Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.npregbw.Rd: npregbw, npreg
  dens_test.Rd: DCdensity
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dfp_auth.Rd: Token-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
possible bashism in configure.ac line 17 (should be 'b = a'):
  if test "${ENDIAN}" == "little"; then
checkRd: (-1) linear_RNDPROJ.Rd:45: Lost braces; missing escapes or markup?
    45 | there is a linear map \eqn{f:R^N} to {R^n} such that
       |                                      ^
checkRd: (-1) halfnorm.like.Rd:105: Lost braces; missing escapes or markup?
   105 |   {f(x|a,b,c_1,c_2,...,c_k) = f(x|a,b)(1 + c(1) h_i1(x) + c(2) h_i2(x) + ... + c(k) h_ik(x)). }
       |   ^
checkRd: (-1) secondDeriv.Rd:15: Lost braces
    15 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
checkRd: (-1) farthest_point_sampling.Rd:28: Lost braces; missing escapes or markup?
    28 | space P = {p_1, ..., p_k}, such that each p_i is the farthest 
       |           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RDML.Rd: R6Class
  adpsType.Rd: R6Class
  annotationType.Rd: R6Class
  baseTemperatureType.Rd: R6Class
  cdnaSynthesisMethodType.Rd: R6Class
  commercialAssayType.Rd: R6Class
  cqDetectionMethodType.Rd: R6Class
  dataCollectionSoftwareType.Rd: R6Class
  dataType.Rd: R6Class
  documentationType.Rd: R6Class
  dyeType.Rd: R6Class
  enumType.Rd: R6Class
  experimentType.Rd: R6Class
  experimenterType.Rd: R6Class
  gradientType.Rd: R6Class
  idReferencesType.Rd: R6Class
  idType.Rd: R6Class
  labelFormatType.Rd: R6Class
  lidOpenType.Rd: R6Class
  loopType.Rd: R6Class
  mdpsType.Rd: R6Class
  measureType.Rd: R6Class
  nucleotideType.Rd: R6Class
  oligoType.Rd: R6Class
  pauseType.Rd: R6Class
  pcrFormatType.Rd: R6Class
  primingMethodType.Rd: R6Class
  quantityType.Rd: R6Class
  quantityUnitType.Rd: R6Class
  rdmlBaseType.Rd: R6Class
  rdmlIdType.Rd: R6Class
  reactIdType.Rd: R6Class
  reactType.Rd: R6Class
  runType.Rd: R6Class
  sampleType.Rd: R6Class
  sampleTypeType.Rd: R6Class
  sequencesType.Rd: R6Class
  stepType.Rd: R6Class
  targetType.Rd: R6Class
  targetTypeType.Rd: R6Class
  temperatureType.Rd: R6Class
  templateQuantityType.Rd: R6Class
  thermalCyclingConditionsType.Rd: R6Class
  xRefType.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) computeCBMeasure.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:56: Lost braces in \itemize; meant \describe ?
possible bashism in configure.ac line 19 (test -a/-o):
  if test [-n "$PKG_CFLAGS" -a -n "$PKG_CPPFLAGS" -a -n "$PKG_LIBS"] ; then
  possible bashism in configure.ac line 22 (test -a/-o):
      if test [-n "$PKG_CFLAGS" -o -n "$PKG_CPPFLAGS" -o -n "$PKG_LIBS"] ; then
  possible bashism in configure.ac line 38 (test -a/-o):
  if test [-z "$FOUND_ALL" -a -n "$DSDP_DIR"] ; then
  possible bashism in configure.ac line 87 (should be 'b = a'):
      if test "${ac_cv_header_declarations_h}" == no; then
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘helpers-process-tracing.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dataDWD.Rd: newFilename
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ReacTran.Rd: ode.1D, ode.2D, ode.3D, steady.1D, steady.2D, steady.3D
  advection.Rd: euler, ode.1D
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘download_data_cube.r’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘download_apra.R’ ‘read_adipops.R’ ‘universal_helpers.R’
checkRd: (-1) reader-package.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:55: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
checkRd: (-1) get.skip.Rd:15: Lost braces
    15 | line in the file to determine the {code{skip}} value.}
       |                                   ^
checkRd: (-1) get.skip.Rd:15: Lost braces
    15 | line in the file to determine the {code{skip}} value.}
       |                                        ^
checkRd: (-1) readMzXmlDir.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlDir.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlDir.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlFile.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlFile.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlFile.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘tidy_rba.R’
checkRd: (-1) ReAD.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{pi}{An estimate of the stationary probabilities of four states {(0,0), (0,1), (1,0), (1,1)}.}
       |                                                                      ^
checkRd: (-1) em_hmm.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{pi}{An estimate of the stationary probabilities of four states {(0,0), (0,1), (1,0), (1,1)}.}
       |                                                                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  melt_delim.Rd: tibble
  read_delim.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘readr/libs/readr.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  readtext.Rd: fread
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cell-specification.Rd: cellranger
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running ‘testthat.R’ [82s/107s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rearrr)
  > 
  > if (require("xpectr")) {
  +   test_check("rearrr")
  + }
  Loading required package: xpectr
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 7341 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_n_fn.R:842:3'): testing quantile_index() ─────────────────────
  xpectr::strip(side_effects_19148[["error"]]) does not match "probs outside 01".
  Actual value: "ℹ In index 1Caused by error in quantiledefault type must be an integer in 19"
  Backtrace:
      ▆
   1. └─testthat::expect_match(...) at test_n_fn.R:842:3
   2.   └─testthat:::expect_match_(...)
  ── Failure ('test_n_fn.R:859:3'): testing quantile_index() ─────────────────────
  xpectr::strip(side_effects_19148[["error"]]) does not match "object a not found".
  Actual value: "ℹ In index 1Caused by error in quantiledefault type must be an integer in 19"
  Backtrace:
      ▆
   1. └─testthat::expect_match(...) at test_n_fn.R:859:3
   2.   └─testthat:::expect_match_(...)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 7341 ]
  Error: Test failures
  Execution halted
checkRd: (-1) Automotive.Rd:29: Lost braces
    29 | Wikipedia (2018): \dQuote{Automobilindustrie --- Wikipedia{,} Die freie Enzyklopaedie}. \url{https://de.wikipedia.org/wiki/Automobilindustrie} (accessed October 14, 2018). Own postprocessing.
       |                                                           ^
checkRd: (-1) Automotive.Rd:33: Lost braces
    33 | Wikipedia (2018): \dQuote{Automobilindustrie --- Wikipedia{,} Die freie Enzyklopaedie}. \url{https://de.wikipedia.org/wiki/Automobilindustrie} (accessed October 14, 2018). 
       |                                                           ^
'library' or 'require' call not declared from: ‘deconvolveR’
'library' or 'require' calls not declared from:
  ‘FNN’ ‘MASS’ ‘e1071’ ‘flexmix’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DateTime.Rd: ClassGroups
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  number_range.Rd: or
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘gg_CD_local.R’ ‘gg_PIT_local.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  add_from_x.Rd: data.table
  comparators.Rd: stringdist
  compare_pairs.Rd: data.table
  compare_vars.Rd: data.table
  get_inspect_pairs.Rd: data.table
  pair.Rd: data.table
  pair_blocking.Rd: data.table
  pair_minsim.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.recmap.SpatialPolygonsDataFrame.Rd: SpatialPolygonsDataFrame
  dot-get_7triangles.Rd: SpatialPolygons
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  parameters.Rd: crop
  spatial.Rd: writeRaster
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) recombinator.Rd:32-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) recombinator.Rd:35-38: Lost braces in \enumerate; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RecLinkData.object.rd: bincombinations
  trainSupv.Rd: rpart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) pseudo.geefit.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.geefit.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simEvent.Rd:112: Lost braces; missing escapes or markup?
   112 | and another argument named {zCoef} for covariate coefficient vector.
       |                            ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘helpers-testing.R’ ‘validate.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘write.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘redSolve.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fLoadAmeriflux22.Rd: read_csv
  fLoadFluxnet15.Rd: cols, read_csv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pullback.Rd: summarize
  redist.compactness.Rd: prep_perims
  redist_map.Rd: tibble
  redist_plans.Rd: dplyr
  scorers.Rd: prep_perims
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘redland/libs/redland.so’:
  Found non-API call to R: ‘SET_S4_OBJECT’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  storr_redis_api.Rd: storr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AutoCorrelationLRtest.Rd: corClasses
  REEMtree.Rd: corClasses, rpart, nlme
  REEMtree.object.Rd: rpart, nlme
  plot.Rd: plot.rpart
  predict.Rd: predict.nlme, predict.rpart
  print.Rd: print.rpart
  tree.Rd: rpart.object
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) make_refreshable.Rd:13: Lost braces
    13 | not that quotes need to be escaped (code{\"}).}
       |                                         ^
Running examples in ‘refseqR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: refseq_AAmol_wt
> ### Title: Extract the molecular weight from a protein accession
> ### Aliases: refseq_AAmol_wt
> 
> ### ** Examples
> 
>  # Get the molecular weight from a single protein accession
>  protein <- "XP_020244413"
>  refseq_AAmol_wt(protein)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [eutils.ncbi.nlm.nih.gov]: Resolving timed out after 10000 milliseconds
Calls: refseq_AAmol_wt ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
refseq_AAlen 0.24  0.043  20.455
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_shiny.Rd: fpca.sc, fpca.face, fpca.ssvd, fpca2s, bayes_fosr,
    mfpca.sc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  associate.Rd: vglm
  build_model.Rd: bestglm, regsubsets
  build_tree.Rd: rpart
  generalization_error.Rd: rpart, randomForest
  getcp.Rd: rpart
  see_models.Rd: regsubsets
  summarize_tree.Rd: rpart, randomForest
  visualize_model.Rd: rpart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘EnvironmentalA.txt’ ‘EnvironmentalB.txt’ ‘Example.txt’
  ‘Example_Predictions.txt’ ‘Example_RRDist.txt’
  ‘Example_RRDistCol.TIF’ ‘Example_RRDistGrey.TIF’ ‘GeneticA.txt’
  ‘GeneticB.txt’ ‘Inds.txt’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘regioncode.R’
checkRd: (-1) impute_down_nuts.Rd:21: Lost braces
    21 | NUTS typologies, defaults to code{"geo_var".}}
       |                                  ^
checkRd: (-1) validate_data_frame.Rd:19: Lost braces
    19 | NUTS typologies, defaults to code{"geo_var".}}
       |                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gfpca_twoStep.Rd: gamm4
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  reglogit.Rd: Matrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mvregmed.graph.attributes.Rd: graph_from_edgelist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) fbase1.binomial.Rd:32: Lost braces; missing escapes or markup?
    32 | In all base log-likelihood functions, we have dropped any additive terms that are independent of the distribution parameter, e.g. constant terms or those terms that are dependent on the response variable only. This is done for computational efficiency. Therefore, these functions cannot be used to obtain the absolute values of log-likelihood functions but only in the context of optimization and/or sampling. Users can write thin wrappers around these functions to add the constant terms to the function value. (Derivatives do not need correction. For binomial family, all factorial terms are ignored since they only depend on \code{n} and {y}.)
