description in Rd file 'isAG.Rd':
  ‘amat’
Undeclared package ‘dwlm’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘sna’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grid’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘scales’, ‘labeling’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Invalid package aliases in Rd file 'package-ggparallel.Rd':
  ‘package-ggparallel-package’
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘ggdensity’ in Rd xrefs
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   1.9Mb
Undeclared packages ‘interp’, ‘akima’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lixoftConnectors’
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.4Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'operator.Rd':
  ‘x’ ‘y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 35 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘car’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘RPostgres’ ‘colourpicker’ ‘dplyr’
  ‘ggpmisc’ ‘ggpubr’ ‘ggrepel’ ‘gridExtra’ ‘markdown’ ‘plotly’
  ‘quantreg’ ‘rlang’ ‘shinyFiles’ ‘shinyjqui’ ‘shinyjs’ ‘survival’
  ‘survminer’ ‘table1’ ‘tidyr’ ‘zoo’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Undeclared package ‘vipor’ in Rd xrefs
Note: found 6242 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘nomogramFormula’ ‘survival’
  All declared Imports should be used.
Note: found 19 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘utils’
  All declared Imports should be used.
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
Undeclared package ‘RColorBrewer’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘rlang’ in Rd xrefs
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Undeclared packages ‘chemometrics’, ‘rlang’ in Rd xrefs
Documented arguments not in \usage in Rd file 'ggplot_gtable.Rd':
  ‘plot’

Documented arguments not in \usage in Rd file 'undocumented.Rd':
  ‘latex’ ‘ggplot’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 138 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc   8.3Mb
Documented arguments not in \usage in Rd file 'add_scale.Rd':
  ‘domain’

Documented arguments not in \usage in Rd file 'bin_vector.Rd':
  ‘width’ ‘origin’ ‘closed’ ‘pad’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 208 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘class’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    Giac  17.8Mb
Note: found 553 marked UTF-8 strings
GNU make is a SystemRequirements.
Found the following significant warnings:
  RcppExports.cpp:44:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:80:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/gif.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    help   2.5Mb
Undeclared package ‘Runuran’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Undeclared packages ‘ineq’, ‘IC2’ in Rd xrefs
Unknown package ‘IC2’ in Rd xrefs
Specified C++11: please drop specification unless essential
File ‘GiRaF/libs/GiRaF.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.
Note: found 1178 marked UTF-8 strings
Note: found 866 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MCMCpack’ ‘ggplot2’ ‘moments’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mlr3proba’
Argument items with no description in Rd file 'GLD.lm.full.surv.Rd':
  ‘maxit’
Argument items with no description in Rd file 'GLD.lm.surv.Rd':
  ‘maxit’
Documented arguments not in \usage in Rd file 'getBeta.Rd':
  ‘thetaConrol’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  phytr.c:2577:78: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
  phytr.c:2664:55: warning: data argument not used by format string [-Wformat-extra-args]
  phytr.c:2668:65: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
  phytr.c:2699:55: warning: data argument not used by format string [-Wformat-extra-args]
  phytr.c:2703:65: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
  phytr.c:2743:65: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
  phytr.c:2821:78: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
  phytr.c:2896:65: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
  phytr.c:2916:65: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
  phytr.c:2943:65: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
  phytr.c:3029:85: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
  phytr.c:3196:65: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
  phytr.c:3219:65: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
  phytr.c:3256:65: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/glinvci.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used Fortran compiler: ‘flang-new version 17.0.5’
File ‘gllm/libs/gllm.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.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.9Mb
File ‘GLMaSPU/libs/GLMaSPU.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: ‘ordinal’
  All declared Imports should be used.
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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Undeclared package ‘GMMBoost’ in Rd xrefs
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc             1.4Mb
    libs            6.4Mb
    test_data       2.2Mb
    vignette_data   1.2Mb
Namespaces in Imports field not imported from:
  ‘AER’ ‘MASS’ ‘Matrix’ ‘censReg’ ‘effects’ ‘foreign’ ‘lme4’ ‘lmtest’
  ‘nnet’ ‘pBrackets’ ‘plm’ ‘pscl’ ‘sandwich’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'glmpathcr-internal.Rd':
  ‘fit’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
File ‘globalOptTests/libs/globalOptTests.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.
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rnaturalearthdata’
  All declared Imports should be used.
Note: found 1191 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘caret’ in Rd xrefs
Documented arguments not in \usage in Rd file 'fun.svd_1.Rd':
  ‘X’

Documented arguments not in \usage in Rd file 'fun.svd_2.Rd':
  ‘X’

Documented arguments not in \usage in Rd file 'fun.svd_3.Rd':
  ‘X’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 2629 marked UTF-8 strings
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'SeqArray', 'SeqVarTools'
Undeclared package ‘glmmLasso’ in Rd xrefs
Undeclared package ‘sandwich’ in Rd xrefs
Undeclared package ‘rms’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Undeclared package ‘repeated’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Undeclared packages ‘openxlsx’, ‘readxl’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘base’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Undeclared package ‘goftest’ in Rd xrefs
Note: found 1352 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘rhandsontable’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BVDWSTOXX.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:16: Escaped LaTeX specials: \& \&
checkRd: (-1) BVDWSTOXX.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:37: Escaped LaTeX specials: \&
Undeclared package ‘fBasics’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘goodpractice-package.Rd’
Note: found 1 marked UTF-8 string
Package suggested but not available for checking: ‘ganalytics’
Documented arguments not in \usage in Rd file 'doHttrRequest.Rd':
  ‘session’ ‘params’

Documented arguments not in \usage in Rd file 'get_google_token.Rd':
  ‘shiny_return_token’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared packages ‘rcmdcheck’, ‘covr’, ‘devtools’, ‘pkgdown’ in Rd xrefs
'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
Undeclared package ‘jsonlite’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘future’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Error(s) in re-building vignettes:
--- re-building ‘GPareto_vignette.Rnw’ using knitr
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Documented arguments not in \usage in Rd file 'estimate_noise_nn.Rd':
  ‘n_thread’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘gvcm.cat’
Specified C++11: please drop specification unless essential
Unknown package ‘gvcm.cat’ in Rd xrefs
Package suggested but not available for checking: ‘maptools’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘gplm/libs/gplm.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) 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:59: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.5Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘speedglm’ in Rd xrefs
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
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    help   5.3Mb
Undeclared package ‘gratia’ in Rd xrefs
Note: found 5030 marked UTF-8 strings
Package suggested but not available for checking: ‘monocle’
Package unavailable to check Rd xrefs: ‘monocle’
'LazyData' is specified without a 'data' directory
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘PairedData’ ‘RColorBrewer’ ‘agricolae’ ‘corrplot’ ‘desplot’
  ‘dplyr’ ‘ggplot2’ ‘ggpubr’ ‘gridGraphics’ ‘gtools’ ‘kableExtra’
  ‘knitr’ ‘magrittr’ ‘pastecs’ ‘reshape2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘summarytools’
  All declared Imports should be used.
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
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  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
Undeclared package ‘glasso’ in Rd xrefs
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'HistPCA.Rd':
  ‘ggplot’
Specified C++11: please drop specification unless essential
Note: found 14768 marked UTF-8 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Found the following significant warnings:
  Cincome_tax.c:162:54: warning: format specifies type 'long long' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  Cincome_tax.c:162:74: warning: format specifies type 'long long' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  Crebate_income.c:54:34: warning: format specifies type 'long long' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  isEquiInt.c:6:72: warning: format specifies type 'long long' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  isEquiInt.c:6:84: warning: format specifies type 'long long' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  sapto.c:268:39: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
  sapto.c:281:43: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
  sapto.c:391:36: warning: format specifies type 'long long' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/grattan.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
Note: found 989 marked UTF-8 strings
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'prCaSetRownames.Rd':
  ‘rownames.fn’

Documented arguments not in \usage in Rd file 'prClearPCAclass.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘msm’
  All declared Imports should be used.
S3 methods shown with full name in Rd file 'groc.fit.Rd':
  ‘groc.fit’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘rjags’
  All declared Imports should be used.
Found the following significant warnings:
  hmg.cpp:202:22: warning: 'operator<<' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  hmg.cpp:203:22: warning: 'operator<<' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  hmg.cpp:453:13: warning: 'operator<<' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/grove.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Found the following significant warnings:
  gpdpmix_moves.cpp:1014:23: warning: 'insert_rows' is deprecated [-Wdeprecated-declarations]
  gpdpmix_moves.cpp:1015:25: warning: 'insert_rows' is deprecated [-Wdeprecated-declarations]
  sppmcarmix_moves.cpp:134:11: warning: 'insert_rows' is deprecated [-Wdeprecated-declarations]
  sppmcarmix_moves.cpp:135:11: warning: 'insert_rows' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/growfunctions.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
Problems with news in ‘NEWS.md’:
No news entries found.
Undeclared packages ‘repeated’, ‘gnlm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  RcppExports.cpp:41:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:79:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:119:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:159:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:193:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:227:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:261:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:295:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:330:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:370:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  RcppExports.cpp:411:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/grpCox.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Invalid package aliases in Rd file 'fit_grp.Rd':
  ‘grplasso-package’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Found the following files/directories:
  ‘p1_20up-vs-p2_25up_in_str1.txt’ ‘p1_20up-vs-p2_25up_in_str2.txt’
  ‘p2_25up-vs-p1_20up_in_str1.txt’ ‘p2_25up-vs-p1_20up_in_str2.txt’
  ‘s0_20up.txt’ ‘s0_30up.txt’ ‘s0_f2up.txt’ ‘strs.vec_01mx.txt’
  ‘strs.vec_02mx.txt’ ‘strs.vec_03mx.txt’ ‘strs.vec_04mx.txt’
  ‘strs.vec_05mx.txt’ ‘strs.vec_06mx.txt’ ‘strs.vec_30up.txt’
  ‘strs.vec_50up.txt’ ‘strs.vec_f2up.txt’ ‘uni_p1_20up-p2_25up.txt’
File ‘grr/libs/grr.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.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘FMD mag discontinuities_disc.png’ ‘FMD mag
  discontinuities_disc1.res’ ‘FMD mag discontinuities_disc2.res’
  ‘IDYLLWILD_bvmed.png’ ‘IDYLLWILD_fig.png’ ‘Schuster's
  diagram_schu.png’ ‘hour.res’
Objects in \usage without \alias in Rd file 'GSA.internal.Rd':
  ‘est.s0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file 'gsb-package.Rd':
  ‘gsb-package’
Undeclared package ‘nflfastR’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  nls.c:226:47: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  nls.c:227:47: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  nls.c:228:42: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  nls.c:652:44: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  nls_large.c:259:47: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  nls_large.c:260:62: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  nls_large.c:261:64: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  nls_large.c:262:42: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  nls_large.c:724:63: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/gslnls.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Malformed Description field: should contain one or more complete sentences.
File ‘gsmoothr/libs/gsmoothr.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.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.3Mb
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.9Mb
Note: found 146 marked UTF-8 strings
Note: found 269 marked UTF-8 strings
Note: found 42384 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RRprof.out’
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
Undeclared package ‘permute’ in Rd xrefs
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Note: found 20255 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘GWASExactHW/libs/GWASExactHW.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
Documented arguments not in \usage in Rd file 'traits.Rd':
  ‘efo_id’ ‘trait’ ‘uri’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 275 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘spgwr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘attempt’ ‘corpcor’ ‘glue’ ‘htmltools’ ‘pkgload’ ‘processx’
  ‘tools’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rgeos’
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Found the following files/directories:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 250.2Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    help    1.0Mb
    java  247.1Mb
'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  8.3Mb
  sub-directories of 1Mb or more:
    HaDeX   4.1Mb
    doc     4.0Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘gsubfn’ ‘stringr’
  All declared Imports should be used.
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 significant warnings:
  ThinImageCpp.cpp:206:15: warning: 'operator<<' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/handwriter.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Undeclared package ‘mnis’ in Rd xrefs
Found the following significant warnings:
  haplo_em_pin.c:236:61: warning: data argument not used by format string [-Wformat-extra-args]
  haplo_em_pin.c:258:75: warning: format specifies type 'long' but the argument has type 'int' [-Wformat]
  haplo_em_pin.c:341:34: warning: format specifies type 'long' but the argument has type 'int' [-Wformat]
  haplo_em_pin.c:419:23: warning: format specifies type 'long' but the argument has type 'int' [-Wformat]
  haplo_em_pin.c:424:42: warning: format specifies type 'long' but the argument has type 'int' [-Wformat]
  haplo_em_pin.c:424:64: warning: format specifies type 'long' but the argument has type 'int' [-Wformat]
  haplo_em_pin.c:424:79: warning: format specifies type 'long' but the argument has type 'int' [-Wformat]
  haplo_em_pin.c:427:23: warning: format specifies type 'long' but the argument has type 'int' [-Wformat]
  haplo_em_pin.c:443:23: warning: format specifies type 'long' but the argument has type 'int' [-Wformat]
  haplo_em_pin.c:448:25: warning: format specifies type 'long' but the argument has type 'int' [-Wformat]
  haplo_em_pin.c:451:23: warning: format specifies type 'long' but the argument has type 'int' [-Wformat]
  haplo_em_pin.c:466:32: warning: format specifies type 'long' but the argument has type 'int' [-Wformat]
  haplo_em_pin.c:1154:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  louis_info.c:468:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/haplo.stats.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Argument items with no description in Rd file 'haplo.em.fitter.Rd':
  ‘random.start ’
Argument items with no description in Rd file 'haplo.model.frame.Rd':
  ‘control’
Note: found 7592 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'modeling-package.Rd':
  ‘modeling-package’
checkRd: (-1) HWAlr.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWAlrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWClr.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) HWClrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWIlr.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) HWf.Rd:25: Escaped LaTeX specials: \&
Found the following significant warnings:
  HARDataCreationC.cpp:43:28: warning: 'operator<<' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/HARModel.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.6Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘dplyr’ in Rd xrefs
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
File ‘hawkes/libs/hawkes.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
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   1.3Mb
GNU make is a SystemRequirements.
Note: found 3 marked UTF-8 strings
Note: found 104392 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is  5.6Mb
  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  6.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'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 significant warnings:
  datatype_export.c:67:19: warning: length modifier 'I64' results in undefined behavior or no effect with 'd' conversion specifier [-Wformat]
  datatype_export.c:67:31: warning: format specifies type '__int64' (aka 'long long') but the argument has type 'hid_t' (aka 'long') [-Wformat]
  convert.c:261:82: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  convert.c:261:98: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  convert.c:2700:13: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  H5Error.c:115:9: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  Wrapper_manual_H5T.c:76:108: warning: format specifies type 'int' but the argument has type 'long long' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/hdf5r.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Documented arguments not in \usage in Rd file 'check_arg_for_hyperslab_func.Rd':
  ‘cur_arg’

Documented arguments not in \usage in Rd file 'extract_dim.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘HDGLM/libs/HDGLM.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.
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘ggjoy’ ‘isotone’ ‘png’ ‘questionr’ ‘rprojroot’
  ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Namespaces in Imports field not imported from:
  ‘TidyDensity’ ‘healthyR’ ‘healthyR.ai’ ‘healthyR.data’ ‘healthyR.ts’
  ‘tidyAML’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Specified C++11: please drop specification unless essential
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'compute_counts.Rd':
  ‘init’ ‘inflow’

Documented arguments not in \usage in Rd file 'compute_values.Rd':
  ‘counts’

Documented arguments not in \usage in Rd file 'create_demographic_table.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'eval_strategy_newdata.Rd':
  ‘model’

Documented arguments not in \usage in Rd file 'get_state_value_names.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared packages ‘Sleuth2’, ‘rrcov’, ‘archdata’, ‘qqtest’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  MHproposal.c:25:4: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  MHproposal.c:38:4: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  changestats.c:1465:181: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  changestats.c:1517:105: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  h_ergm.c:1910:84: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
  model.c:58:3: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  model.c:69:3: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/hergm.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.1Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'check.Rd':
  ‘inner_class’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'check_known_repos.Rd':
  ‘known_packages’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘hexfont-Ex.R’ failed
The error most likely occurred in:

> ### Name: unifont
> ### Title: Load Unifont font
> ### Aliases: unifont
> 
> ### ** Examples
> 
> # Much faster to load only the subset of GNU Unifont one needs
> # Mandarin Chinese
> if (require("bittermelon")) {
+   s <- "\uff32\u5f88\u68d2\uff01"
+   font <- unifont(ucp = str2ucp(s))
+   bm <- as_bm_bitmap(s, font = font)
+   print(bm, px = px_ascii)
+ }
Loading required package: bittermelon

Attaching package: ‘bittermelon’

The following object is masked from ‘package:base’:

    which

Error in vector("list", n_orig - n_combining) : vector size cannot be NA
Calls: as_bm_bitmap -> as_bm_bitmap.character -> lapply -> FUN
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Undeclared package ‘lme4’ in Rd xrefs
Found the following significant warnings:
  HHG.cpp:76:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  rcpp_internals.cpp:66:13: warning: format specifies type 'int' but the argument has type 'typename storage_type<14>::type' (aka 'double') [-Wformat]
  rcpp_internals.cpp:66:31: warning: format specifies type 'int' but the argument has type 'typename storage_type<14>::type' (aka 'double') [-Wformat]
  rcpp_internals.cpp:66:48: warning: format specifies type 'int' but the argument has type 'typename storage_type<14>::type' (aka 'double') [-Wformat]
  rcpp_internals.cpp:66:65: warning: format specifies type 'int' but the argument has type 'typename storage_type<14>::type' (aka 'double') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/HHG.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'HH-defunct.Rd':
  ‘anova.mean’ ‘print.glht.mmc.multicomp’ ‘coef.arima.HH’ ‘glht.mmc’
  ‘plot.odds.ratio’ ‘persp.plane’ ‘persp.floor’ ‘persp.back.wall.x’
  ‘persp.back.wall.y’ ‘persp.setup’ ‘plot.hov’ ‘plot.hov.bf’
  ‘plot.matchMMC’ ‘seqplot.forecast’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd file 'residual.plots.lattice.Rd':
  ‘X’
File ‘HiCseg/libs/HiCseg.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.
Found export directives that require package ‘methods’:
  ‘exportClasses’ ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
File ‘HiDimDA/libs/HiDimDA.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: ‘RiskPortfolios’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'qcplate.Rd':
  ‘dat’
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
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: ‘rgdal’
'LazyData' is specified without a 'data' directory
Undeclared packages ‘Guerry’, ‘alr4’, ‘agridat’, ‘coin’ in Rd xrefs
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Auto-generated content requiring editing in Rd file 'HistDAWass-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
Invalid package aliases in Rd file 'histogram-package.Rd':
  ‘histogramtools-package’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘trackr’
Package which this enhances but not available for checking: ‘HadoopStreaming’
Note: found 9638 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
html_describe_con: multiple local function definitions for ‘g’ with
  different formal arguments
Documented arguments not in \usage in Rd file 'bootstrapfun.Rd':
  ‘DoF’ ‘n_sample’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
Undeclared package ‘genalg’ in Rd xrefs
Auto-generated content requiring editing in Rd file 'HMVD-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Invalid package aliases in Rd file 'hoardeR-package.Rd':
  ‘R/hoardeR-package’
Argument items with no description in Rd file 'bid2.Rd':
  ‘numattable1’ ‘playerseats1’ ‘blinds1’ ‘dealer1’ ‘b3’ ‘b4’ ‘round1’
  ‘ntable1’ ‘decision1’
Argument items with no description in Rd file 'calcwin1.Rd':
  ‘numattable1’ ‘playerseats1’ ‘b3’ ‘b7’
Argument items with no description in Rd file 'mycount1.Rd':
  ‘x’
Argument items with no description in Rd file 'mygraphics1.Rd':
  ‘numattable1’ ‘playerseats1’ ‘chips1’ ‘blinds1’ ‘dealer1’ ‘b3’ ‘b4’
  ‘b5’ ‘b6’ ‘b7’ ‘chips2’ ‘ntable1’ ‘myfast1’ ‘chipstart1’ ‘name1’
  ‘lowercut1’
Argument items with no description in Rd file 'nothing1.Rd':
  ‘x’
Argument items with no description in Rd file 'onepair1.Rd':
  ‘x’
Argument items with no description in Rd file 'straight1.Rd':
  ‘x’
Argument items with no description in Rd file 'straightdraw1.Rd':
  ‘x’
Argument items with no description in Rd file 'strflsh1.Rd':
  ‘x’ ‘y’
Argument items with no description in Rd file 'trip1.Rd':
  ‘x’
Argument items with no description in Rd file 'twopair1.Rd':
  ‘x’
Argument items with no description in Rd file 'writebets1.Rd':
  ‘b9’ ‘y1’ ‘numattable1’ ‘b3’ ‘playerseats1’ ‘chips1’ ‘chips2’ ‘over1’
  ‘myfast1’ ‘name1’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    app   1.7Mb
    doc   3.3Mb
Undeclared package ‘rgl’ in Rd xrefs
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'plot.hopitCP.Rd':
  ‘plotf’

Documented arguments not in \usage in Rd file 'sigma.hopit.Rd':
  ‘model’

Documented arguments not in \usage in Rd file 'summary.hopit.Rd':
  ‘control’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 124 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘hpoPlot-package.Rd’
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'dot-E3.Rd':
  ‘i’ ‘M’

Documented arguments not in \usage in Rd file 'dot-E4.Rd':
  ‘i’ ‘M’

Documented arguments not in \usage in Rd file 'hrm.0w.2s.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.0w.3s.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.0w.4s.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.0w.5s.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.1f.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.1w.0f.Rd':
  ‘factor1’

Documented arguments not in \usage in Rd file 'hrm.2w.2f.Rd':
  ‘factor’

Documented arguments not in \usage in Rd file 'hrm.mv.1w.1f.Rd':
  ‘H’ ‘text’

Documented arguments not in \usage in Rd file 'hrm.mv.internal.Rd':
  ‘alpha’ ‘H’ ‘text’

Documented arguments not in \usage in Rd file 'hrm.test.1.none.Rd':
  ‘factor1’ ‘factor2’

Documented arguments not in \usage in Rd file 'hrm.test.1.one.Rd':
  ‘group’ ‘factor2’

Documented arguments not in \usage in Rd file 'hrm.test.2.one.Rd':
  ‘factor2’