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
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}}.
       |                                ^
File ‘rehh/libs/rehh.so’:
  Found non-API call to R: ‘SETLENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) polarizacion_Dalton.Rd:26: Lost braces; missing escapes or markup?
    26 | {Pd = sqrt(sum(p_j*(x_j-mean(x_p))/4.5)^2)}
       | ^
checkRd: (-1) reparto_div.Rd:37: Lost braces; missing escapes or markup?
    37 | The set of divisors is formed by the odd numbers, that is {1,3,..,2n+1}.
       |                                                           ^
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.
       |                                                                                                                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  anomalize.Rd: calc, writeRaster
  covWeight.Rd: getValues
  deseason.Rd: writeRaster
  predict.Rd: calc
  remote-package.Rd: raster-package
  writeEot.Rd: writeRaster
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running examples in ‘rempsyc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cormatrix_excel
> ### Title: Easy export of correlation matrix to Excel
> ### Aliases: cormatrix_excel
> ### Keywords: Excel correlation matrix
> 
> ### ** Examples
> 
> ## Don't show: 
> if (requireNamespace("correlation", quietly = TRUE) && requireNamespace("openxlsx2", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ ## Don't show: 
+ .old_wd <- setwd(tempdir())
+ ## End(Don't show)
+ # Basic example
+ cormatrix_excel(mtcars, select = c("mpg", "cyl", "disp", "hp", "carb"), filename = "cormatrix1")
+ cormatrix_excel(iris, p_adjust = "none", filename = "cormatrix2")
+ cormatrix_excel(airquality, method = "spearman", filename = "cormatrix3")
+ ## Don't show: 
+ setwd(.old_wd)
+ ## End(Don't show)
+ ## Don't show: 
+ }) # examplesIf
> .old_wd <- setwd(tempdir())
> cormatrix_excel(mtcars, select = c("mpg", "cyl", "disp", "hp", "carb"), 
+     filename = "cormatrix1")
# Correlation Matrix (pearson-method)

Parameter |      mpg |      cyl |     disp |       hp |    carb
---------------------------------------------------------------
mpg       |          | -0.85*** | -0.85*** | -0.78*** | -0.55**
cyl       | -0.85*** |          |  0.90*** |  0.83*** |  0.53**
disp      | -0.85*** |  0.90*** |          |  0.79*** |   0.39*
hp        | -0.78*** |  0.83*** |  0.79*** |          | 0.75***
carb      |  -0.55** |   0.53** |    0.39* |  0.75*** |        

p-value adjustment method: none
Error: x must be class wbColour
Execution halted
Running ‘testthat.R’ [19s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rempsyc)
  Suggested APA citation: Thériault, R. (2023). rempsyc: Convenience functions for psychology. 
  Journal of Open Source Software, 8(87), 5466. https://doi.org/10.21105/joss.05466
  > 
  > test_check("rempsyc")
  [ FAIL 1 | WARN 0 | SKIP 19 | PASS 46 ]
  
  ══ Skipped tests (19) ══════════════════════════════════════════════════════════
  • On CRAN (19): 'test-best_duplicate.R:8:3', 'test-extract_duplicates.R:8:3',
    'test-find_mad.R:2:3', 'test-format_value.R:2:3',
    'test-nice_assumptions.R:9:3', 'test-nice_contrasts.R:7:3',
    'test-nice_lm.R:5:3', 'test-nice_lm_contrasts.R:12:3',
    'test-nice_lm_slopes.R:5:3', 'test-nice_mod.R:4:3', 'test-nice_na.R:2:3',
    'test-nice_randomize.R:5:3', 'test-nice_reverse.R:3:3',
    'test-nice_slopes.R:4:3', 'test-nice_t_test.R:5:3', 'test-nice_table.R:13:3',
    'test-nice_var.R:2:3', 'test-scale_mad.R:2:3', 'test-winsorize_mad.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cormatrix_excel.R:5:3'): cormatrix_excel ───────────────────────
  Error: x must be class wbColour
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-cormatrix_excel.R:5:3
   2.   └─rlang::cnd_signal(state$error)
  
  [ FAIL 1 | WARN 0 | SKIP 19 | PASS 46 ]
  Error: Test failures
  Execution halted
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NBlevy.Rd: glm.nb
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) rentrez.Rd:17-21: Lost braces
    17 | /enumerated{
       |            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  entrez_link.Rd: xmlTreeParse
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.
       |                                          ^
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
checkRd: (-1) method.A.Rd:231-236: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.A.Rd:237-242: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:201-206: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:207-212: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:232-237: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:238-243: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  source_XlsxData.Rd: httr
  source_data.Rd: fread, httr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘PackageCites.bib’
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  reportr.Rd: es
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addLineBreak.Rd: xtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate_impact.R’ ‘plot_repsd.R’ ‘repsd_pval.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘Require2.R’ ‘helpers.R’ ‘pak.R’ ‘pkgDep3.R’
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}
       |      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mbl_control.Rd: foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) cast.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) cast.Rd:46: Escaped LaTeX specials: \_
File ‘reshape2/libs/reshape2.so’:
  Found non-API call to R: ‘STRING_PTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) as-data-frame-cast-df-v7.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-matrix-59.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-df-bu.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-matrix-2y.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) cast-9g.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:46: Escaped LaTeX specials: \_ \_
checkRd: (-1) clean-vars-rc.rd:13: Escaped LaTeX specials: \_
checkRd: (-1) expand-kx.rd:15: Escaped LaTeX specials: \_
checkRd: (-1) reshape-4u.rd:17: Escaped LaTeX specials: \_ \_
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘to_df.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  resi.Rd: boot, vcovHC
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) resistance.Rd:52: Lost braces
    52 |     \item B. Bollob\'{a}s, 1998.  \emph{Modern Graph Theory}.  Springer.
       |                      ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘specta_data_processing.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  format_time.Rd: lubridate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘resp_distributions.R’ ‘util.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  invert_vector.Rd: SpatExtent
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bind.R’ ‘result.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  etel.Rd: nloptr
  retel.Rd: nloptr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) harmonize_values.Rd:44: Lost braces; missing escapes or markup?
    44 | \item{perl}{Use perl-like regex? Defaults to {FALSE}.}
       |                                              ^
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.
       |          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  content.Rd: XMLInternalDocument-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.}
       |               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  revealjs_presentation.Rd: includes, render
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
Packages required but not available:
  'BSgenome', 'BSgenome.Hsapiens.UCSC.hg38'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
       |                                                                         ^
'::' or ':::' import not declared from: ‘Matrix’
'library' or 'require' call not declared from: ‘Matrix’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bic.regs.Rd: logistic_only, poisson_only
  circ.cor1.Rd: spml.reg
  cor_test.Rd: allbetas, univglms
  el.cor.test.Rd: permcor
  fedhc.skel.Rd: data.frame.to_matrix
  fp.Rd: logistic_only, poisson_only
  is.skew.symmetric.Rd: cholesky, cora, cova
  mmhc.skel.Rd: data.frame.to_matrix
  pc.sel.Rd: pc.skel, omp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) fs_search.Rd:76: Lost braces
    76 | \\code{\link{fs_auth}} \code{\link{fs_browse}}
       |       ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘common_names.R’ ‘distribution.R’ ‘fb_tbl.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fish_draw.Rd: aes, geom_path
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' calls not declared from:
  ‘rpanel’ ‘tkrplot’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotProximity.Rd: ggplot
  rfPermute.Rd: randomForest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.funts.Rd: fd, fts, create.bspline.basis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ee_install_set_pyenv.Rd: py_install
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) GenDataPopulation.Rd:21: Lost braces
    21 | {data}{Population of data}
       |       ^
checkRd: (-1) GenDataSample.Rd:23: Lost braces
    23 | {data}{Sample of data}
       |       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CCGammaToBlockmatrix.Rd: blockmatrix
  omega.Rd: normalCopula, pcopula
  omega_inv.Rd: nearPD, normalCopula, pcopula
  omega_root.Rd: normalCopula, pcopula
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  generate.Rd: varest-class, varest2-class, inv_GPCA,
    GPCAvarest2-class, adddate, getVARmodel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘connection.R’ ‘level-set.R’ ‘lie-group.R’ ‘manifold.R’ ‘open-set.R’
    ‘spd-matrices.R’ ‘utils.R’
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")) {
       |                                                   ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_Rgff.Rmd’ using rmarkdown

Quitting from lines 344-349 [unnamed-chunk-23] (Using_Rgff.Rmd)
Error: processing vignette 'Using_Rgff.Rmd' failed with diagnostics:
Package "rtracklayer" is required to convert from GTF to GFF3. Please install it.
--- failed re-building ‘Using_Rgff.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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 ?
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:
       |                                                                                                                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ReadMapTile.Rd: readPNG
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  H2Connection-class.Rd: JDBC, JDBCDriver-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) rhandsontable-package.Rd:8: Lost braces
     8 | R interface for creating tables using Handsontable, url{https://handsontable.com/}
       |                                                        ^
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘RHRVEasy.R’ ‘easyStatsFunctions.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  conduct_ri.Rd: declare_ra, obtain_permutation_matrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ts_utils.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bvm.Rd: sdetorus
  bwc.Rd: sdetorus
  bwn.Rd: sdetorus
  ridge_fourier_fit.Rd: sphunif
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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: \&
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
Found the following assignments to the global environment:
File ‘rim/R/engine.R’:
  assign(varname, output.data, envir = knitr::knit_global())
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  inat_map.Rd: map
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘population_utils.R’
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.}
       |                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CSC.Rd: coxph
  FGR.Rd: Hist
  ate.Rd: as.data.table
  plot.riskRegression.Rd: SmartControl
  plotBrier.Rd: SmartControl
  plotCalibration.Rd: SmartControl
  plotEffects.Rd: SmartControl
  plotPredictRisk.Rd: SmartControl
  plotROC.Rd: SmartControl
  plotRisk.Rd: SmartControl
  selectCox.Rd: fastbw
  summary.ate.Rd: as.data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘15_SCORE2-Diabetes_func.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cv_risk_mod.Rd: foreach
  cv_risk_mod_random_start.Rd: foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fititcdata.Rd: nls.lm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.balancetest.Rd: ggplot, scale_color_manual
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘plotdensity.R’
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}}
       |                                                                                                                                                                                                                                                   ^
possible bashism in configure.ac line 24 (test -a/-o):
           if test [ -z "${JAGS_LIBS}" -a -z "${JAGS_CFLAGS}" ] ; then
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)
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-clang/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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  adiff.Rd: madness
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘flatten.R’ ‘patch.R’ ‘rquerypivot.R’
File ‘RJSONIO/libs/RJSONIO.so’:
  Found non-API call to R: ‘VECTOR_PTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘higher_order_metadata.R’
'::' or ':::' imports not declared from:
  ‘htmlwidgets’ ‘rmarkdown’ ‘shiny’ ‘vcd’
'library' or 'require' calls not declared from:
  ‘htmlwidgets’ ‘httpuv’ ‘httr2’ ‘kableExtra’ ‘knitr’ ‘purrrlyr’
  ‘raster’ ‘rmarkdown’ ‘tidyverse’ ‘vcd’
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: \$
File ‘rlang/libs/rlang.so’:
  Found non-API calls to R: ‘ENVFLAGS’, ‘FRAME’, ‘HASHTAB’, ‘LEVELS’,
    ‘NAMED’, ‘PRENV’, ‘PRVALUE’, ‘RDEBUG’, ‘R_PromiseExpr’,
    ‘Rf_findVarInFrame3’, ‘SETLENGTH’, ‘SET_BODY’, ‘SET_CLOENV’,
    ‘SET_ENCLOS’, ‘SET_ENVFLAGS’, ‘SET_FORMALS’, ‘SET_GROWABLE_BIT’,
    ‘SET_RDEBUG’, ‘SET_TRUELENGTH’, ‘SET_TYPEOF’, ‘STRING_PTR’,
    ‘XTRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  chartEvent.Rd: App
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' calls not declared from:
  ‘Mcomp’ ‘RODBC’ ‘dplyr’ ‘ggplot2’
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.