Documented arguments not in \usage in Rd file 'hrm.test.2.two.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.test.3.three.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.test.4.four.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.test.5.five.Rd':
  ‘group’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘quantreg’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'imageplot.Rd':
  ‘\dots’
File ‘hsphase/libs/hsphase.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: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'FramedHTML.Rd':
  ‘DiagnosticsPath’
Namespaces in Imports field not imported from:
  ‘recipes’ ‘tune’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    2.1Mb
    help   1.0Mb
Invalid package aliases in Rd file 'httkpop.Rd':
  ‘httkpop-package’
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'as-redactor.Rd':
  ‘expr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
File ‘humaniformat/libs/humaniformat.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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘xml2’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shiny’ ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Package suggested but not available for checking: ‘microViz’
Invalid package aliases in Rd file 'HydroMe-package.Rd':
  ‘HydroMe2-package’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
Packages suggested but not available for checking: 'flowCore', 'rgeos'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
Documented arguments not in \usage in Rd file 'read.txt.Witec.Rd':
  ‘nwl’ ‘remove.zerospc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 38558 marked UTF-8 strings
Note: found 1058038 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
Note: found 359 marked UTF-8 strings
Objects in \usage without \alias in Rd file 'btibgen.Rd':
  ‘ibdgen’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  lsConstrain.c:304:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/ibdreg.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Argument items with no description in Rd file 'pairSum.Rd':
  ‘cov1’ ‘cov2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘ibmcraftr/libs/ibmcraftr.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.
Package suggested but not available for checking: ‘SparkR’
Specified C++11: please drop specification unless essential
File ‘ibm/libs/ibm.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.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'GetCustomKmerCounts.Rd':
  ‘custom.range’

Documented arguments not in \usage in Rd file 'GetMutationLoadsFromStrelkaIDVCFs.Rd':
  ‘list.of.vcfs’

Documented arguments not in \usage in Rd file 'GetMutationLoadsFromStrelkaSBSVCFs.Rd':
  ‘split.vcfs’

Documented arguments not in \usage in Rd file 'PlotPPM.Rd':
  ‘pwm’

Documented arguments not in \usage in Rd file 'PlotPPMToPdf.Rd':
  ‘list.of.pwm’

Documented arguments not in \usage in Rd file 'ReadStrelkaSBSVCF.Rd':
  ‘suppress.discarded.variants.warnings’

Documented arguments not in \usage in Rd file 'ReadVCF.Rd':
  ‘num.of.cores’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 356712 marked UTF-8 strings
Package suggested but not available for checking: ‘icd’
Note: found 55 marked UTF-8 strings
Undeclared package ‘tibble’ in Rd xrefs
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Found the following significant warnings:
  ./icenReg_files/basicUtilities.cpp:589:64: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/icenReg.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
Namespaces in Imports field not imported from:
  ‘digest’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 10 marked UTF-8 strings
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
Undeclared packages ‘mlogit’, ‘logitr’ in Rd xrefs
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rggobi’
'LazyData' is specified without a 'data' directory
Undeclared package ‘tibble’ in Rd xrefs
Specified C++11: please drop specification unless essential
Undeclared packages ‘sfsmisc’, ‘RColorBrewer’, ‘hexbin’ in Rd xrefs
Objects in \usage without \alias in Rd file 'pkg-internal.Rd':
  ‘iplotMain’ ‘segments.circle’ ‘griddat’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'pkg-internal.Rd':
  ‘plot.page’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
File ‘ieeeround/libs/ieeeround.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.
Note: found 366 marked UTF-8 strings
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 40 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘IFCdata’
File ‘IFP/libs/IFP.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:
  ‘kableExtra’ ‘knitr’ ‘xtable’
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rinterface_extra.c:255:16: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/igraph.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   1.5Mb
    libs   3.4Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.5Mb
Undeclared packages ‘bmp’, ‘jpeg’, ‘png’, ‘tiff’ in Rd xrefs
Documented arguments not in \usage in Rd file 'dot-compl.Rd':
  ‘imgfile’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘tesseract’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.2Mb
    extdata   1.1Mb
    include   3.0Mb
    libs      4.9Mb
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'image-package.Rd':
  ‘image-package’
Specified C++11: please drop specification unless essential
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggseqlogo’

Imports includes 38 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘accdata’
Documented arguments not in \usage in Rd file 'new_impactr_peaks.Rd':
  ‘acc_signal:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘haven’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pscl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘imputeYn-package.Rd’
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Undeclared package ‘minfi’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 151 marked UTF-8 strings
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Package which this enhances but not available for checking: ‘gurobi’
File ‘infotheo/libs/infotheo.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.
Found the following files/directories:
  ‘c.txt’ ‘rho.txt’ ‘sta.txt’ ‘topo.txt’
'LazyData' is specified without a 'data' directory
File ‘INLAspacetime/libs/INLAspacetime.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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
File ‘INSPIRE/libs/INSPIRE.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.
Package suggested but not available for checking: ‘cmdstanr’
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘splines2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Error_Estimation_Response_1.tiff’ ‘Error_Estimation_Response_2.tiff’
  ‘Error_Estimation_Response_3.tiff’
Undeclared packages ‘quantreg’, ‘effects’, ‘Hmisc’, ‘rockchalk’, ‘pequod’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘colorspace’ in Rd xrefs
'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
Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘readxl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'IntervalSurgeon-package.Rd':
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc  10.0Mb
Undeclared package ‘DT’ in Rd xrefs
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'selectRuleRRF.Rd':
  ‘target’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'rawAvgCost-deprecated.Rd':
  ‘cost.transf’ ‘in.millions’ ‘confidence.interval’ ‘minimum.year’
  ‘maximum.year’ ‘final.year’ ‘incomplete.year.threshold’
  ‘incomplete.year.weights’ ‘gam.k’ ‘mars.nprune’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 12106 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared packages ‘nlstools’, ‘lme4’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘fdrtool’ ‘nimble’
  All declared Imports should be used.
Package suggested but not available for checking: ‘surveyspec’
Note: found 102 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
Documented arguments not in \usage in Rd file 'chars_collapse.Rd':
  ‘collapse’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’
File ‘iotools/libs/iotools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
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
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘expm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gmodels’ ‘lmtest’ ‘testthat’ ‘tidyverse’ ‘zoo’
  All declared Imports should be used.
Note: found 46 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘Rpadrino’ in Rd xrefs
Found the following significant warnings:
  Rip-host-info.c:514:20: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  ./templates/Rip-bsearch-template.c:889:38: warning: data argument not used by format string [-Wformat-extra-args]
  Rip-match.c:467:34: warning: data argument not used by format string [-Wformat-extra-args]
  Rip-match.c:1125:26: warning: data argument not used by format string [-Wformat-extra-args]
  Rip-match.c:1173:24: warning: data argument not used by format string [-Wformat-extra-args]
  Rip-match.c:1407:26: warning: data argument not used by format string [-Wformat-extra-args]
See ‘/data/gannet/ripley/R/packages/tests-clang/IP.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Invalid package aliases in Rd file 'iprior_package.Rd':
  ‘iprior_package-package’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘seqinr’
  All declared Imports should be used.
Argument items with no description in Rd file 'mrbayes.Rd':
  ‘unlink’ ‘constraint’
Argument items with no description in Rd file 'mrbayes.lset.Rd':
  ‘partition’
Argument items with no description in Rd file 'multistate.Rd':
  ‘model’
File ‘iRafNet/libs/iRafNet.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:
  ‘Rdpack’ ‘glmnet’
  All declared Imports should be used.
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
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: \&
Undeclared package ‘irr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'print.cat_output.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'sub-subset-Itempool-numeric-missing-method.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'sub-subset-Response_set-numeric-missing-method.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'sub-subset-Testlet-numeric-missing-method.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'print.Item.Rd':
  ‘print.Item’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 117 marked UTF-8 strings
Package suggested but not available for checking: ‘xcms’
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
Note: found 104 marked UTF-8 strings
File ‘isingLenzMC/libs/isingLenzMC.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.
Objects in \usage without \alias in Rd file 'islasso-internal.Rd':
  ‘modelX’ ‘.checkinput’ ‘.startpoint’ ‘.islasso’
  ‘checkinput.islasso.path’ ‘startpoint.islasso.path’
  ‘islasso.path.fit.glm’ ‘islasso.path.fitter2’ ‘interpolate’ ‘makeHyp’
  ‘printHyp’ ‘cislasso’ ‘ci.fitted.islasso’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'dot-assignmentMaker.Rd':
  ‘.precip_raster’ ‘.precip_SD_raster’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘Unicode’ in Rd xrefs
Note: found 7542 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Undeclared package ‘multtest’ in Rd xrefs
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: \$
Specified C++14: please drop specification unless essential
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.3Mb
    libs   4.1Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Undeclared package ‘surveillance’ in Rd xrefs
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 87 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Found the following files/directories:
  ‘RMTplot.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘AER’ in Rd xrefs
Package suggested but not available for checking: ‘gurobi’
Note: found 58 marked UTF-8 strings
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Invalid package aliases in Rd file 'ivprobit-package.Rd':
  ‘ivProbit-package’
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
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Rd files without \alias:
  ‘jackknifeKME-package.Rd’
Namespaces in Imports field not imported from:
  ‘fBasics’ ‘reshape’ ‘tidyr’ ‘utils’
  All declared Imports should be used.
Note: found 2261 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 1984 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘mcmcplots’ ‘tidyverse’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘GA’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.4Mb
Namespace in Imports field not imported from: ‘ids’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   3.7Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 87 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 16726 marked UTF-8 strings
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
Specified C++11: please drop specification unless essential
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    i18n   6.5Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
  ‘afex’ ‘car’ ‘dplyr’ ‘emmeans’ ‘ggrepel’ ‘ggridges’ ‘lavaan’
  ‘multcomp’ ‘mvnormtest’ ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘remMap’
Documented arguments not in \usage in Rd file 'paste_coef.Rd':
  ‘parlemts’

Documented arguments not in \usage in Rd file 'paste_linpred.Rd':
  ‘parlemts’ ‘matname’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
Note: found 925830 marked UTF-8 strings
Note: found 176 marked UTF-8 strings
Undeclared package ‘later’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    examples      2.9Mb
    htmlwidgets   1.1Mb
    www           2.7Mb
Note: found 17 marked UTF-8 strings
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:
    pre-release juicr (2017 - 2021)
Specified C++14: please drop specification unless essential
Undeclared package ‘ggplot2’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Superpower’ ‘pwr’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 111752 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘kappalab/libs/kappalab.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.
Rd files without \alias:
  ‘karaoke-package.Rd’
Found the following files/directories:
  ‘song.wav’ ‘song4karaoke.wav’
Namespace in Imports field not imported from: ‘gifski’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘EQL’ ‘univariateML’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
prepare_Rd: NEWS.Rd:58: Dropping empty section ‘kelvin INITIAL VERSION 1.0-0 (2012-05-30)’
'LazyData' is specified without a 'data' directory
File ‘Kendall/libs/Kendall.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:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
File ‘KERE/libs/KERE.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.
Argument items with no description in Rd file 'covQualNested.Rd':
  ‘covBet’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘KernSmoothIRT/libs/KernSmoothIRT.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.
S3 methods shown with full name in Rd file 'bw.abram.temp.Rd':
  ‘bw.abram.temp’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'calc_PGtheta_R.Rd':
  ‘model’ ‘iter’

Documented arguments not in \usage in Rd file 'make_wsz_cpp.Rd':
  ‘info’ ‘initialized’