       |             ^
Running examples in ‘rllama-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_defillama_stablecoin_data
> ### Title: Stablecoins Data
> ### Aliases: get_defillama_stablecoin_data
> 
> ### ** Examples
> 
> stablecoin_data = get_defillama_stablecoin_data()
Error in circulating * price : non-numeric argument to binary operator
Calls: get_defillama_stablecoin_data -> [ -> [.data.table -> eval -> eval
Execution halted
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  app_RLum.Rd: runApp, plot_AbanicoPlot, plot_Histogram, plot_KDE,
    plot_RadialPlot, plot_DRTResults, calc_CosmicDoseRate, CW2pHMi,
    CW2pLM, CW2pLMi, CW2pPMi, plot_FilterCombinations, calc_FastRatio,
    analyse_FadingMeasurement, calc_FadingCorr, plot_RLum
  jscolorInput.Rd: animationOptions, sliderInput, checkboxGroupInput,
    checkboxInput, dateInput, dateRangeInput, fileInput, numericInput,
    passwordInput, radioButtons, selectInput, selectizeInput,
    submitButton, textInput
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LRParser.Rd: R6Class
  LexToken.Rd: R6Class
  Lexer.Rd: R6Class
  NullLogger.Rd: R6Class
  RlyLogger.Rd: R6Class
  YaccProduction.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ms_simplify.Rd:36: Lost braces
    36 | \url{https://github.com/mbloch/mapshaper/wiki/Simplification-Tips}{link}
       |                                                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_flame.Rd: layer
  geom_lolli.Rd: layer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.
       |               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NewVAReventRealization.Rd: VAR
  VAR_mod.Rd: VAR
  arch_test.Rd: arch.test
  findDate.Rd: date.mdy
  forecastEV.Rd: VAR
  forecastResidual.Rd: VAR
  generateTemperatureTimeseries.Rd: VAR
  getVARmodel.Rd: VAR, VARselect
  normality_test.Rd: normality.test
  removeNAs.Rd: VAR, VARselect
  serial_test.Rd: serial.test
  varest-class.Rd: VAR
  varest2-class.Rd: VAR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  weightedMscale.Rd: normal_consistency_constants
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘replace_doi.R’
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘model-table.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ci.Rd: lavaan
  mbco.Rd: mxOption
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DCCfilter-class.Rd: GARCHfilter-class, rGARCH-class
  DCCfit-class.Rd: GARCHfit-class, rGARCH-class
  DCCforecast-class.Rd: GARCHforecast-class, rGARCH-class
  DCCroll-class.Rd: GARCHroll-class, rGARCH-class
  DCCsim-class.Rd: GARCHsim-class, rGARCH-class
  DCCspec-class.Rd: GARCHspec-class, rGARCH-class
  cGARCHfilter-class.Rd: GARCHfilter-class, rGARCH-class
  cGARCHfit-class.Rd: GARCHfit-class, rGARCH-class
  cGARCHsim-class.Rd: GARCHsim-class, rGARCH-class
  cGARCHspec-class.Rd: GARCHspec-class, rGARCH-class
  cgarchfit-methods.Rd: uGARCHmultifit-class
  cgarchspec-methods.Rd: uGARCHmultispec-class, multispec
  dccfit-methods.Rd: uGARCHmultifit-class
  dccsim-methods.Rd: setfixed<-
  dccspec-methods.Rd: uGARCHmultispec-class, multispec
  goGARCHfilter-class.Rd: GARCHfilter-class, rGARCH-class
  goGARCHfit-class.Rd: GARCHfit-class, rGARCH-class
  goGARCHforecast-class.Rd: GARCHforecast-class, rGARCH-class
  goGARCHroll-class.Rd: GARCHroll-class, rGARCH-class
  goGARCHsim-class.Rd: GARCHsim-class, rGARCH-class
  goGARCHspec-class.Rd: GARCHspec-class, rGARCH-class
  mGARCHfilter-class.Rd: GARCHfilter-class, rGARCH-class
  mGARCHfit-class.Rd: GARCHfit-class, rGARCH-class
  mGARCHforecast-class.Rd: GARCHforecast-class, rGARCH-class
  mGARCHroll-class.Rd: GARCHroll-class, rGARCH-class
  mGARCHsim-class.Rd: GARCHsim-class, rGARCH-class
  mGARCHspec-class.Rd: GARCHspec-class, rGARCH-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RMixtComp-package.Rd: createAlgo, availableModels,
    RMixtCompUtilities-package, getBIC, getICL, getCompletedData,
    getParam, getProportion, getTik, getEmpiricTik, getPartition,
    getType, getModel, getVarNames, computeDiscrimPowerClass,
    computeDiscrimPowerVar, computeSimilarityClass,
    computeSimilarityVar, plot.MixtComp, heatmapClass,
    heatmapTikSorted, heatmapVar, histMisclassif, plotConvergence,
    plotDataBoxplot, plotDataCI, plotDiscrimClass, plotDiscrimVar,
    plotProportion, RMixtCompIO-package
  mixtCompLearn.Rd: createAlgo, availableModels, heatmapVar
  plot.MixtCompLearn.Rd: plotDataCI, plotDataBoxplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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)
       |                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  harmonized_dossier_summarize.Rd: valueType_list
  harmonized_dossier_visualize.Rd: valueType_list
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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’.
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}}
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MR.loops.Rd: biglm
  background.resp.rd: biglm
  rMR-package.Rd: biglm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rmw_partial_dependencies.Rd: partial
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) myTarGetClientList.Rd:33: Lost braces
    33 | {MyTarget API Documenation}{https://target.my.com/doc/api/detailed/#resource_agency_clients}
       |                            ^
Package required but not available: ‘ensembldb’

Package suggested but not available for checking: ‘recount3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gaston2neiGWAS.Rd: gaston, bed.matrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
File ‘RNetCDF/libs/RNetCDF.so’:
  Found non-API call to R: ‘Rf_findVarInFrame3’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) 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 ?
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  robreg3S.Rd: GSE
  simulation-tools.Rd: generate.randcorr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
possible bashism in configure.ac line 34 (test -a/-o):
           if test [ -z "${JAGS_LIBS}" -a -z "${JAGS_CFLAGS}" ] ; then
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  case_resampling.Rd: foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  robustbetareg.Rd: betareg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FaCov.Rd: CovControl-class, CovControlMcd-class, CovMcd, CovClassic
  myplotDD.Rd: CovClassic, getDistance
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  compare.Rd: xtable, print.xtable
  fitDatasets.Rd: lmer
  getME.Rd: merMod-class, fixef, glmer, glmerControl, ranef
  prepareMixedEffectDataset.Rd: lmer
  processFit.Rd: lmer
  rlmer.Rd: lmer
  rlmerMod-class.Rd: lmer, fixef.merMod, isGLMM, isLMM, isNLMM, isREML,
    predict.merMod, ranef.merMod, VarCorr.merMod, merMod
  robustlmm-package.Rd: lmer, lme4
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  surerob.Rd: lmrob
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) descriptiveTable.Rd:18: Lost braces
    18 | other object type that does not fail in code{model.frame(object)}.}
       |                                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  newDB.Rd: R6, DBI
  rocker-R6-class.Rd: R6, DBI
  rocker-S3-functions.Rd: R6, DBI
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  show_methods.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
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
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘flat_table.R’ ‘geoattribute.R’ ‘geolayer.R’ ‘refresh.R’
    ‘star_database.R’ ‘star_database_export.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  scrollama.Rd: html_document2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RollingLDA.Rd: LDA
  updateRollingLDA.Rd: LDA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rologit.Rd: coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) update_tidy_omic.Rd:16-17: Lost braces
    16 | in \code{updated_tidy_data} (names) and the table {features, samples,
       |                                                   ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘add_longwave.R’ ‘convert_to_efi_standard.R’ ‘daily_to_hourly.R’
    ‘get_climate_projections.R’ ‘get_ensemble_forecast.R’
    ‘get_forecast.R’ ‘get_historical_weather.R’ ‘get_seasonal_forecast.R’
    ‘parse_ensemble.R’ ‘read_url.R’ ‘six_hourly_to_hourly.R’
    ‘write_glm_format.R’
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}".}
       |                                                                                                                                                                                                                                                                                                                                                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fanova.Rd: leveneTest, lmer, Anova
  formatPvalue.Rd: noZero, formatCI
  formatR.Rd: noZero, formatCI
  ggBoxplot.Rd: ggplot, geom_boxplot
  ggqq.Rd: ggplot
  oneway.Rd: leveneTest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
       |                                                  ^
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  prp.Rd: rpart, rpart.object, text.rpart, plot.rpart
  rpart.plot.Rd: rpart, text.rpart, plot.rpart
  rpart.predict.Rd: predict.rpart
  rpart.rules.Rd: rpart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addLabels.Rd: text3d
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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) 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
       |                                                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  postgres-query.Rd: dbConnect, dbGetRowsAffected
  postgres-tables.Rd: dbAppendTable, dbWriteTable, dbQuoteIdentifier,
    SQL
  postgresHasDefault.Rd: dbConnect
  postgresIsTransacting.Rd: dbBegin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nb2.Rd: negative.binomial
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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)
       |                                                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  all_markets.Rd: tibble
  format_market_data.Rd: tibble
  historical_plot.Rd: xts
  markets_table.Rd: shiny, tibble
  parse_historical_csv.Rd: xts
  single_market.Rd: tibble
  tweet_markets.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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)}
       |                                                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_btg.Rd: igraph, igraph.plotting
  psel.Rd: group_by
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  to_data_frame.Rd: rbind.fill
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.}
       |                                                                                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rpt.Rd: lmer
  rptBinary.Rd: lmer
  rptGaussian.Rd: lmer
  rptPoisson.Rd: lmer
  rptProportion.Rd: lmer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
possible bashism in configure.ac line 70 (should be 'b = a'):
  if test x"${QUANTLIB}" == x"yes" ; then
  possible bashism in configure.ac line 95 (should be 'b = a'):
  elif test "`uname`" == "Darwin" ; then
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()}
       |                                                                                                            ^
File ‘rrapply/libs/rrapply.so’:
  Found non-API call to R: ‘Rf_isValidString’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
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.