Documented arguments not in \usage in Rd file 'read_dfm_cpp.Rd':
  ‘W_raw’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  keyring_secret_service.c:188:23: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  keyring_secret_service.c:351:23: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/keyring.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Documented arguments not in \usage in Rd file 'b_wincred_get.Rd':
  ‘backend’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘splines’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.2Mb
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘Rsamtools’ ‘rtracklayer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fitdistrplus’ ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘kknn/libs/kknn.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.
Package which this enhances but not available for checking: ‘rkward’
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘SnowballC’ ‘stringi’
  All declared Imports should be used.
'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
Undeclared package ‘kml3d’ in Rd xrefs
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
S3 methods shown with full name in Rd file 'unlist.constr.Rd':
  ‘unlist.constr’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘maptools’
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
Found the following files/directories:
  ‘Killed after ’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'knotR-package.Rd':
  ‘knot-package’
Note: found 9 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘mice’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘kriging/libs/kriging.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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘KSEA Bar Plot.tiff’ ‘KSEA Kinase Scores.csv’
  ‘KSEA.Merged.Heatmap.png’ ‘Kinase-Substrate Links.csv’
Package suggested but not available for checking: ‘FactoClass’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RUnit’
  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: ‘robustbase’
  All declared Imports should be used.
Undeclared package ‘fso’ in Rd xrefs
File ‘labdsv/libs/labdsv.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.
Undeclared packages ‘carData’, ‘factoextra’, ‘labstatR’ in Rd xrefs
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
Undeclared package ‘spdep’ in Rd xrefs
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Undeclared package ‘plyr’ in Rd xrefs
Undeclared package ‘gsl’ in Rd xrefs
GNU make is a SystemRequirements.
Undeclared package ‘raster’ in Rd xrefs
'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) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Note: found 6 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘glmnet’ in Rd xrefs
File ‘LassoNet/libs/LassoNet.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 ‘lassoshooting/libs/lassoshooting.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
Package suggested but not available for checking: ‘ergm.userterms’
checkRd: (-1) simulate.ergmm.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) simulate.ergmm.Rd:36: Escaped LaTeX specials: \$
Unknown package ‘ergm.userterms’ in Rd xrefs
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘akmedoids’
Unknown package ‘akmedoids’ in Rd xrefs
Objects in \usage without \alias in Rd file 'latrend-generics.Rd':
  ‘nClusters’ ‘clusterProportions’ ‘clusterTrajectories’ ‘compose’
  ‘converged’ ‘externalMetric’ ‘estimationTime’ ‘fit’
  ‘fittedTrajectories’ ‘getArgumentDefaults’ ‘getArgumentExclusions’
  ‘getLabel’ ‘getLcMethod’ ‘getName’ ‘getShortName’ ‘idVariable’
  ‘metric’ ‘plotFittedTrajectories’ ‘plotClusterTrajectories’ ‘postFit’
  ‘postprob’ ‘predictAssignments’ ‘predictForCluster’ ‘predictPostprob’
  ‘prepareData’ ‘preFit’ ‘qqPlot’ ‘responseVariable’ ‘strip’
  ‘timeVariable’ ‘trajectoryAssignments’ ‘validate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Undeclared package ‘ggplot2’ in Rd xrefs
checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'moments2.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'skeleton.Rd':
  ‘endogeneous’ ‘...’

Documented arguments not in \usage in Rd file 'vcov2-internal.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘R6’
  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
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘gridExtra’ in Rd xrefs
Found the following files/directories:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
Found the following significant warnings:
  R_Interface/R_Lcm_CR.cpp:66:16: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  daniel2/R_Environ_Simple.cpp:85:19: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  daniel2/R_Environ_Simple.cpp:98:16: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  daniel2/R_Environ_Simple.cpp:138:19: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  daniel2/R_Environ_Simple.cpp:354:19: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/LCMCR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   5.4Mb
Packages suggested but not available for checking: 'xcms', 'MSnbase'
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘cli’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘chinese.misc’ ‘dplyr’ ‘factoextra’ ‘glasso’
  ‘highcharter’ ‘htmlwidgets’ ‘ldatuning’ ‘qgraph’ ‘quanteda’ ‘rvest’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinybusy’ ‘shinycssloaders’
  ‘shinydashboard’ ‘shinyjs’ ‘stringr’ ‘textmineR’ ‘textplot’ ‘tidyr’
  ‘topicmodels’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'dot-choose_best_subjects.Rd':
  ‘best’ ‘candidate’

Documented arguments not in \usage in Rd file 'dot-normalize_props.Rd':
  ‘keep_all_items’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd file 'top.topic.words.Rd':
  ‘alpha’
File ‘lda/libs/lda.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.
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘beepr’ ‘broom’ ‘chinese.misc’ ‘dplyr’ ‘highcharter’
  ‘htmlwidgets’ ‘ldatuning’ ‘parallel’ ‘plotly’ ‘purrr’ ‘quanteda’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinycssloaders’ ‘shinyjs’
  ‘stringr’ ‘textmineR’ ‘tidyr’ ‘tidytext’ ‘topicmodels’
  All declared Imports should be used.
Undeclared package ‘tm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘RcppProgress’ ‘rgen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'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.
Note: found 75 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  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:
    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
Namespace in Imports field not imported from: ‘leaflet’
  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
Invalid package aliases in Rd file 'LEANR-package.Rd':
  ‘LEAN-package’
checkRd: (-1) leaps.Rd:38: Escaped LaTeX specials: \&
File ‘leaps/libs/leaps.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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘pracma’ in Rd xrefs
Note: found 78 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Invalid package aliases in Rd file 'learnn.Rd':
  ‘learnn-package’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   8.0Mb
Documented arguments not in \usage in Rd file 'backward_step.Rd':
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in Rd file 'backward_step_IM.Rd':
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in Rd file 'forward_step.Rd':
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in Rd file 'forward_step_IM.Rd':
  ‘empty_start_dataset’ ‘fit’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Undeclared packages ‘purrr’, ‘dplyr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘maptools’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   6.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs   3.9Mb
GNU make is a SystemRequirements.
Undeclared package ‘MESS’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get_generic.Rd':
  ‘mismatch’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 3 marked UTF-8 strings
Found the following significant warnings:
  utils.c:34:85: warning: format specifies type 'int' but the argument has type 'mybigint_t' (aka 'long') [-Wformat]
  utils.c:283:16: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/lfe.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘knitr’ ‘purrr’ ‘rmarkdown’
  All declared Imports should be used.
File ‘lgarch/libs/lgarch.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.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Note: found 22 marked UTF-8 strings
Found the following significant warnings:
  linear.cpp:31:10: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  tron.cpp:33:10: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/LiblineaR.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Undeclared package ‘future’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘data.table’ ‘e1071’ ‘fastmatch’
  All declared Imports should be used.
Undeclared package ‘tidyselect’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) LIMEcoli.Rd:125: Escaped LaTeX specials: \_
checkRd: (-1) Read.Rd:88: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:92: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:98: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:104: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:105: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:106: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:107: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:108: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:109: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:110: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:111: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:112: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:114: Escaped LaTeX specials: \# \#
Specified C++11: please drop specification unless essential
S3 methods shown with full name in Rd file 'BIC.threshold.Rd':
  ‘BIC.threshold’

S3 methods shown with full name in Rd file 'BIC.threshold.ggm.Rd':
  ‘BIC.threshold.ggm’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘linERR/libs/linERR.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
Undeclared package ‘magrittr’ in Rd xrefs
Note: found 60714 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'MassAcylCer.Rd':
  ‘glccer’

Documented arguments not in \usage in Rd file 'MassPEo.Rd':
  ‘PEp’

Documented arguments not in \usage in Rd file 'findMS2precursor.Rd':
  ‘minint’ ‘maxint’

Documented arguments not in \usage in Rd file 'joinAnnotationResults.Rd':
  ‘simplifyAnnotation’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 32 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘keras’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get_variable.Rd':
  ‘x’ ‘name’ ‘mustExist’ ‘create’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  combine.c:664:49: warning: format specifies type 'double' but the argument has type 'int' [-Wformat]
  combine.c:664:58: warning: data argument not used by format string [-Wformat-extra-args]
  subroutines.c:57:52: warning: data argument not used by format string [-Wformat-extra-args]
See ‘/data/gannet/ripley/R/packages/tests-clang/list.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
'LazyData' is specified without a 'data' directory
Note: found 888 marked UTF-8 strings
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
File ‘ljr/libs/ljr.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) MHDI.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    testdata   1.3Mb
Undeclared packages ‘sfsmisc’, ‘mnormt’ in Rd xrefs
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘agridat’ ‘ggplot2’ ‘maps’ ‘sf’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R              1.2Mb
    doc-software   2.4Mb
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: \_
File ‘lmPerm/libs/lmPerm.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
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tTestTable.rda’
Note: found 1 marked UTF-8 string
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Author
    Maintainer
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘base’ ‘qpdf’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) SPSloess.Rd:71: Escaped LaTeX specials: \^ \^
File ‘localgauss/libs/localgauss.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: ‘checkmate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) ACS.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) EmployedACS.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSale.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleCA.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleCanton.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleNY.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:24: Escaped LaTeX specials: \$
checkRd: (-1) SalaryGender.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) SandP500.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) SandwichAnts.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) SandwichAnts2.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) TrafficFlow.Rd:18: Escaped LaTeX specials: \#
Invalid package aliases in Rd file 'Lock5Data-package.Rd':
  ‘Lock5Data-package’
Namespace in Imports field not imported from: ‘lestat’
  All declared Imports should be used.
Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’
Note: skipping ‘locuszoomr.Rmd’ due to unavailable dependencies:
  'EnsDb.Hsapiens.v75'
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'spec.emb.Rd':
  ‘A’
File ‘loe/libs/loe.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.
Found the following significant warnings:
  solvoptweights.c:569:54: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/LogConcDEAD.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Undeclared package ‘colorspace’ in Rd xrefs
Note: found 12 marked UTF-8 strings
File ‘logisticPCA/libs/logisticPCA.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
Argument items with no description in Rd file 'dlogitnorm.Rd':
  ‘sigma’
Argument items with no description in Rd file 'invlogit.Rd':
  ‘q’ ‘\dots’
Argument items with no description in Rd file 'logit.Rd':
  ‘p’ ‘\dots’
Argument items with no description in Rd file 'plogitnorm.Rd':
  ‘sigma’ ‘\dots’
Argument items with no description in Rd file 'qlogitnorm.Rd':
  ‘sigma’ ‘\dots’
Argument items with no description in Rd file 'twCoefLogitnorm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'twCoefLogitnormE.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘apollo’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Argument items with no description in Rd file 'levopt.Rd':
  ‘x’ ‘alpha’ ‘fmax’ ‘tm’
Argument items with no description in Rd file 'pershow.Rd':
  ‘object’
Argument items with no description in Rd file 'norpt.Rd':
  ‘alist’
Found the following significant warnings:
  t_chol.c:883:31: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
  t_chol.c:913:29: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/longclust.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
checkRd: (-1) butstrap.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.nri.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.s.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.s.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) nri.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) roc.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) roc.s.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.s.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 994 marked Latin-1 strings
Namespace in Imports field not imported from: ‘cli’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   1.5Mb
    tcl   1.3Mb
Auto-generated content requiring editing in Rd file 'LoopAnalyst-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Found the following files/directories:
  ‘Model_1.cm’ ‘dambacher.dot’ ‘levins.dot’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'importance_sampling.array.Rd':
  ‘is_method’