       |                                                                              ^
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}.
       |                                                                                  ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘sort_tips.r’ ‘tips.r’ ‘validate_rankedPhylo.r’
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RRmixed.Rd: lme4, glmer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RSA.Rd: sem
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  account.Rd: authenticate
  queryAPI.Rd: VERB, content
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.
       |                                                                                                                                                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  author_df.Rd: add_headers, GET
  author_retrieval.Rd: add_headers, GET
  author_search.Rd: add_headers, GET
  author_search_by_affil.Rd: GET
  elsevier_authenticate.Rd: add_headers, GET
  generic_elsevier_api.Rd: add_headers, GET
  get_affiliation_info.Rd: add_headers, GET
  get_complete_author_info.Rd: add_headers, GET
  get_links.Rd: GET
  object_retrieval.Rd: GET, add_headers
  process_author_name.Rd: add_headers, GET
  scopus_search.Rd: add_headers, GET
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rmad.Rd: Matrix
  rsc.Rd: Matrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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",
       |                                 ^
'library' or 'require' call not declared from: ‘selectr’
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-clang/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_Outputfile’,
    ‘R_TempDir’, ‘R_Visible’, ‘R_curErrorBuf’, ‘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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  iwlsm.Rd: lqs
  plot.sienaTimeTest.Rd: xyplot
  sienaDependent.Rd: Matrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bilinearInterpolator.Rd: interp.surface.grid
  computeStatisticalQuantitiesTile.Rd: readJPEG
  getCloseMatch.Rd: nn2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘get_stac_data.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  selectobject.Rd: funSource
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' call not declared from: ‘plot3D’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rSpectral.Rd: igraph
  spectral_igraph_communities.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘geom-funs.R’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rstanarm.Rcheck/00install.out’ for details.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rstan_create_package.Rd: Rcpp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  stata.Rd: write.dta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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) 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}}.
       |                                                                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  terms_graph.Rd: tkplot, plot.igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
checkRd: (-1) tw_options.Rd:22: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  markdown_rtl.Rd: knitr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getRtopParams.Rd: gstat
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) grapes-.-times-grapes.Rd:6-9: Lost braces
     6 | "round.torch.Tensor" <- function(input) {
       |                                         ^
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})}
       |     ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ma_support.R’ ‘mb_support.R’ ‘mb_timeline.R’ ‘memory_alpha.R’
    ‘memory_beta.R’ ‘tiles.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  TRNG.Engine.Rd: Rcpp, Module-class
  rTRNG-package.Rd: dependsAttribute
  rbinom_trng.Rd: RcppParallel, setThreadOptions
  rlnorm_trng.Rd: RcppParallel, setThreadOptions
  rnorm_trng.Rd: RcppParallel, setThreadOptions
  rpois_trng.Rd: RcppParallel, setThreadOptions
  runif_trng.Rd: RcppParallel, setThreadOptions
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Colors.Rd: xts
  rtsplot.Rd: xts
  rtsplot.candle.Rd: xts
  rtsplot.fake.stock.data.Rd: xts
  rtsplot.hl.Rd: xts
  rtsplot.lines.Rd: xts
  rtsplot.matplot.Rd: xts
  rtsplot.ohlc.Rd: xts
  rtsplot.polygon.Rd: xts
  rtsplot.scale.volume.Rd: xts
  rtsplot.text.Rd: xts
  rtsplot.volume.Rd: xts
  rtsplot.x.highlight.Rd: xts
  rtsplot2Y.Rd: xts
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}}.
       |                                                                                                       ^
Found the following files/directories:
  ‘Tsttwalk.dat’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘auth.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  predict.ucm.Rd: predict.SSModel
  ucm.Rd: SSModel, KFAS
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_path.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
       |                                                                    ^
'library' or 'require' calls in package code:
  ‘nimble’ ‘nimbleAPT’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  TimeoutException.Rd: Exception
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GPA.test.Rd: GPA
  MVA.cor.Rd: GPA
  MVA.scoreplot.Rd: GPA
  MVA.scores.Rd: GPA
  MVA.synt.Rd: GPA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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) }
       |                                                                                   ^
'::' or ':::' import not declared from: ‘purrr’
'library' or 'require' call not declared from: ‘tidyr’
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}).
       |                               ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘wcvp_checklist.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  wcvp_summary_gt.Rd: gt
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 
       | ^
'::' or ':::' imports not declared from:
  ‘changepoint’ ‘strucchange’
'library' or 'require' calls not declared from:
  ‘changepoint’ ‘strucchange’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  load.trees.Rd: read.nexus, read.tree
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) plot.eff.ridge.Rd:6: Lost braces
     6 |  emph{Single Interior Knot} at the MSE Optimal m-Extent of Shrinkage. The
       |      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  eff.biv.Rd: ellipse.lm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' call not declared from: ‘Ryacas’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ZabbixAPI.Rd: POST, user_agent, content_type, response, fromJSON
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}}.}
       |                              ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘s3_check_for_file.R’ ‘s3_file_size.R’ ‘s3_get_files.R’
    ‘s3_parse_uri.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘fit_density_ratio.R’ ‘fit_plug_and_play.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BCs4vd.Rd: biclust, Biclust
  BCssvd.Rd: biclust, Biclust
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ICtab.Rd: mle2-class
  fitrad-class.Rd: mle2, mle2-class
  fitsad-class.Rd: mle2, mle2-class
  fitsadC-class.Rd: mle2, mle2-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mvrnormSeries.Rd: mvrnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  npdeSaemix.Rd: npde, NpdeObject, npde.graphs, gof.test,
    npde.plot.select, autonpde, npde.plot.scatterplot, npde.plot.dist
  xbinning.Rd: npde, autonpde
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sim.Rd: parallelStart, parallelLibrary, parallelExport
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  compare_pred.Rd: emdi
  write.excel.Rd: openxlsx
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘class-2-differential.r’ ‘dual-apply.r’ ‘dual-math.r’
    ‘dual-summary.r’ ‘dual-test-near-equality.r’ ‘dual.r’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘Bivdiff.R’ ‘Output_Tables.R’
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
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: \#
checkRd: (-1) ModelHMMR-class.Rd:37: Lost braces; missing escapes or markup?
    37 |         class {StatHMMR}).
       |               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_RuleBook.Rd: RLumModel-package
  measure_SAR_OSL.Rd: RLumModel-package
  set_Rule.Rd: RLumModel-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sfn_plot.Rd: geom_point, geom_col
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘h-fun.R’ ‘mc-test.R’ ‘tshift.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  computeCritCutLength.Rd: snowprofileSet, snowprofile,
    snowprofileLayers
  computePunstable.Rd: snowprofileSet, snowprofile, snowprofileLayers
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  az_rec_service.Rd: az_subscription, az_resource_group
  create_rec_service.Rd: az_template
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SASmarkdown-package.rd: knitr-package
  sas_enginesetup.rd: knit_engines
  saslog_hookset.rd: knit_hooks
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.}
       |         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  alignGeometry.Rd: resample, projectRaster
  calcTopoCorr.Rd: hillShade, writeRaster
  crop.Rd: extent
  demTools.Rd: hillShade
  satellite.Rd: raster
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  crop.Rd: getpoly
  isolines.Rd: convCP, PolySet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
       |                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Shift.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  summary.sbde.Rd: geweke.diag
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
'library' or 'require' calls not declared from:
  ‘maps’ ‘sp’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  custom_scaffold_py_function_wrapper.Rd: py_function_docs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) get.events.Rd:51: Lost braces
    51 |   code{\link[deSolve]{events}}
       |       ^
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}
       |                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PermBiclust.beta.ks.Rd: KMeansSparseCluster
  PermBiclust.sigclust.Rd: sigclust, KMeansSparseCluster
  PermBiclust.sigclust_stop.Rd: sigclust, KMeansSparseCluster
  PermHclust.sigclust.Rd: HierarchicalSparseCluster, sigclust
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' calls not declared from:
  ‘doSNOW’ ‘foreach’ ‘iterators’ ‘reshape’ ‘rlecuyer’ ‘snow’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘nap.R’ ‘randomization_test.R’ ‘scdtb.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  barplot.SCGLRTHM.Rd: theme
  plot.SCGLR.Rd: ggplot
  plot.SCGLRTHM.Rd: ggplot
  scglrThemeBackward.Rd: Formula
  screeplot.SCGLRTHM.Rd: theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_scholar_resp.Rd: response, GET
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  step_aggregate_hclust.Rd: selections, bake, prep
  step_aggregate_list.Rd: selections, bake, prep
  step_rownormalize_tss.Rd: selections, bake, prep
  step_select_background.Rd: selections, bake, prep
  step_select_cv.Rd: selections, bake, prep
  step_select_kruskal.Rd: selections, bake, prep
  step_select_wilcoxon.Rd: selections, bake, prep
  step_taxonomy.Rd: selections, bake, prep
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fitSCI.Rd: mledist, fitdistrplus
  genlog.Rd: pdfglo, quaglo, cdfglo
  pe3.Rd: pdfpe3, quape3, cdfpe3
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  correlation.Rd: plotcorr
  panels.Rd: rlm, ellipse
  pcomp.Rd: cov.mve, cov.mcd
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sclr.Rd: broom
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  spatialPreprocess.Rd: BiocSingularParam-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.}
       |                                                                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  xtable.SK.Rd: xtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running examples in ‘ScottKnott-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SK