Documented arguments not in \usage in Rd file 'importance_sampling.default.Rd':
  ‘is_method’

Documented arguments not in \usage in Rd file 'importance_sampling.matrix.Rd':
  ‘is_method’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘scio’
Malformed Description field: should contain one or more complete sentences.
File ‘lorec/libs/lorec.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
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'LotkasXX.Rd':
  ‘Table’
Argument items with no description in Rd file 'LotkasXY.Rd':
  ‘Table’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘lowmemtkmeans/libs/lowmemtkmeans.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.
Undeclared package ‘forecastLSW’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'followx.Rd':
  ‘Xi’ ‘x0’ ‘h’ ‘t0’ ‘iter’ ‘way’ ‘weights’ ‘pen’ ‘phi’
  ‘lasteigenvector’ ‘rho0’ ‘boundary’ ‘convergence.at’ ‘cross’
'LazyData' is specified without a 'data' directory
checkRd: (-1) lpepa.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:90: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:65: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  hbio.c:1629:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/lpSolve.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
File ‘LRcontrast/libs/LRcontrast.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: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘kerdiest’
Note: found 55 marked UTF-8 strings
checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
Namespace in Imports field not imported from: ‘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
'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
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) spectral.density.Rd:55: Escaped LaTeX specials: \&
Note: found 2096 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘Icens’ ‘interval’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ltsa/libs/ltsa.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
Namespace in Imports field not imported from: ‘rpostgis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'setlogdata.Rd':
  ‘logdata’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘depth’
Undeclared package ‘zoo’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  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
Package suggested but not available for checking: ‘orthogene’
Namespace in Imports field not imported from: ‘fmsb’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘orthogene’
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shinythemes’ ‘topicmodels’
  All declared Imports should be used.
Note: found 134 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘rlang’ ‘torch’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 27 marked UTF-8 strings
Packages suggested but not available for checking: 'lpjmlkit', 'quitte'
Undeclared packages ‘rlang’, ‘vctrs’ in Rd xrefs
Packages suggested but not available for checking:
  'SeqArray', 'SeqVarTools'
Package suggested but not available for checking: ‘tesseract’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Argument items with no description in Rd file 'plot.magree.Rd':
  ‘xlab’ ‘ylab’ ‘main’ ‘\dots’
Argument items with no description in Rd file 'print.summary.magree.Rd':
  ‘x’ ‘\dots’
Argument items with no description in Rd file 'summary.magree.Rd':
  ‘object’ ‘\dots’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocCheck’
Note: found 41 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
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cli’ ‘nomnoml’
  All declared Imports should be used.
Argument items with no description in Rd file 'alignPeaks.Rd':
  ‘\dots’
Undeclared package ‘tibble’ in Rd xrefs
Note: found 17524 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
Note: found 328 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 55 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.5Mb
Undeclared packages ‘CompQuadForm’, ‘car’ in Rd xrefs
Note: found 3 marked UTF-8 strings
Package suggested but not available for checking: ‘RSiena’
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 3058 marked UTF-8 strings
Note: found 11396 marked UTF-8 strings
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
Specified C++11: please drop specification unless essential
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data          1.2Mb
    doc           1.6Mb
    htmlwidgets   2.3Mb
    libs          2.6Mb
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fixes
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
Note: found 29618 marked UTF-8 strings
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
Namespace in Imports field not imported from: ‘pbmcapply’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 55 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 1056 marked UTF-8 strings
Note: found 13138 marked UTF-8 strings
Note: found 1810 marked UTF-8 strings
Found the following significant warnings:
  mapget.c:251:43: warning: data argument not used by format string [-Wformat-extra-args]
  mapget.c:325:48: warning: data argument not used by format string [-Wformat-extra-args]
  mapget.c:354:41: warning: data argument not used by format string [-Wformat-extra-args]
See ‘/data/gannet/ripley/R/packages/tests-clang/maps.Rcheck/00install.out’ for details.
Undeclared package ‘chromote’ in Rd xrefs
Note: found 1 marked UTF-8 string
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
checkRd: (-1) Interpolation-class.Rd:41: Escaped LaTeX specials: \#
checkRd: (-1) MareyMap-class.Rd:85: Escaped LaTeX specials: \_
checkRd: (-1) MareyMap-methods.Rd:11: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) MareyMap-methods.Rd:12: Escaped LaTeX specials: \_
checkRd: (-1) SpeciesMaps-methods.Rd:11: Escaped LaTeX specials: \_
checkRd: (-1) interpolation-methods.Rd:13: Escaped LaTeX specials: \_
Note: found 5210 marked UTF-8 strings
Argument items with no description in Rd file 'bias.factor.Rd':
  ‘RRud’ ‘RReu’ ‘rr’ ‘s2’
'LazyData' is specified without a 'data' directory
checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'mark_my_dir.Rd':
  ‘mark_file’

Documented arguments not in \usage in Rd file 'path_type.Rd':
  ‘github_token’

Documented arguments not in \usage in Rd file 'read_assignment_yml.Rd':
  ‘path’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘marssTMB’
Objects in \usage without \alias in Rd file 'utility_functions.Rd':
  ‘fully.spec.x’ ‘marssMODEL.to.list’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'NewPackage-package.Rd':
  ‘NewPackage-package’
Auto-generated content requiring editing in Rd file 'NewPackage-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Package suggested but not available for checking: ‘gurobi’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
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) size_t-class.Rd:6: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
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
'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 significant warnings:
  binCounts.c:25:85: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  binMeans.c:26:70: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  binMeans.c:26:74: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  binMeans.c:33:85: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  colOrderStats.c:58:51: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  indexByRow.c:30:72: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  indexByRow.c:33:15: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  indexByRow.c:33:22: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  indexByRow.c:69:131: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
  rowOrderStats.c:58:51: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  weightedMean.c:26:70: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  weightedMean.c:26:74: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  weightedMedian.c:26:70: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  weightedMedian.c:26:74: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/matrixStats.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Found the following files/directories:
  ‘utilities.R’
'LazyData' is specified without a 'data' directory
checkRd: (-1) maxControl.Rd:83: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘geohashTools’ in Rd xrefs
Note: found 18 marked UTF-8 strings
Note: found 54 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Found the following files/directories:
  ‘map_5.png’ ‘maze_5.html’
'LazyData' is specified without a 'data' directory
Undeclared packages ‘logistf’, ‘brglm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘raster’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘effsize’ ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 6 marked Latin-1 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
File ‘mbrglm/libs/mbrglm.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: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lars’ ‘methods’ ‘parallel’ ‘smoothmest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd file 'mccca-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
File ‘mcclust/libs/mcclust.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
File ‘mcemGLM/libs/mcemGLM.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: ‘boot.heterogeneity’
  All declared Imports should be used.
checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
Note: found 46 marked UTF-8 strings
Undeclared package ‘NLP’ in Rd xrefs
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
Specified C++11: please drop specification unless essential
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘coda’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Package suggested but not available for checking: ‘cmdstanr’
Note: found 496 marked UTF-8 strings
Found the following significant warnings:
  nsga2.c:303:11: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  nsga2.c:303:31: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  nsga2.c:308:13: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  nsga2.c:308:33: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  nsga2.c:339:13: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  nsga2.c:339:34: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  nsga2.c:344:15: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  nsga2.c:344:36: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/mco.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'geom_cp_density.Rd':
  ‘include’

Documented arguments not in \usage in Rd file 'get_simulate.Rd':
  ‘par_trials’ ‘pars_pop’ ‘pars_varying’

Documented arguments not in \usage in Rd file 'pp_eval.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘cli’ in Rd xrefs
'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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2866 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MethylCapSig’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  score.c:87:3: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
  score.c:88:3: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/meanr.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Package suggested but not available for checking: ‘cmdstanr’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'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:
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
File ‘MediaK/libs/MediaK.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: ‘vroom’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Data_Correlation.txt’ ‘correlation_FDR_table.txt’
'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 significant warnings:
  dta-for-R.c:516:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/memisc.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   3.1Mb
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  getPointer.c:126:70: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
  getPointer.c:139:70: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/memo.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'buildModelMatrix.Rd':
  ‘character’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
GNU make is a SystemRequirements.
Note: found 37 marked UTF-8 strings
Packages suggested but not available for checking: 'ropls', 'xcms'
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Invalid package aliases in Rd file 'taxa-package.Rd':
  ‘taxa-package’
Documented arguments not in \usage in Rd file 'limited_print.Rd':
  ‘trunc’

Documented arguments not in \usage in Rd file 'parse_heirarchies_to_taxonomy.Rd':
  ‘A’

Documented arguments not in \usage in Rd file 'parse_raw_heirarchies_to_taxonomy.Rd':
  ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘gbm’ ‘ggplot2’ ‘graphics’ ‘randomForest’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'ClusterMF-deprecated.Rd':
  ‘formula’ ‘data’ ‘vi’ ‘study’ ‘whichweights’ ‘num.trees’ ‘mtry’
  ‘method’ ‘tau2’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking: 'Rcgmin', 'Rvmmin'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.3Mb
Unknown packages ‘Rcgmin’, ‘Rvmmin’ in Rd xrefs
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’
  ‘readr’
  All declared Imports should be used.
Suggests orphaned package: ‘udunits2’
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data       3.0Mb
    examples  10.3Mb
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmerTest’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'plot.metaplot_gtable.Rd':
  ‘y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ade4’ ‘dendextend’ ‘ggforce’ ‘ggrepel’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
Undeclared packages ‘netmeta’, ‘metasens’, ‘robumeta’ in Rd xrefs
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
Note: found 1496 marked UTF-8 strings
Note: found 3300 marked UTF-8 strings
Specified C++11: please drop specification unless essential
checkRd: (-1) cardiac.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) plvol.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) sbp.Rd:16: Escaped LaTeX specials: \&
Undeclared package ‘R2WinBUGS’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Note: found 1 marked UTF-8 string
Undeclared package ‘rlang’ in Rd xrefs
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.8Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
Note: found 6 marked UTF-8 strings
Note: found 7 marked Latin-1 strings
  Note: found 14 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Argument items with no description in Rd file 'predict.mfp.Rd':
  ‘safe’
Namespace in Imports field not imported from: ‘fs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘boot’ ‘energy’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  matrix.c:144:66: warning: data argument not used by format string [-Wformat-extra-args]
  misc.c:31:48: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/mgcv.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
File ‘MGL/libs/MGL.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
Namespaces in Imports field not imported from:
  ‘R6’ ‘reticulate’
  All declared Imports should be used.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'Rpackage-package.Rd':
  ‘Rpackage-package’
Auto-generated content requiring editing in Rd file 'Rpackage-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
File ‘mhsmm/libs/mhsmm.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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'DAPAR', 'ProteoMM'
S3 methods shown with full name in Rd file 'complete.miceadds.Rd':
  ‘complete.mids.nmi’ ‘complete.mids.1chain’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared packages ‘micEconAids’, ‘micEconSNQP’ in Rd xrefs
Specified C++11: please drop specification unless essential
Note: found 9345 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘utils’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
Undeclared package ‘tibble’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  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: ‘testthat’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'changeDevSettings.Rd':
  ‘defaultsSettings’