> ### Title: The SK Test for Single Experiments
> ### Aliases: SK SK.default SK.aov SK.lm SK.formula SK.aovlist SK.lmerMod
> ### Keywords: package
> 
> ### ** Examples
> 
> ##
> ## Examples:Randomized Complete Block Design (RCBD)
> ## More details: demo(package='SK')
> ##
> 
> ## The parameters can be: formula, aov, lm, aovlist and lmerMod
> 
> data(RCBD)
> 
> ## From: formula
> sk1 <- with(RCBD,
+             SK(y ~ blk + tra,
+                data=dfm,
+                which='tra'))
Error in data.frame(means = aux_mt1, reps = reps) : 
  arguments imply differing number of rows: 0, 5
Calls: with ... eval -> SK -> SK.formula -> SK -> SK.lm -> data.frame
Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘clipboard.R’ ‘display.R’ ‘locate_image.R’ ‘screenshot.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘plotting.R’
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]}}
       |                                                          ^
Found the following files/directories:
  ‘untitled_consensus_cluster’
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  modRisk.Rd: loglm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) sdc_extabs.Rd:59: Lost braces
    59 | (including ]code{forcelist} variables) that can be used to form tables.}
       |                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  create_raster.Rd: raster
  protect_smooth.Rd: focal
  sdc_raster.Rd: raster, brick
  smooth_raster.Rd: focal
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘sde/libs/sde.so’:
  Found non-API call to R: ‘SET_TYPEOF’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘fit.R’
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} .}
       |                                           ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘series.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  casecross.Rd: coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cla_secsse_ml.Rd: DDD
  cla_secsse_ml_func_def_pars.Rd: DDD
  default_params_doc.Rd: DDD
  secsse_ml.Rd: DDD
  secsse_ml_func_def_pars.Rd: DDD
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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"}.}
       |                                                                                                                                   ^
Packages required but not available: 'msa', 'GenomicFeatures'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  seeds-package.Rd: Deriv, ode
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  noisew.Rd: pulse
  synth.Rd: pulse
  synth2.Rd: pulse
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  garch.seg-class.Rd: foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘selcorr.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DearBegg.Rd: DEoptim
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  checkResponse.Rd: VERB
  errorContent.Rd: content
  errorResponse.Rd: VERB
  getPageSource.Rd: read_html
  queryDriver.Rd: VERB, content
  takeElementScreenshot.Rd: base64_dec
  takeScreenshot.Rd: base64_dec
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  est_change_plot.Rd: ggplot2
  index_plot.Rd: ggplot2
  influence_plot.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘boot_utils.R’
'library' or 'require' call not declared from: ‘swirl’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  spm.Rd: gam, lme, glmmPQL
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SemNetCleaner-package.Rd: SemNetDictionaries
  best.guess.Rd: SemNetDictionaries
  textcleaner.Rd: SemNetDictionaries
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  convert2igraph.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  semPaths.Rd: qgraph.layout.fruchtermanreingold
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AVE.Rd: lavaan-class
  auxiliary.Rd: lavaan-class
  chisqSmallN.Rd: lavaan-class
  compRelSEM.Rd: lavaan-class
  compareFit.Rd: fitMeasures, lavaan-class
  discriminantValidity.Rd: lavaan-class
  lavTestScore.mi.Rd: lavTestScore, standardizedSolution, lavInspect
  lavaan.mi-class.Rd: lavaanList-class, lavaan-class
  maximalRelia.Rd: lavaan-class
  measEq.syntax.Rd: lavaan-class
  measurementInvariance-deprecated.Rd: cfa
  measurementInvarianceCat-deprecated.Rd: cfa
  modindices.mi.Rd: lavInspect
  monteCarloCI.Rd: lavaan-class
  plausibleValues.Rd: lavaan-class
  probe2WayMC.Rd: lavaan-class
  probe2WayRC.Rd: lavaan-class
  probe3WayMC.Rd: lavaan-class
  probe3WayRC.Rd: lavaan-class
  reliability-deprecated.Rd: lavaan-class
  reliabilityL2-deprecated.Rd: lavaan-class
  twostage-class.Rd: lavaan-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  evaluateDataLikelihood.Rd: OpenMx
  semtree.Rd: OpenMx, mxModel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sobol_dummy.Rd: boot
  sobol_indices.Rd: boot
  sobol_matrices.Rd: sobol, randomLHS
  sobol_ode.Rd: ode
  vars_matrices.Rd: sobol
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  WordCountAna.Rd: textual, MFA
  analyse_holos.Rd: MFA, FactoMineR, MCA, HMFA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.LocationDatum.Rd: qmap, geom_point
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.data.table.sento_measures.Rd: as.data.table
  plot.attributions.Rd: ggplot
  plot.sento_measures.Rd: ggplot
  plot.sento_modelIter.Rd: ggplot
  predict.sento_model.Rd: predict.glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                               ^
checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                                                          ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                              ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                                                     ^
Found the following files/directories:
  ‘assocpointpair_result.csv’ ‘foundereffectfinder_result.csv’
  ‘getfreqs_result.csv’ ‘getfreqs_result.png’ ‘orPlot.pdf1_1.pdf’
  ‘orPlot.pdf2_1.pdf’ ‘orPlot.pdf3_1.pdf’ ‘orPlot.pdf4_1.pdf’
  ‘orPlot.pdf5_1.pdf’ ‘orPlot.pdf6_1.pdf’ ‘orPlot.pdf7_1.pdf’
  ‘orPlot.pdf8_1.pdf’ ‘q-values_result.csv’ ‘rewritetuple_result.csv’
  ‘tartan_plot.pdf’ ‘vispair_plot.pdf’ ‘vispairfeat_plot.pdf’
  ‘volcano_plot.pdf’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  seq2qha.Rd: seqdef
  seq_heatmap.Rd: seqdef, agnes, seqIplot
  seqi1epi.Rd: seqdef, seqistatd
  seqifpos.Rd: seqdef, seqistatd
  seqinepi.Rd: seqdef, seqistatd
  seqsmooth.Rd: seqdef
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fit_model.Rd: nloptr
  hidden_paths.Rd: seqIplot
  mssplot.Rd: seqplot, plot.stslist
  plot.hmm.Rd: igraph.plotting, seqplot, plot.igraph
  plot.mhmm.Rd: igraph.plotting, seqplot, plot.igraph
  seqHMM-deprecated.Rd: nloptr
  ssp.Rd: seqplot, plot.stslist
  ssplot.Rd: seqplot, plot.stslist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘consensus.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_modules.Rd: igraph
  plot_network.Rd: igraph
  plot_network_diff.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘seqtrie/libs/seqtrie.so’:
  Found non-API call to R: ‘STRING_PTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  avg.modindices.Rd: sem
  bin.results.Rd: sem
  bin.rsquare.Rd: sem
  gam.path.Rd: sem, gam
  modelsummary.Rd: sem
  plotmodelfit.Rd: sem
  plotpath.Rd: sem
  runModels.Rd: lavaan, sem
  sesem-package.Rd: sem, lavaan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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: \&
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘sd_box.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sd_distance.Rd: sf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘sfheaders/libs/sfheaders.so’:
  Found non-API call to R: ‘STRING_PTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘st_transform_outline.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘st_augment.R’ ‘st_bridges.R’ ‘st_check_islands.R’
    ‘st_manual_cut_nb.R’ ‘st_manual_join_nb.R’ ‘st_quickmap_nb.R’
    ‘st_quickmap_preds.R’
possible bashism in configure.ac line 25 (test -a/-o):
      if test [$RVER_MAJOR -lt 3] -o [$RVER_MAJOR -eq 3 -a $RVER_MINOR -lt 3]; then
  possible bashism in configure.ac line 120 (test -a/-o):
  if test [${GDAL_MAJ_VER} -eq 3] -a [${GDAL_MIN_VER} -eq 6] -a [${GDAL_PATCH_VER} -eq 0] ; then
'::' or ':::' import not declared from: ‘wkb’
'library' or 'require' calls not declared from:
  ‘RgoogleMaps’ ‘animation’ ‘cshapes’ ‘ggmap’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fPCAassessment.Rd: fda
  fPCAcapacity.Rd: fda
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' call not declared from: ‘microbenchmark’
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},
       |                                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gPLS.Rd: cim
  gPLSda.Rd: plotIndiv, plotVar, cim, network
  sPLSda.Rd: plotIndiv, plotVar, cim, network
  sgPLSda.Rd: plotIndiv, plotVar, cim, network
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘sgraph_utils.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘sample_systematic.R’
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cluster.plot.Rd: vegan
  detect.outline.Rd: pixmap
  generateShapeCoefficients.Rd: wd, wavethresh
  plotWaveletShape.Rd: wavethresh
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ClusteringPerformance.Rd: SimulateClustering
  GraphComparison.Rd: SimulateGraphical, SimulateRegression
  SelectionPerformance.Rd: SimulateRegression, SimulateComponents,
    SimulateGraphical, BlockStructure
  SelectionPerformanceGraph.Rd: SimulateGraphical, SimulateRegression
  plot.clustering.Rd: Heatmap
  plot.roc_band.Rd: ROC
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package unavailable to check Rd xrefs: ‘rCOSA’
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})}
       |                              ^
checkRd: (-1) shiftrPrepare.Rd:37: Lost braces
    37 |     See code{\link{shiftrPermBinary}} function and the respective example.
       |             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Buttons.Rd: actionButton, checkboxInput
  Collapses.Rd: tabsetPanel, shinyServer
  Modals.Rd: tabPanel
  Tooltips_and_Popovers.Rd: renderUI
  bsButton.Rd: icon
  bsExample.Rd: runApp
  popify.Rd: renderUI
  tipify.Rd: renderUI
  updateButton.Rd: icon, submitButton
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘filter_discrete.R’ ‘filter_query.R’ ‘renders.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  renderDropdownMenu.Rd: HTML
  renderMenu.Rd: HTML, uiOutput
  renderValueBox.Rd: HTML
  tabBox.Rd: tabPanel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘destroyModule.R’ ‘makeModule.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  downloadablePlot.Rd: renderPlot
  downloadablePlotUI.Rd: plotOutput
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.}
       |                    ^
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.
       |                                                     ^
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shiny.info)
  > 
  > test_check("shiny.info")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 24 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-lintr.R:1:1'): (code run outside of `test_that()`) ─────────────
  Error: Function with_defaults was deprecated in lintr version 3.0.0. Use linters_with_defaults or modify_defaults instead.
  Backtrace:
      ▆
   1. └─lintr::with_defaults(...) at test-lintr.R:1:1
   2.   └─lintr:::lintr_deprecated(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 24 ]
  Error: Test failures
  Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘continue_sequence.R’ ‘get_exchange_rates.R’
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 ?
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}
       |            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  displayCodeModal.Rd: icon
  metaObserve.Rd: observe, req
  metaReactive.Rd: reactive, req
  metaRender.Rd: req
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  connect_sqlite.Rd: RSQLite, DBI
  create_schema.Rd: RSQLite, DBI
  db.read_table.Rd: DBI, tibble
  db.write_table.Rd: DBI
  shinynotes.Rd: DBI
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
checkRd: (-1) addValidationSuffix.Rd:13: Lost braces; missing escapes or markup?