Documented arguments not in \usage in Rd file 'getResultPerScheme.Rd':
  ‘criteria’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
    lib   1.7Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘curl’ ‘jsonlite’ ‘parallel’ ‘tools’ ‘vctrs’
  All declared Imports should be used.
Argument items with no description in Rd file 'micSimParallel.Rd':
  ‘transitionMatrix’ ‘absStates’ ‘varInitStates’ ‘initStatesProb’
  ‘fixInitStates’ ‘maxAge’ ‘simHorizon’ ‘fertTr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'MIDASwrappeR-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
Package suggested but not available for checking: ‘midfielddata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'getvol.Rd':
  ‘data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  subfunc.cpp:275:14: warning: 'operator<<' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  subfunc.cpp:310:16: warning: 'operator<<' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  subfunc.cpp:322:16: warning: 'operator<<' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/minimaxdesign.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘gmp’ ‘jpeg’
  All declared Imports should be used.
':::' call which should be '::': ‘parallel:::detectCores’
  See the note in ?`:::` about the use of this operator.
Namespaces in Imports field not imported from:
  ‘markdown’ ‘metafor’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Namespaces in Imports field not imported from:
  ‘pracma’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
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
Undeclared package ‘scatterplot3d’ in Rd xrefs
Undeclared packages ‘pspline’, ‘lme4’ in Rd xrefs
File ‘MiSPU/libs/MiSPU.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.
Undeclared package ‘list’ in Rd xrefs
Documented arguments not in \usage in Rd file 'logAdd.Rd':
  ‘x’ ‘y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘mcmcr’
  All declared Imports should be used.
Argument items with no description in Rd file 'randomizationTest.Rd':
  ‘R’
checkRd: (-1) AKMCS.Rd:215: Escaped LaTeX specials: \&
checkRd: (-1) BMP.Rd:164: Escaped LaTeX specials: \&
checkRd: (-1) IRW.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) IRW.Rd:151: Escaped LaTeX specials: \&
checkRd: (-1) MP.Rd:142: Escaped LaTeX specials: \&
checkRd: (-1) MetropolisHastings.Rd:58: Escaped LaTeX specials: \&
checkRd: (-1) SubsetSimulation.Rd:152: Escaped LaTeX specials: \&
checkRd: (-1) oscillator_d6.Rd:14: Escaped LaTeX specials: \&
Packages suggested but not available for checking:
  'karyoploteR', 'regioneR'
Found the following files/directories:
  ‘par-7269706c6579’
Found the following significant warnings:
  ./AK_Basic.h:576:32: warning: format specifies type 'double' but the argument has type 'int' [-Wformat]
  ./AK_Basic.h:584:30: warning: format specifies type 'double' but the argument has type 'int' [-Wformat]
  ./AK_Basic.h:587:61: warning: format specifies type 'double' but the argument has type 'int' [-Wformat]
  GLMM_MCMC.cpp:191:100: warning: data argument not used by format string [-Wformat-extra-args]
  GLMM_NMixRelabel.cpp:157:81: warning: data argument not used by format string [-Wformat-extra-args]
  GLMM_dY_meanY.cpp:101:69: warning: data argument not used by format string [-Wformat-extra-args]
  NMix_NMixRelabel.cpp:110:81: warning: data argument not used by format string [-Wformat-extra-args]
See ‘/data/gannet/ripley/R/packages/tests-clang/mixAK.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Found the following significant warnings:
  ClusterLauncher.cpp:201:16: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  ClusterLauncher.cpp:291:16: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  KmmLauncher.cpp:283:16: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  KmmLauncher.cpp:392:16: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  LearnLauncher.cpp:202:16: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  LearnLauncher.cpp:289:16: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/MixAll.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'mixAR-internal.Rd':
  ‘p’ ‘value’ ‘tau’ ‘etk’ ‘parscore’ ‘sigma’ ‘logpdf’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'rigaussian.Rd':
  ‘mu’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'Sn_A.Rd':
  ‘data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
File ‘mixexp/libs/mixexp.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.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
Auto-generated content requiring editing in Rd file 'mixl-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
Specified C++11: please drop specification unless essential
checkRd: (-1) mixmeta-package.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) mixmeta.ml.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ml.igls.Rd:62: Escaped LaTeX specials: \&
Undeclared package ‘mvmeta’ in Rd xrefs
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mixRasch’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘ashr’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘rms’ in Rd xrefs
Undeclared packages ‘rms’, ‘Hmisc’, ‘genefilter’ in Rd xrefs
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Texture.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:33: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘ConfusionTableR’ ‘OddsPlotty’ ‘caret’ ‘dplyr’ ‘ggplot2’ ‘parsnip’
  ‘ranger’ ‘recipes’ ‘rsample’ ‘varhandle’ ‘workflows’
  All declared Imports should be used.
checkRd: (-1) gp.list.Rd:16: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'

Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘ClusterR’ ‘MASS’ ‘Rdpack’ ‘multiwave’ ‘randomForest’ ‘ranger’
  All declared Imports should be used.
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    include  10.1Mb
    libs     25.2Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘randomForest’
  All declared Imports should be used.
Undeclared package ‘htmlwidgets’ in Rd xrefs
Running examples in ‘mlr3pipelines-Ex.R’ failed
The error most likely occurred in:

> ### Name: mlr_pipeops_colroles
> ### Title: Change Column Roles of a Task
> ### Aliases: mlr_pipeops_colroles PipeOpColRoles
> 
> ### ** Examples
> 
> library("mlr3")
> 
> task = tsk("boston_housing")
> pop = po("colroles", param_vals = list(
+   new_role = list(cmedv = "order")
+ ))
> 
> pop$train(list(task))
Error: Cannot change the role of a target.
This happened PipeOp colroles's $train()
Execution halted
Namespaces in Imports field not imported from:
  ‘DT’ ‘Metrics’ ‘data.table’ ‘dplyr’ ‘mlr3’ ‘mlr3learners’
  ‘mlr3measures’ ‘mlr3pipelines’ ‘patchwork’ ‘plyr’ ‘purrr’
  ‘shinyWidgets’ ‘shinyalert’ ‘shinydashboard’ ‘shinyjs’ ‘stats’
  ‘stringr’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'cpoTemplate.Rd':
  ‘affect.names’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'mlVARsim0.Rd':
  ‘nPerson’ ‘nNode’ ‘nTime’ ‘sparsity’ ‘parRange’ ‘propPositive’
  ‘diagPositive’ ‘diagIncluded’ ‘sdRange’ ‘shrinkFactor’
  ‘residualStyle’ ‘residualShared’ ‘residualSDrange’ ‘verbose’
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.pdf’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
Namespaces in Imports field not imported from:
  ‘Cairo’ ‘DT’ ‘XML’ ‘caTools’ ‘data.table’ ‘dplyr’ ‘ggplot2’
  ‘htmltools’ ‘leaflet’ ‘lubridate’ ‘plotly’ ‘shinyjs’ ‘stringr’ ‘xts’
  ‘zoo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ActCR’ ‘ActFrag’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘doParallel’ ‘parallel’
  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
Undeclared package ‘geeM’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./covariance.h:177:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  ./covariance.h:164:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/mmrm.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'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
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘magrittr’ ‘reticulate’ ‘tensorflow’ ‘usethis’
  All declared Imports should be used.
Rd files without \alias:
  ‘mnlfa-package.Rd’
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘energy’ in Rd xrefs
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Undeclared package ‘geomorph’ in Rd xrefs
Packages suggested but not available for checking: 'optiSel', 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Packages suggested but not available for checking:
  'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene'

Imports includes 34 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: 'purrr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘caret’ in Rd xrefs
Note: found 313 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘DALEX’ ‘DT’ ‘auditor’ ‘breakDown’ ‘drifter’ ‘svglite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 18 marked Latin-1 strings
Undeclared packages ‘lme4’, ‘rstanarm’, ‘dplyr’ in Rd xrefs
Documented arguments not in \usage in Rd file 'check_augment_data_specification.Rd':
  ‘strict’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘parsnip’
  All declared Imports should be used.
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘tidymodels’ ‘tidyverse’
  All declared Imports should be used.
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘crayon’ ‘dials’ ‘glue’ ‘parsnip’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 5238 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 20578 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Warning: no function found corresponding to methods exports from ‘moko’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
Argument items with no description in Rd file 'as.difftime.rd':
  ‘tim’ ‘format’
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘seewave’ in Rd xrefs
Note: found 13 marked UTF-8 strings
File ‘morse/libs/morse.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.
Note: found 56 marked UTF-8 strings
Note: found 7 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
Undeclared package ‘cubature’ in Rd xrefs
Namespace in Imports field not imported from: ‘NlcOptim’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘graphlayouts’ in Rd xrefs
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'create_barrier_cs.Rd':
  ‘fields’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 3 marked UTF-8 strings
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
Specified C++11: please drop specification unless essential
Undeclared package ‘lme4’ in Rd xrefs
checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
checkRd: (-1) genotype_data.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) phenotype_data.Rd:15: Escaped LaTeX specials: \_
Rd files without \alias:
  ‘MPLikelihoodWB-package.Rd’
Documented arguments not in \usage in Rd file 'addHeaderToSavedata.Rd':
  ‘director’

Documented arguments not in \usage in Rd file 'extractIndirect.Rd':
  ‘curFile’

Documented arguments not in \usage in Rd file 'extractIndirect_section.Rd':
  ‘curFile’

Documented arguments not in \usage in Rd file 'graphModel.Rd':
  ‘The’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘mpmi/libs/mpmi.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
Undeclared package ‘proxy’ in Rd xrefs
File ‘mp/libs/mp.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
Objects in \usage without \alias in Rd file 'Mqrcm-internal.Rd':
  ‘check.in’ ‘check.out’ ‘start.theta’ ‘iMqr.internal’ ‘cov.theta’
  ‘iobjfun’ ‘sortH’ ‘isigma’ ‘iMqr.newton’ ‘num.fun’ ‘make.bfun’
  ‘apply_bfun’ ‘p.bisec’ ‘slp.basis’ ‘is.slp’ ‘iqr.waldtest’
  ‘extract.p’ ‘pred.beta’ ‘print.iMqr’ ‘print.summary.iMqr’
  ‘terms.iMqr’ ‘model.matrix.iMqr’ ‘vcov.iMqr’ ‘nobs.iMqr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) F.huggins.estim.Rd:199: Escaped LaTeX specials: \$ \$
checkRd: (-1) F.huggins.estim.Rd:205: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:206: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:207: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:208: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:209: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:210: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:212: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:213: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:214: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:215: Escaped LaTeX specials: \$
checkRd: (-1) lines.cjs.Rd:15: Escaped LaTeX specials: \$
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Auto-generated content requiring editing in Rd file 'mrbsizer-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rgdal', 'rgeos'
Undeclared package ‘processx’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘speedglm’ in Rd xrefs
Found the following significant warnings:
  main.cpp:41:31: warning: 'operator<<' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
  recursion.cpp:645:10: warning: 'operator<<' is deprecated: use braced initialiser list instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/MRS.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 75 marked UTF-8 strings
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Argument items with no description in Rd file 'msda.Rd':
  ‘sml’
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    data   4.4Mb
Documented arguments not in \usage in Rd file 'CalcMPDynamics.Rd':
  ‘M_ageArray’ ‘TAC_f’ ‘E_f’ ‘SizeLim_f’ ‘FinF’ ‘Spat_targ’
  ‘CAL_binsmid’ ‘Linf’ ‘Len_age’ ‘maxage’ ‘nareas’ ‘Asize’ ‘nCALbins’
  ‘qs’ ‘qvar’ ‘qinc’

Documented arguments not in \usage in Rd file 'popdynCPP.Rd':
  ‘SSBcurr’

Documented arguments not in \usage in Rd file 'popdynOneMICE.Rd':
  ‘nyears’

Documented arguments not in \usage in Rd file 'qestMICE.Rd':
  ‘mod’ ‘plusgroup.’ ‘WtC’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/sglOptim/include/rtools.h:29:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  /data/gannet/ripley/R/test-clang/sglOptim/include/rtools.h:33:16: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/msgl.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Found the following files/directories:
  ‘test.txt’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R   5.9Mb
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘datasets’ ‘grDevices’ ‘graphics’ ‘iterators’ ‘methods’
  All declared Imports should be used.
Argument items with no description in Rd file 'DAGOSTINO.Rd':
  ‘data’
Argument items with no description in Rd file 'HZ.test.Rd':
  ‘data’
Argument items with no description in Rd file 'MardiaTest.Rd':
  ‘data’
Argument items with no description in Rd file 'Royston.test.Rd':
  ‘data’
Argument items with no description in Rd file 'gen.var.Rd':
  ‘\dots’
Argument items with no description in Rd file 'larg.ellip.Rd':
  ‘n’ ‘box’ ‘add’ ‘xlim’ ‘ylim’ ‘zlim’ ‘xlab’ ‘ylab’ ‘zlab’ ‘col’
  ‘alpha’ ‘\dots’
Argument items with no description in Rd file 'prism.Rd':
  ‘add’
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ms_sev.Rd:31: Escaped LaTeX specials: \_
Invalid package aliases in Rd file 'ms_sev-package.Rd':
  ‘ms_sev-package’
Found the following significant warnings:
  PF.cpp:44:57: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  laplace.cpp:519:65: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  laplace.cpp:560:17: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  laplace.cpp:560:27: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  laplace.cpp:628:38: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  laplace.cpp:631:17: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  problem_data.cpp:60:27: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/mssm.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘utils’
  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:
  ‘markdown’ ‘methods’ ‘vctrs’
  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
S3 methods shown with full name in Rd file 'data.visualisation.Rd':
  ‘lda.plot.wrap.1’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘tidyr’ in Rd xrefs
checkRd: (-1) mkjnw.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) mkjnw.Rd:6: Escaped LaTeX specials: \&
Note: found 303 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
Note: found 2632 marked UTF-8 strings
'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
Specified C++11: please drop specification unless essential
Undeclared package ‘slam’ in Rd xrefs
Documented arguments not in \usage in Rd file 'plotBoxes.Rd':
  ‘lwd’ ‘T.base’ ‘font.family’ ‘fig’ ‘mar’

Documented arguments not in \usage in Rd file 'plotLetters.Rd':
  ‘width’ ‘lwd’ ‘label.groups’ ‘T.base’ ‘orientation’

Documented arguments not in \usage in Rd file 'plotTs.Rd':
  ‘font.family’ ‘fig’ ‘mar’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Specified C++11: please drop specification unless essential
File ‘MultiBD/libs/MultiBD.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
Namespace in Imports field not imported from: ‘plsgenomics’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'Trace.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'iteraite_fun_Iter.Rd':
  ‘The’

Documented arguments not in \usage in Rd file 'prepare_data.Rd':
  ‘The’

Documented arguments not in \usage in Rd file 'project.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'select_initial_Iter.Rd':
  ‘X’ ‘parametrs’

Documented arguments not in \usage in Rd file 'similarity_function.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'similarity_noncum.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘cmdstanr’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
Undeclared packages ‘shiny’, ‘shinystan’, ‘gtable’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 15 marked UTF-8 strings
Specified C++14: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  10.2Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rrelaxiv’
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘fields’ ‘optmatch’ ‘rcbalance’ ‘utils’
  All declared Imports should be used.
checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    help   2.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘poweRlaw’ ‘rmutil’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Specified C++11: please drop specification unless essential
Note: found 6 marked UTF-8 strings
Undeclared package ‘lfe’ in Rd xrefs
Specified C++11: please drop specification unless essential
Undeclared packages ‘AICcmodavg’, ‘bbmle’, ‘glmulti’, ‘arm’, ‘performance’, ‘wgeesel’, ‘ape’, ‘bestglm’, ‘leaps’, ‘glmmTMB’, ‘brglm’, ‘quantreg’, ‘maxlike’, ‘RMark’ in Rd xrefs
Documented arguments not in \usage in Rd file 'check_mnsl.Rd':
  ‘fix’

Documented arguments not in \usage in Rd file 'text_colour.Rd':
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
Undeclared package ‘dosresmeta’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘grDevices’ ‘knitr’ ‘utils’
  All declared Imports should be used.
Undeclared package ‘VGAM’ in Rd xrefs
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
Undeclared package ‘mev’ in Rd xrefs
Undeclared package ‘sampleSelection’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
Packages suggested but not available for checking: 'BioNet', 'DLBCL'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘glue’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rTubeDB’
Package unavailable to check Rd xrefs: ‘rTubeDB’
Note: found 4 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
Note: found 50 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Kendall’ ‘perm’
  All declared Imports should be used.
Note: found 63 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘mlr3learners’ ‘rpart’
  All declared Imports should be used.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
Argument items with no description in Rd file 'check_subject_pattern.Rd':
  ‘subject.vec’ ‘pattern’
Argument items with no description in Rd file 'names_or_error.Rd':
  ‘pattern’
Argument items with no description in Rd file 'only_captures.Rd':
  ‘match.mat’ ‘pattern’
Argument items with no description in Rd file 'stop_for_names.Rd':
  ‘pattern’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs     2.0Mb
    models   1.1Mb
Note: found 47936 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spatialClust’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Crashpad’
Package suggested but not available for checking: ‘gurobi’
Packages suggested but not available for checking:
  'rgeos', 'rgdal', 'maptools'
Note: found 5 marked Latin-1 strings
  Note: found 7187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    1.7Mb
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    6.5Mb
GNU make is a SystemRequirements.
Undeclared package ‘CBPS’ in Rd xrefs
Note: found 140 marked UTF-8 strings
Invalid package aliases in Rd file 'NBBttest-package.Rd':
  ‘NBBtatest-package’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘rrpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘sSeq’
Package unavailable to check Rd xrefs: ‘sSeq’
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Namespace in Imports field not imported from: ‘magick’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Undeclared package ‘reader’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'Moth.Rd':
  ‘delta.ident’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
Undeclared package ‘DescTools’ in Rd xrefs
Note: found 7332 marked UTF-8 strings
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
'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.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Note: found 21 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘RSiena’
':::' call which should be '::': ‘lhs:::maximinLHS’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_ \_
checkRd: (-1) makeNetwork.Rd:31: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Package required but not available: ‘RSiena’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Undeclared package ‘crossnma’ in Rd xrefs
Note: found 2 marked UTF-8 strings
Found the following significant warnings:
  mmsbm_fit.cpp:162:55: warning: format specifies type 'double' but the argument has type 'arma::uword' (aka 'unsigned int') [-Wformat]
  mmsbm_fit.cpp:162:63: warning: data argument not used by format string [-Wformat-extra-args]
See ‘/data/gannet/ripley/R/packages/tests-clang/NetMix.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
File ‘NetPreProc/libs/NetPreProc.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) NetworkChange.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  wtedgetree.c:628:28: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/networkDynamic.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Argument items with no description in Rd file 'print.networkDynamic.Rd':
  ‘\dots’
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map.png’ ‘maze.html’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: found 2 marked Latin-1 strings
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
'LazyData' is specified without a 'data' directory
File ‘neuroim/libs/neuroim.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.
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
Note: found 318 marked UTF-8 strings
Note: found 4894 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘quickcode’ ‘utils’
  All declared Imports should be used.
Undeclared packages ‘compositions’, ‘robCompositions’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘curl’ ‘mathjaxr’
  All declared Imports should be used.
Undeclared package ‘yaml’ in Rd xrefs
Namespace in Imports field not imported from: ‘nflfastR’
  All declared Imports should be used.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  asweka.c:117:8: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/ngram.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'NH-MSAR-package.Rd':
  ‘NH-MSAR-package’
Argument items with no description in Rd file 'ENu_graph.Rd':
  ‘N.s.data’
Argument items with no description in Rd file 'Estep.MSAR.VM.Rd':
  ‘verbose’
Auto-generated content requiring editing in Rd file 'NH-MSAR-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Argument items with no description in Rd file 'init.theta.MSAR.Rd':
  ‘\dots’
Argument items with no description in Rd file 'init.theta.MSAR.VM.Rd':
  ‘\dots’
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NHSRdatasets’ ‘grid’ ‘utils’
  All declared Imports should be used.
Found the following significant warnings:
  get_my_priority.c:44:17: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  get_my_priority.c:51:17: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/nice.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
File ‘nice/libs/nice.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: ‘rJava’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Found the following significant warnings:
  eigenUsingClasses.cpp:33:5: warning: format specifies type 'char *' but the argument has type 'SEXP' (aka 'SEXPREC *') [-Wformat]
  eigenUsingClasses.cpp:42:7: warning: format specifies type 'char *' but the argument has type 'SEXP' (aka 'SEXPREC *') [-Wformat]
  eigenUsingClasses.cpp:55:5: warning: format specifies type 'char *' but the argument has type 'SEXP' (aka 'SEXPREC *') [-Wformat]
  eigenUsingClasses.cpp:64:7: warning: format specifies type 'char *' but the argument has type 'SEXP' (aka 'SEXPREC *') [-Wformat]
  ../include/nimble/RcppNimbleUtils.h:242:11: warning: format specifies type 'char *' but the argument has type 'SEXP' (aka 'SEXPREC *') [-Wformat]
  ../include/nimble/RcppNimbleUtils.h:246:17: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  ../include/nimble/RcppNimbleUtils.h:255:7: warning: format specifies type 'char *' but the argument has type 'SEXP' (aka 'SEXPREC *') [-Wformat]
  Utils.cpp:65:36: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  ../inst/include/nimble/RcppNimbleUtils.h:242:11: warning: format specifies type 'char *' but the argument has type 'SEXP' (aka 'SEXPREC *') [-Wformat]
  ../inst/include/nimble/RcppNimbleUtils.h:246:17: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  ../inst/include/nimble/RcppNimbleUtils.h:255:7: warning: format specifies type 'char *' but the argument has type 'SEXP' (aka 'SEXPREC *') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/nimble.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    CppCode        2.7Mb
    R              7.5Mb
    classic-bugs   1.6Mb
    include       10.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘jpndistrict’
Undeclared packages ‘cshapes’, ‘mapdata’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
Note: found 170 marked UTF-8 strings
Objects in \usage without \alias in Rd file 'internalRK.Rd':
  ‘brkCalc’ ‘findPowerR’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  RcppExports.cpp:59:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  rprintf.c:44:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  rprintf.c:49:19: warning: data argument not used by format string [-Wformat-extra-args]
  rprintf.c:55:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/nlmixr2est.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'Rvmmin', 'Rcgmin'
Specified C++11: please drop specification unless essential
Undeclared package ‘tm’ in Rd xrefs
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   3.7Mb
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'nldoc_write_nldoc.Rd':
  ‘number_ections’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
Package suggested but not available for checking: ‘mail’
Documented arguments not in \usage in Rd file 'ccSpec.Rd':
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  logistf.c:118:79: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/nncc.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
Invalid package aliases in Rd file 'logistf-package.Rd':
  ‘logistf-package’ ‘{logistf}-package’
Undeclared package ‘sfheaders’ in Rd xrefs
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’ ‘forcats’
  ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘digest’ ‘hash’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'noise-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get_max_stat.Rd':
  ‘statfunc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘noncompliance/libs/noncompliance.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:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'StatQQVPC.Rd':
  ‘mapping’ ‘data’ ‘geom’ ‘position’ ‘na.rm’ ‘show.legend’
  ‘inherit.aes’ ‘...’