    13 | A string `"{tagId}-shinyreforms-validation"`.
       |            ^
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
Running ‘testthat.R’ [10s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shinystan)
  Loading required package: shiny
  
  This is shinystan version 2.6.0
  
  > 
  > test_check("shinystan")
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 125 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test_creating_sso.R:197:3'
  • {rstanarm} is not installed (5): 'test_creating_sso.R:45:3',
    'test_creating_sso.R:60:3', 'test_creating_sso.R:135:3',
    'test_creating_sso.R:150:3', 'test_creating_sso.R:161:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_misc.R:2:1'): (code run outside of `test_that()`) ──────────────
  <packageNotFoundError/error/condition>
  Error in `library(rstanarm)`: there is no package called 'rstanarm'
  Backtrace:
      ▆
   1. └─base::library(rstanarm) at test_misc.R:2:1
  
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 125 ]
  Error: Test failures
  Execution halted
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}.
       |                                                                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  numberInput.Rd: validateCssUnit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘app_server.R’ ‘function.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AppDriver.Rd: ChromoteSession
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) run_shinytitle_example.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) run_shinytitle_example.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MrBayes.Rd:24: Lost braces
    24 | \item{contype}{A character string; the type of consensus tree calculated from the posterior distribution of trees}{either "halfcompat" (majority-rule consensus tree) or "allcombat" (strict consensus tree)}
       |                                                                                                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ShopifyShop.Rd: R6
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  shrinkDSM.Rd: shrinkTVP
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  shrinkDTVP.Rd: stochvol, svsample
  shrinkTVP.Rd: stochvol, svsample
  simTVP.Rd: svsim
  updateTVP.Rd: stochvol, svsample
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.'
       |                       ^
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}. 
       |                                                                                                                                                                                                                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mutation.network.Rd: plot.network
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
       |              ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘show_group_enrichment.R’
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  survivalForest.Rd: forestplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘p_sie.R’ ‘prp.R’ ‘siie.R’
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘resilp.R’
checkRd: (-1) sim_Y_Binary_X.Rd:51: Lost braces
    51 |     \item \code{dist = "binomial"} is drawn from eqn{Bin(XB, XB(1-XB))}
       |                                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  window.PMCMC.Rd: window.mcmc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ermvnorm.Rd: rmvnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SplineFitDepFct.Rd: solve.QP
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘formula_interface.r’ ‘node_time_to_event.r’
File ‘Sim.DiffProc/libs/Sim.DiffProc.so’:
  Found non-API call to R: ‘SET_TYPEOF’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot-methods.Rd: plot.deSolve
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  msq.Rd: rstream
  simEd-package.Rd: rstream
  ssq.Rd: rstream
  ssqvis.Rd: rstream
  vbeta.Rd: rstream, rstream.sample
  vbinom.Rd: rstream, rstream.sample
  vcauchy.Rd: rstream, rstream.sample
  vchisq.Rd: rstream, rstream.sample
  vexp.Rd: rstream, rstream.sample
  vfd.Rd: rstream, rstream.sample
  vgamma.Rd: rstream, rstream.sample
  vgeom.Rd: rstream, rstream.sample
  vlnorm.Rd: rstream, rstream.sample
  vlogis.Rd: rstream, rstream.sample
  vnbinom.Rd: rstream, rstream.sample
  vnorm.Rd: rstream, rstream.sample
  vpois.Rd: rstream, rstream.sample
  vt.Rd: rstream, rstream.sample
  vunif.Rd: rstream, rstream.sample
  vweibull.Rd: rstream, rstream.sample
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cvx.lip.reg.Rd: nnls
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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) {
       |                         ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘call_api.R’ ‘sfa_load__shares_outstanding.R’ ‘sfa_load_companies.R’
    ‘sfa_load_shareprices.R’ ‘sfa_load_statement.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sfa_load_common_shares_outstanding.Rd: data.table
  sfa_load_shareprices.Rd: data.table
  sfa_load_statements.Rd: data.table
  sfa_load_weighted_shares_outstanding.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bootstrap-projection.R’ ‘bundle_sim.R’ ‘calc_coverage.R’
    ‘calc_rejection.R’ ‘utilities.R’
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.trajectory.Rd: grViz, render_graph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package required but not available: ‘BSgenome’

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coxsimInteract.Rd: coxph, survival, strata
  coxsimLinear.Rd: coxph, survival, strata
  coxsimPoly.Rd: coxph, survival, strata
  coxsimSpline.Rd: coxph, pspline, survival, strata
  coxsimtvc.Rd: coxph, survival, strata
  ggfitStrata.Rd: plot.survfit, survfit, strata
  simGG.siminteract.Rd: scale_colour_brewer, discrete_scale
  simGG.simlinear.Rd: scale_colour_brewer, discrete_scale
  simGG.simpoly.Rd: scale_colour_brewer, discrete_scale
  simGG.simtvc.Rd: scale_colour_brewer, discrete_scale
  simPH.Rd: coxph
  tvc.Rd: survival, coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘anon.R’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘markdown_block.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘imgocr.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  residuals.simplexreg.Rd: simplex
  simplexreg.Rd: simplex
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  print.powerSim.Rd: binom.confint
  simrOptions.Rd: Anova
  tests.Rd: summary.merMod, anova.merMod, Anova
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  device.Rd: pdf.end
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'::' or ':::' import not declared from: ‘codetools’
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.
       |                                                                                                                                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  analyze.Rd: lavaan-class
  getExtraOutput.Rd: lavaan-class
  likRatioFit.Rd: lavaan-class
  modelLavaan.Rd: lavaan-class
  pValue.Rd: lavaan-class
  pValueNested.Rd: lavaan-class
  pValueNonNested.Rd: lavaan-class
  sim.Rd: lavaan-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  land.Rd: getData
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
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
       |                                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  expand_tibble.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  stat_hollow_contour.Rd: aes, aes_, borders, layer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
       |                                                     ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘calculate-effect-sizes.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘debug.R’
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘predict.sitar.R’
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)}).}
       |                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  anova.sitar.Rd: anova.lme
  sitar.Rd: nlme, nlmeObject
  summary.sitar.Rd: summary.lme, lmeObject
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.
       |                                                                                                  ^
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.
       |                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sizeestima.Rd: rtnorm, rinvgamma, dtnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘SiZer.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  to_value.Rd: set_labels
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running examples in ‘skellam-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: skellam.reg
> ### Title: Regression assuming a Skellam distribution
> ### Aliases: skellam.reg
> ### Keywords: Skellam regression
> 
> ### ** Examples
> 
> require('skellam')
> 
> set.seed(0)
> 
> x <- rnorm(1000)
> y1 <- rpois(1000, exp(1 + 1 * x) )
> y2 <- rpois(1000 , exp(-1 + 1 * x) )
> y <- y2 - y1
> skellam.reg(y, x)
Error in stats::optim(mod$estimate, skelreg, hessian = TRUE, control = list(maxit = 5000)) : 
  function cannot be evaluated at initial parameters
Calls: skellam.reg -> <Anonymous>
Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ext-annotate_expr.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rM.Rd: mvrnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  knit_print.Rd: collapse
  print.Rd: tbl_format_setup
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sklars.omega.Rd: hjkb
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘add_ci_bounds_mc_power.R’ ‘calculate_gefficiency.R’
    ‘eval_design_custom_mc.R’ ‘eval_design_survival_mc.R’ ‘skprGUI.R’
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.
       |                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bout_analysis.Rd: data.table, behavr
  curate_dead_animals.Rd: data.table, behavr
  sleep_annotation.Rd: data.table, behavr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
       |                                                                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  slideView.Rd: levelplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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] +
       |          ^
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) cities_lon_lat.Rd:6: Lost braces
     6 | A subset of world.cities{maps}. Extracted in order to shink number of dependencies. 
       |                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  remove_empty_features.Rd: futile.logger
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) trlong.Rd:17: Lost braces
    17 |     \item{\code{resp}}{a factor indicating the transport mode choice, and \code{B} denotes taking the bus, code{D} denotes driving one's own vehicle, \code{F} denotes getting a ride with a friend, \code{O} denotes other, and \code{W} denotes walking}
       |                                                                                                                ^
checkRd: (-1) smdocker_log.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:35-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                  ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                            ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                          ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                                    ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                              ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                        ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                      ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                                ^
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.
       |                        ^
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)) 
       |                                                              ^
checkRd: (-1) getKernel.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getKernel.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smoof_function.Rd:10: Lost braces
    10 | or code{smoof_multi_objective_function}. Both single- and multi-objective functions share the following attributes.
       |        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  smoother.Rd: TTR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.idm.Rd: SmartControl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_paths.Rd: facet_wrap
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  funcen.Rd: kde
  smoothROCtime-package.Rd: ks
  stRoc.Rd: kde
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}
       |             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  smoothtail-package.Rd: logConDens
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
Found the following files/directories:
  ‘my_new_social_media_plot.png’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  evol_auc.Rd: ggplot
  explore_table.Rd: flextable
  probs_pred.Rd: ggplot
  sMSROC_plot.Rd: plotROC
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) SnakesAndLaddersGame.Rd:25: Lost braces; missing escapes or markup?
    25 | {Hector Haffenden} {haffendenh@cardiff.ac.uk}
       |                    ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘sk.R’ ‘sk_export.R’ ‘sk_index.R’ ‘sk_pars.R’ ‘sk_plot.R’
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')
       |                                  ^
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.
       |   ^
Packages required but not available: 'GWASTools', 'gdsfmt', 'SNPRelate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  snplist-package.Rd: Rcpp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  createSaturated.Rd: FrF2, DoE.base
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
       |                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  map.active.Rd: geom_text_repel, geom_label_repel, guides, theme
  map.add.Rd: geom_text_repel, geom_label_repel, guides, theme
  map.csa.mca.Rd: geom_smooth
  map.ctr.Rd: geom_text_repel, geom_label_repel, guides, theme
  map.ind.Rd: geom_text_repel, geom_label_repel, guides, theme
  map.mod.Rd: geom_text_repel, geom_label_repel, guides, theme
  map.path.Rd: geom_path, geom_point, geom_text
  map.select.Rd: geom_text_repel, geom_label_repel, guides, theme,
    guide_legend
  map.sup.Rd: geom_text_repel, geom_label_repel, guides, theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘PowerRelation.R’ ‘SocialRanking.R’ ‘copeland.R’ ‘generator.R’
    ‘makePowerRelationMonotonic.R’
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
       |                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Incomplete-class.Rd: dgCMatrix-class, CsparseMatrix-class,
    dsparseMatrix-class, generalMatrix-class, dMatrix-class,
    sparseMatrix-class, compMatrix-class, Matrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  soilhypfit_control_fit_wrc_hcc.Rd: nloptr
  soilhypfit_fit_wrc_hcc.Rd: nloptr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘meteoReaders.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  window-methods.Rd: window.zoo
  writeSolar.Rd: read.zoo, write.zoo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) solr_mlt.Rd:70: Lost braces; missing escapes or markup?
    70 | TermVector DEFAULT_FIELD_NAMES = new String[] {"contents"}
       |                                               ^
checkRd: (-1) solve_pH_from_AT.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:93: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  superClass.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' call not declared from: ‘RColorBrewer’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  somsp.Rd: kohonen
  somspa.Rd: kohonen, som
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘objects.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  graphsoptd.mae.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SpaDES.core-package.Rd: copy, equalExtent, getColors,
    divergentColors, layerNames, numLayers, Plot, clearPlot,
    clickValues, clickExtent, clickCoordinates, dev, newPlot, rePlot
  depsLoadOrder.Rd: igraph
  downloadData.Rd: prepInputs
  emptyEventList.Rd: data.table
  moduleDiagram.Rd: igraph
  moduleGraph.Rd: igraph
  simList-accessors-events.Rd: data.table
  simList-class.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  corMatern.Rd: glmmPQL, lme
  spaMM_boot.Rd: boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘spaMM/libs/spaMM.so’:
  Found non-API call to R: ‘PRVALUE’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘available-data.R’ ‘convert.R’ ‘duckdb-helpers.R’ ‘get-zones.R’
    ‘internal-utils.R’ ‘quick-get.R’
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
       |                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  xgboost_classifier.Rd: ft_r_formula
  xgboost_regressor.Rd: ft_r_formula, ml_save
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sparrpowR-package.Rd: sparr, spatstat.random, spatstat.geom, terra,
    doFuture, doRNG
  spatial_data.Rd: spatstat.random
  spatial_power.Rd: spatstat.random
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ElasticNet_HJBiplot.Rd: spca
  Plot_Biplot.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sparseFLMM.Rd: mgcv, s, te, bam, pffr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}
       |                                  ^
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.
       |                                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  model_parallel.Rd: future_lapply
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}{
       |            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sparsesvd.Rd: dgCMatrix-class, sparseMatrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.tscgm.Rd: network
  plot.tscgm.ar2.Rd: network
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘sim_functional_process.R’
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘dnnModel.R’ ‘interGradientsDL.R’ ‘loadData.R’ ‘spatialClustering.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FEMdensity.Rd: basisfd
  smooth.FEM.basis.Rd: lambda2df, lambda2gcv, df2lambda
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) distSG.Rd:40: Lost braces; missing escapes or markup?