Documented arguments not in \usage in Rd file 'StatQQnorm.Rd':
  ‘mapping’ ‘data’ ‘geom’ ‘position’ ‘na.rm’ ‘show.legend’
  ‘inherit.aes’ ‘...’

Documented arguments not in \usage in Rd file 'StatQQrefline.Rd':
  ‘mapping’ ‘data’ ‘geom’ ‘position’ ‘na.rm’ ‘show.legend’
  ‘inherit.aes’ ‘...’

Documented arguments not in \usage in Rd file 'covload.sub.table.Rd':
  ‘nrows’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  ./parseSyntaxErrors.h:391:30: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  abbrev.c:1048:39: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
  abbrev.c:1052:39: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
See ‘/data/gannet/ripley/R/packages/tests-clang/nonmem2rx.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   3.4Mb
    mods   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘e1071’ ‘glmnet’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'nose-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Documented arguments not in \usage in Rd file 'FunctionSanityChecks.Rd':
  ‘structure’

Documented arguments not in \usage in Rd file 'newLine.Rd':
  ‘current.in’

Documented arguments not in \usage in Rd file 'nosoiSimConstructor.Rd':
  ‘pres.time’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'read.Rd':
  ‘dots’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
checkRd: (-1) prepareplot.Rd:64: Escaped LaTeX specials: \#
checkRd: (-1) prepareplot.Rd:68: Escaped LaTeX specials: \#
Undeclared package ‘tidyselect’ in Rd xrefs
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
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.
Documented arguments not in \usage in Rd file 'Create_P.Rd':
  ‘y_zx_dependent’

Documented arguments not in \usage in Rd file 'make_proposer.Rd':
  ‘N’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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:
    data   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’ ‘base’ ‘graphics’ ‘parallel’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘forecast’ ‘rlang’ ‘tsibble’ ‘viridis’
  All declared Imports should be used.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘optparse’ ‘vcfR’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'exp_hclust.Rd':
  ‘df_allele’

Documented arguments not in \usage in Rd file 'log_mem.Rd':
  ‘msg’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘pedtools’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  nro_train.cpp:79:34: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
See ‘/data/gannet/ripley/R/packages/tests-clang/Numero.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
Note: found 6409 marked UTF-8 strings
Note: found 7284 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared packages ‘ensurer’, ‘validate’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 7 marked UTF-8 strings
Note: found 6986 marked UTF-8 strings
Note: found 1242 marked UTF-8 strings
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    doc       5.7Mb
    extdata   1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   1.0Mb
    doc    1.7Mb
    help   3.2Mb
Argument items with no description in Rd file 'plot.comphat.Rd':
  ‘\dots’
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Found the following significant warnings:
  nanodbc/nanodbc.cpp:301:32: warning: 'codecvt_utf8_utf16<char16_t>' is deprecated [-Wdeprecated-declarations]
  nanodbc/nanodbc.cpp:301:16: warning: 'wstring_convert<std::codecvt_utf8_utf16<char16_t>, char16_t>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/odbc.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Rd files without \alias:
  ‘odbc-package.Rd’
Note: found 4 marked UTF-8 strings
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’ ‘ggthemes’ ‘mlbench’ ‘rmarkdown’ ‘tidymodels’
  All declared Imports should be used.
Undeclared package ‘gam’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
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: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘sp’ in Rd xrefs
Note: found 12 marked UTF-8 strings
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘olctools/libs/olctools.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
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Note: found 842 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘crayon’ ‘testthat’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘gdata’ ‘genefilter’ ‘maftools’ ‘readxl’
  All declared Imports should be used.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgdal’
Undeclared package ‘lubridate’ in Rd xrefs
Note: found 32 marked UTF-8 strings
Note: found 34 marked UTF-8 strings
Rd files without \alias:
  ‘ontologyPlot-package.Rd’
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  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
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘glue’ ‘httpcode’ ‘httr’ ‘jsonlite’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
License stub is invalid DCF.
GNU make is a SystemRequirements.
Note: found 4 marked UTF-8 strings
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'unary_ops.Rd':
  ‘log10.ProcessNode’ ‘log10.ProcessGraphParameter’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
Note: found 2524 marked UTF-8 strings
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'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:
    R        2.6Mb
    data     1.4Mb
    libs     5.7Mb
    models   4.8Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
possible bashism in configure line 52 (test -a/-o):
  if test ${java_version_maj} -ge 5 || \
      test ${java_version_maj} -eq 1 -a ${java_version_min} -ge 5;
Package suggested but not available for checking: ‘openNLPmodels.en’
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Documented arguments not in \usage in Rd file 'clique_color_pals.Rd':
  ‘aplha’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in Rd file 'bertinBase.Rd':
  ‘x’ ‘ratings’ ‘trim’

Documented arguments not in \usage in Rd file 'biplot3dBase2.Rd':
  ‘ext.sphere’

Documented arguments not in \usage in Rd file 'convertImportObjectToRepGridObject.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'convertScivescoImportObjectToRepGridObject.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'mapCoordinatesToColor.Rd':
  ‘color’

Documented arguments not in \usage in Rd file 'quasiDistributionDistanceSlater.Rd':
  ‘rep’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking: 'maptools', 'rgeos'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Note: found 10 marked UTF-8 strings
Note: found 167 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
File ‘OptHedging/libs/OptHedging.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.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Undeclared package ‘tibble’ in Rd xrefs
Package suggested but not available for checking: ‘rrelaxiv’
Namespaces in Imports field not imported from:
  ‘boot’ ‘splines’
  All declared Imports should be used.
Undeclared package ‘vegan’ in Rd xrefs
File ‘optpart/libs/optpart.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.
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
Package suggested but not available for checking: ‘gurobi’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'dsevdist.Rd':
  ‘x’ ‘sevdist’
Found the following significant warnings:
  count.cpp:397:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  count.cpp:556:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  count.cpp:956:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  count.cpp:1451:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/orca.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Specified C++11: please drop specification unless essential
File ‘orca/libs/orca.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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Note: found 36 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Undeclared package ‘VGAM’ in Rd xrefs
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Undeclared package ‘pillar’ in Rd xrefs
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘scales’ ‘tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘microplot’ in Rd xrefs
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
Documented arguments not in \usage in Rd file 'distsuml2.Rd':
  ‘partial’

Documented arguments not in \usage in Rd file 'distsumlp.Rd':
  ‘partial’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
Documented arguments not in \usage in Rd file 'dosepred.Rd':
  ‘w’

Documented arguments not in \usage in Rd file 'surv_dm_solver.Rd':
  ‘bw_optim’

Documented arguments not in \usage in Rd file 'surv_forward_solver.Rd':
  ‘Phit’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tibble’
  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
'LazyData' is specified without a 'data' directory
Undeclared package ‘knitr’ in Rd xrefs
Note: found 5889 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    help   1.1Mb
Note: found 34 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rcplex’
Namespaces in Imports field not imported from:
  ‘R6’ ‘openssl’
  All declared Imports should be used.
Rd files without \alias:
  ‘otp-package.Rd’
'LazyData' is specified without a 'data' directory
Undeclared package ‘survey’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘astsa’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'packagetracker.Rd':
  ‘packagetracker-package’
'LazyData' is specified without a 'data' directory
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘flexsurv’ ‘nlme’ ‘tibble’ ‘tidyverse’ ‘tm’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'prediction_regression.Rd':
  ‘dataset’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
'LazyData' is specified without a 'data' directory
Undeclared package ‘devtools’ in Rd xrefs
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘e1071’
  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
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  progress.c:98:37: warning: data argument not used by format string [-Wformat-extra-args]
  handle.c:115:20: warning: field precision should have type 'int', but argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  utils.c:42:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  utils.c:78:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  utils.c:87:29: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  parse.c:38:32: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  push_parser.c:71:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  hbio.c:1629:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  create-time.c:147:61: warning: data argument not used by format string [-Wformat-extra-args]
See ‘/data/gannet/ripley/R/packages/tests-clang/pak.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 17.0.5’
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    library   7.9Mb
Note: found 314 marked UTF-8 strings
Package which this enhances but not available for checking: ‘CorShrink’
Documented arguments not in \usage in Rd file 'other.Rd':
  ‘trial’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'dplyr_verbs.Rd':
  ‘funs’ ‘.dots’ ‘keep_attributes’

Documented arguments not in \usage in Rd file 'nest_tdc.Rd':
  ‘vars’ ‘id’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'pamr.internal.Rd':
  ‘print.nsc’ ‘print.nsccv’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘pamr/libs/pamr.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: ‘smoothmest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Undeclared package ‘AER’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'getOption2.Rd':
  ‘envvar’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘BayesFM’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Undeclared packages ‘tidygraph’, ‘htmlwidgets’ in Rd xrefs
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rgdal’
Note: found 16 marked UTF-8 strings
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/ast2ast/include/etr_bits/util.hpp:32:16: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/paropt.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 17.0.5’
Documented arguments not in \usage in Rd file 'expect_missing_argument.Rd':
  ‘message’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++14: please drop specification unless essential
Undeclared packages ‘partykit’, ‘Cubist’, ‘rules’, ‘h2o’, ‘agua’, ‘baguette’, ‘ipred’, ‘dbarts’, ‘lightgbm’, ‘bonsai’, ‘mboost’, ‘mda’, ‘sda’, ‘sparsediscrim’, ‘klaR’, ‘workflows’, ‘brulee’, ‘glmnet’, ‘rstan’, ‘rstanarm’, ‘naivebayes’, ‘plsmod’, ‘pscl’, ‘aorsf’, ‘randomForest’, ‘xrf’, ‘flexsurv’, ‘broom’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.5Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'as_partition.Rd':
  ‘.partition_step’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Found the following files/directories:
  ‘co2’ ‘co2.1’ ‘co2.2’ ‘co2s.1’ ‘co2s.2’ ‘ctm.1’ ‘ctm.2’ ‘m’ ‘m.1’
  ‘m.2’ ‘test’ ‘test.1’ ‘test.2’ ‘testa.1’ ‘testa.2’ ‘xfile.1’
  ‘xfile.2’
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Documented arguments not in \usage in Rd file 'fixvar_of_red_mod.Rd':
  ‘data’

Documented arguments not in \usage in Rd file 'get_ndf.Rd':
  ‘data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'vec_cast.partial_time.Rd':
  ‘vec_cast.partial_time’

S3 methods shown with full name in Rd file 'vec_cast.timespan.Rd':
  ‘vec_cast.timespan’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \# \# \#
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \#
Namespace in Imports field not imported from: ‘logger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
    data   1.5Mb
Undeclared package ‘pathfindR’ in Rd xrefs
Note: found 180 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘testthat’ ‘usethis’ ‘utils’
  All declared Imports should be used.