    40 |   matrix and weight matrix (plus a matrix with {eID} identifiers
       |                                                ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘kinetic_ising_ensemble.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  grf.Rd: ranger
  grf.bw.Rd: ranger
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rasterReilly.Rd: ratify
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘highest_concentration.R’ ‘plot_points.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SpatDensReg.Rd: Surv
  SuperSurvRegBayes.Rd: Surv
  anovaDDP.Rd: Surv
  cox.snell.survregbayes.Rd: Surv
  frailtyGAFT.Rd: Surv, rdist
  indeptCoxph.Rd: Surv
  spCopulaCoxph.Rd: Surv
  spCopulaDDP.Rd: Surv
  survregbayes.Rd: Surv, rdist, rdist.earth
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  surfacemodel.Rd: rpart.control, rpart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) NEWS.Rd:137: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CompactStratification-class.Rd: SpatialPixels-class,
    SpatialPoints-class, SpatialPixelsDataFrame-class
  CompactStratificationEqualArea-class.Rd: SpatialPixels-class,
    SpatialPoints-class
  CompactStratificationPriorPoints-class.Rd: SpatialPoints-class,
    SpatialPixels-class
  SamplingPattern-class.Rd: SpatialPoints-class
  SamplingPatternCentroids-class.Rd: SpatialPoints-class
  SamplingPatternPriorPoints-class.Rd: SpatialPoints-class
  SamplingPatternPurposive-class.Rd: SpatialPoints-class
  SamplingPatternRandom-class.Rd: SpatialPoints-class
  SamplingPatternRandomComposite-class.Rd: SpatialPoints-class,
    SpatialPointsDataFrame-class
  SamplingPatternRandomSamplingUnits-class.Rd: SpatialPoints-class
  stratify-methods.Rd: SpatialPixels-class, SpatialGrid-class,
    SpatialPolygons-class, SpatialPoints-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘federov.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  forecast.spdur.Rd: forecast
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
possible bashism in configure.ac line 109 (should be 'b = a'):
  AS_IF([test "x$enable_system_arpack" == "xno"], [
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  speck.Rd: Ckmeans.1d.dp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  continuum_removal.Rd: baseline
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
Running ‘testthat.R’ [4s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spectralGraphTopology)
  
  Attaching package: 'spectralGraphTopology'
  
  The following object is masked from 'package:stats':
  
      D
  
  > 
  > test_check("spectralGraphTopology")
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-learnGraphTopology.R:21:1'): (code run outside of `test_that()`) ──
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  ── Error ('test-learnSmoothSignalGraph.R:9:1'): (code run outside of `test_that()`) ──
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  ── Error ('test-operators.R:122:1'): (code run outside of `test_that()`) ───────
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ]
  Error: Test failures
  Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘analysis_age.R’ ‘analysis_alpha.R’ ‘analysis_helpers.R’
    ‘analysis_helpers_table.R’ ‘analysis_photo.R’ ‘analysis_radio.R’
    ‘analysis_setup.R’ ‘export_Output_Settings.R’ ‘export_download.R’
    ‘export_helpers.R’ ‘export_helpers_plot.R’ ‘export_helpers_table.R’
    ‘import_examples.R’ ‘import_examples_box.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘innprod.R’ ‘utils.R’
checkRd: (-1) speech_recompiler.Rd:25: Lost braces; missing escapes or markup?
    25 | The default compilation is that of \ code {speech_build (., compiler = TRUE}).
       |                                           ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘import_qiime2_tax_table.R’ ‘import_sintax_tax_table.R’
Found the following files/directories:
  ‘.neig’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  qml.SARspARCH.Rd: solnp
  qml.spARCH.Rd: solnp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
    61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc}, 
       |                                                   ^
checkRd: (-1) adaptIntegrateSpherePolar.Rd:14: Lost braces
    14 | code{adaptIntegrateBallPolar()} will likely miss these abrupt changes and give
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  F_from_f.Rd: tang-norm-decomp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bestCloseMatch.Rd: dist.dna
  localMinima.Rd: dist.dna
  monophyly.Rd: prop.part, root, boot.phylo
  monophylyBoot.Rd: prop.part, root, boot.phylo
  nearNeighbour.Rd: dist.dna
  polyBalance.Rd: balance
  read.GB.Rd: read.GenBank
  rosenberg.Rd: nodelabels
  slideAnalyses.Rd: dist.dna
  spider-package.Rd: ape-package, pegas-package
  tajima.K.Rd: dist.dna
  tclust.Rd: dist.dna
  threshID.Rd: dist.dna
  tree.comp.Rd: dist.topo, node.depth
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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’
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})
       |                                                                                                                                                                  ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘addlearn_local.R’
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.
       |                                                  ^
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.idigbio.Rd: idig_search_records
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘summary.spjctest.R’ ‘summary.spqtest.R’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ce.dat.prep.Rd: Surv
  kaplan.meier.location.Rd: survfit
  lifedata.MLE.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  onNextInput.Rd: observeEvent
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}
       |                                                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  inipopFun.Rd: lhs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 
       |                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  impactspsur.Rd: impacts
  spsur-package.Rd: impacts
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running examples in ‘spsurv-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bppo
> ### Title: Bernstein Polynomial Based Proportional Odds Model
> ### Aliases: bppo
> 
> ### ** Examples
> 
> 
> library("spsurv")
> data("veteran")
Warning in data("veteran") : data set ‘veteran’ not found
> 
> fit <- bppo(Surv(time, status) ~ karno + celltype,
+ data = veteran)
Error in optimHess(theta, fn, gr, control = list(fnscale = -1)) : 
  non-finite value supplied by optim
Calls: bppo ... spbp.mle -> <Anonymous> -> <Anonymous> -> .local -> optimHess
Execution halted
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
       |                                             ^
'library' or 'require' calls not declared from:
  ‘MBA’ ‘akima’ ‘colorspace’ ‘fields’ ‘maps’
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fitDistances.Rd: fitdistr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.Rd: viridis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) sqldf.Rd:248: Lost braces
   248 | and code{port} arguments of sqldf.
       |         ^
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. 
       |                                                                        ^
'library' or 'require' call not declared from: ‘interval’
checkRd: (-1) squidR.Rd:83: Lost braces; missing escapes or markup?
    83 |   \item \code{X1_sto_shared} (default \code{TRUE}): {logical}; if \code{TRUE}, the stochastic environmental effect included in the environmental effect x1 will be shared between individuals. If \code{FALSE}, each individual will experience a different stochastic environmental effect x1 (i.e. a new stochastic environmental effect is generated for each individual).
       |                                                     ^
checkRd: (-1) plot.SRCS.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:56-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:77-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:87-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:143-144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:145: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:146-148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:149: Lost braces in \itemize; meant \describe ?
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.
       |               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sscor.Rd: Qn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.Rd: levelplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_moran.Rd: nb2listw
  ssfa.Rd: nb2listw, maxNR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ssize.twoSampVaryDelta.Rd: ssize.twoSamp, ssize.twoSampVary,
    ssize.oneSamp, ssize.oneSampVary, ssize.F, ssize.Fvary
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LinearTSVMSSLR.Rd: SVM
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) new.distance.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:35-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:30-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:38-40: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_ssp.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
       |                                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gplot.SSrat.Rd: gplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
       |       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LearnerList.Rd: ctree
  accuracy.Rd: classAgreement
  stabletree-coercion.Rd: randomForest, RandomForest-class, cforest,
    ranger
  stabletree.Rd: as.party
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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"}.}
       |                    ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘classification.R’ ‘regression.R’ ‘staccuracy.R’ ‘unpackaged_utils.R’
checkRd: (-1) stackExample.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stackExample.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stamppFst.Rd:20: Lost braces
    20 | \code{Fsts}{a matrix of pairwise Fst values between populations}
       |            ^
checkRd: (-1) stamppFst.Rd:21: Lost braces
    21 | \code{Pvalues}{a matrix of p-values for each of the pairwise Fst values containined in the 'Fsts' matrix}
       |               ^
checkRd: (-1) stamppFst.Rd:22: Lost braces
    22 | \code{Bootstraps}{a dataframe of each Fst value generated during Bootstrapping and the associated confidence intervals}
       |                  ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘stamp.direction.r’
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
       |                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  staple.Rd: readNifti
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
       |             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggeem.Rd: eem_extract
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.}
       |                                                                         ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘stat_frequency.R’
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
       |                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Statamarkdown-package.rd: knitr-package
  stata_engine.rd: knit_engines
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  elapsed.Rd: week, month, year
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}.
       |                                                                                                    ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘od_list.R’ ‘od_resource.R’ ‘od_utils.R’ ‘other_endpoints.R’
    ‘sc_data.R’ ‘schema.R’ ‘schema_uri.R’ ‘sdmx_table.R’ ‘table.R’
    ‘table_as_data_frame.R’ ‘table_json.R’ ‘table_meta.R’ ‘table_saved.R’
possible bashism in configure.ac line 31 (should be 'b = a'):
  if test x"${RSysinfoName}" == x"Darwin"; then
  possible bashism in configure.ac line 42 (should be 'b = a'):
     if test x"${hasOpenMP}" == x""; then
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  runMultiTraitGwas.Rd: GWAS
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘tables.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  quote_cloud.Rd: wordcloud
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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)}
       |                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Heat.Rd: pheatmap
  ImpPlot.Rd: randomForest, gbm
  cv_glmnet_plot.Rd: glmnet
  esSim.Rd: lmFit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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)}
       |                                                                                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  STB-Package.Rd: VCA
  stb.VCA.Rd: residuals.VCA, ranef.VCA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘coxph_methods.R’ ‘glm_methods.R’ ‘standardize_custom.R’ ‘utils.R’
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 ?
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
       |                                                                ^
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")}
       | ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘do_bma.R’ ‘evaluate_models.R’ ‘gam_model_probs.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  STLK.Rd: Kest
  STLg.Rd: pcf
  as.lpp.stlpp.Rd: as.lpp, lpp
  as.stlpp.Rd: ppp, lpp, linnet
  as.tpp.stlpp.Rd: lpp, as.lpp
  density.stlpp.Rd: density.lpp, densityQuick.lpp, bw.scott.iso
  densityVoronoi.stlpp.Rd: densityVoronoi.lpp
  densityVoronoi.tpp.Rd: densityVoronoi.lpp
  methods.stlpp.Rd: as.linim
  rpoistlpp.Rd: ppp
  rthin.stlpp.Rd: rthin
  stlpp.Rd: as.ppp, lpp, linnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘corrviz.html’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘stm_diag.R’ ‘stm_effects.R’ ‘stm_network.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  labelTopics.Rd: lda
  topicLasso.Rd: glmnet, cv.glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  stochBlockORP.Rd: genRandomPar
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘Functions.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘sepstlppm.R’ ‘sepstppm.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  globaldiag.Rd: STIKhat, STLKinhom
  localSTLKinhom.Rd: STLKinhom, STLginhom
  localdiag.Rd: KLISTAhat
  localtest.Rd: KLISTAhat, LISTAhat
  plot.globaldiag.Rd: STLKinhom
  plot.locstppm.Rd: OS
  plot.sepstppm.Rd: OS
  plot.stlgcppm.Rd: OS
  plot.stlp.Rd: plot3D
  plot.stppm.Rd: OS
  sepstlppm.Rd: lppm
  sepstppm.Rd: ppm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘defStormsList.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  storr.Rd: R6Class
  storr_dbi.Rd: digest
  storr_environment.Rd: digest
  storr_rds.Rd: digest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_publication.Rd: rvest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}{
       |                            ^
Found the following files/directories:
  ‘myNewStrat.R’
possible bashism in configure.ac line 35 (should be 'b = a'):
  if test x"${RSysinfoName}" == x"Darwin"; then
  possible bashism in configure.ac line 46 (should be 'b = a'):
     if test x"${hasOpenMP}" == x""; then
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
       | ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getSummary.StratSel.Rd: mtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘apportion_inverse.R’ ‘apportion_polygon.R’ ‘apportion_web.R’
    ‘prep_reach_dist.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DSClassifier_SlidingWindow.Rd: rpart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘stringfish/libs/stringfish.so’:
  Found non-API calls to R: ‘LEVELS’, ‘STDVEC_DATAPTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
possible bashism in configure.ac line 18 (should be '.', not 'source'):
      source tarball as suggested by BR)
File ‘stringi/libs/stringi.so’:
  Found non-API calls to R: ‘LEVELS’, ‘NAMED’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  str_replace.Rd: stri_replace
  str_split.Rd: stri_split
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  flankingRegions.Rd: tibble
  genotypeList.Rd: tibble
  noiseList.Rd: tibble
  stringCoverageGenotypeList.Rd: tibble
  stringCoverageList.Rd: tibble
  workflow.control.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘generic_stroke.R’ ‘index_plot.R’ ‘mfi_calc.R’ ‘pase_calc.R’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
checkRd: (-1) calculateStatistics.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{quant}{numeric quantile to calculate {0,1}, default 0.95.}
       |                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calculateAllele.Rd: data.table
  calculateSpike.Rd: data.table
  combine_gui.Rd: rbind.fill
  editData_gui.Rd: gdf, gtable
  ggsave_gui.Rd: ggsave
  plotDistribution_gui.Rd: geom_density
  plotGroups_gui.Rd: stat_ecdf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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} ) |}
       |                                                                                                                                            ^
checkRd: (-1) subdetect-package.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subdetect-package.Rd:12: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotAnnGraph.Rd: plot.igraph
  plotGraphL.Rd: plot.igraph, layout.random
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) P3C.Rd:18: Lost braces; missing escapes or markup?
    18 |  used for this will be 1.00*10^{-PoissonThreshold}.}
       |                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  subspace.Rd: ggvis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘geom_glyph_ribbon.R’
checkRd: (-1) suggests.Rd:14: Lost braces; missing escapes or markup?
    14 | {suggests} aims to make that workflow as minimal and painless as possible,
       | ^
File ‘sumR/libs/sumR.so’:
  Found non-API call to R: ‘STRING_PTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) 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},
       |                                ^
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.}
       |                                                                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mice.impute.SuperLearner.Rd: SuperLearner
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  KNNTrainer.Rd: R6Class
  LabelEncoder.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  level_pairs.Rd: tibble
  new_pairwise_tbl.Rd: tibble
  row_blank.Rd: tibble_row
  row_error.Rd: tibble_row
  row_term.Rd: tibble_row
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ANOVA_exact.Rd: aov_car, emmeans
  emmeans_power.Rd: aov_car, emmeans
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) getFittedProbs.Rd:6-8: Lost braces
     6 | getFittedValues <- function(object) {
       |                                     ^
checkRd: (-1) getFittedProbs.Rd:14-16: Lost braces
    14 | getFittedValues <- function(object) {
       |                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  surrosurv.Rd: optimx
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  survexp_plot.Rd: plot.survfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  svycoplot.Rd: xyplot
  svycoxph.Rd: coxph, predict.coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
possible bashism in configure.ac line 72 (should be 'b = a'):
  if test x"${PKGCONFIG}" == x"yes"; then
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘make.surv.R’ ‘plot_tranformed_km.R’ ‘utils_make_surv.R’
    ‘utils_plot_survHE.R’
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  forest_plot.Rd: draw_label
  forest_plot_grid.Rd: plot_grid
  kaplan_meier_grid.Rd: ggsurvplot, save_pdf, marrangeGrob
  kaplan_meier_plot.Rd: ggsurvplot, save_pdf
  pluck_multivariate_analysis.Rd: coxph
  pluck_survival_analysis.Rd: survfit, survdiff, coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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)}
       |                                                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  predict.coxph_mpl.Rd: predict.coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hybridFit.Rd: quadprog, ipop, nearPD
  regFit.Rd: quadprog, ipop, nearPD
  survivalsvm.Rd: quadprog, ipop, nearPD, Surv
  vanbelle1Fit.Rd: quadprog, ipop, nearPD
  vanbelle2Fit.Rd: quadprog, ipop, nearPD
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘add.R’ ‘filters.R’ ‘get.R’ ‘helpers.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘scoreFull.R’ ‘scoreHalf.R’ ‘scoreLVCF.R’ ‘scoreNVCF.R’
checkRd: (-1) sf.Rd:66: Lost braces; missing escapes or markup?
    66 | A {data.table} which is stored as an attribute of
       |   ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘survival_class.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ConvertWeibull.Rd: survreg
  NormalMeanDiffCens.Rd: Surv
  ParamSampleCens.Rd: Surv
  SurvRegCens.Rd: Surv, survreg
  WeibullDiag.Rd: Surv, plot.survfit
  WeibullReg.Rd: survreg, Surv
  censorContVar.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
       |                                                        ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘suso_gql_helpers.R’ ‘suso_gql_uploadMap.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.sValues.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  stability.Rd: VAR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  svDialogstcltk-package.Rd: dlg_message, dlg_input, dlg_list,
    dlg_open, dlg_save, dlg_dir
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
       |                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  svy_vglm.Rd: vglm, svydesign, svrepdesign
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}
       |                                                                                      ^
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.
       |                                                                                                                                                                                                                                                                                                                                                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sw_sweep.Rd: tk_make_future_timeseries
  tidiers_bats.Rd: bats, tbats
  tidiers_ets.Rd: ets
  tidiers_nnetar.Rd: nnetar
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  import_local_nut.Rd: rem_reps, all_params, all_params_dtrng,
    single_param
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
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}.}
       |                                                                                                   ^
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
       |                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cor.matrix.Rd: mantel, mantel.partial, procrustes
  matrix.x.Rd: gowdis
  optimal.Rd: gowdis
  permut.vector.Rd: shuffleSet
  procrustes.syncsa.Rd: procrustes
  rao.diversity.Rd: gowdis
  syncsa.Rd: gowdis, mantel, procrustes, vegdist
  var.type.Rd: gowdis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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")}}/}
       |                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fn.V.Rd: ipop
  synth.Rd: ipop, optimx
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘test.csv’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bordear.Rd: createStyle
  escribirTabla.Rd: createStyle
  tablaxlsx.estilos.set.Rd: createStyle
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tableHTML_output.Rd: uiOutput
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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)")}.}
       |       ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘class_methods.R’ ‘convert.R’ ‘freq.R’ ‘lilypond.R’ ‘lp_render.R’
    ‘midi.R’ ‘modes.R’ ‘notes.R’ ‘plot.R’ ‘scales.R’ ‘sf.R’ ‘snippet.R’
    ‘strings.R’ ‘transpose.R’
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}}]...'.
       |                      ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘fmt_class.R’ ‘jmvtab.b.R’ ‘tab.R’ ‘tab_classes.R’ ‘tab_xl.R’
    ‘utils.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  xyplot.Arima.Rd: xyplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  zoom.Rd: print.trellis, Lattice, xyplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  smoothPalette.Rd: brewer.pal
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘plott.R’ ‘read_cats_csv.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘add_lines.R’ ‘init.R’ ‘plots.R’ ‘report.R’ ‘tokenize.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  medic.Rd: bind
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  IRT.threshold.Rd: IRT.irfprob
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ASTBranch.Rd: R6Class
  ASTFunction.Rd: R6Class
  ASTMultiply.Rd: R6Class
  ASTPlus.Rd: R6Class
  ASTTableFormula.Rd: R6Class
  ASTVariable.Rd: R6Class
  Parser.Rd: R6Class
  Token.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘auth0.R’ ‘config.R’ ‘entra_id.R’ ‘google.R’ ‘utils.R’
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.
       |                                                                                   ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘depreciation_interest.R’ ‘friction_period.R’ ‘nl_med_prices.R’
    ‘nl_pat_fam_prices.R’ ‘nl_ppp.R’ ‘nl_price_index.R’
    ‘nl_prod_oth_prices.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Tagged_table.Rd: data.table
  as.data.table.Mashed_table.Rd: as.data.table, data.table
  as_workbook.Rd: openxlsx
  cmash.Rd: data.table
  write_worksheet.Rd: openxlsx
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘parse_schema.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as_data_frame.Rd: as_tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘format_code.R’
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
       |                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gm_mean_ci.Rd: boot.ci, boot
  mean_ci.Rd: boot.ci, boot
  median_ci.Rd: boot.ci, boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}.}
       |                                                                                                                                                                                                                                                                                                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot1GS.Rd: element_text, +.gg
  plotFit.GS.Rd: +.gg
  plotMultipleGS.Rd: element_text, +.gg
  plotPat.1GS.Rd: element_text, +.gg
  plotSelect.GS.Rd: element_text, +.gg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) windows/tk2reg.Rd:17: Escaped LaTeX specials: \_
checkRd: (-1) windows/tk2reg.Rd:18: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) windows/tk2reg.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) windows/tk2reg.Rd:52: Escaped LaTeX specials: \_ \_
checkRd: (-1) windows/tk2reg.Rd:53: Escaped LaTeX specials: \_ \_
checkRd: (-1) windows/tk2reg.Rd:57: Escaped LaTeX specials: \_ \_
checkRd: (-1) windows/tk2reg.Rd:58: Escaped LaTeX specials: \_ \_
checkRd: (-1) windows/tk2reg.Rd:60: Escaped LaTeX specials: \_
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘tcplCytoPt.R’ ‘tcplFit2.R’ ‘tcplQueryAPI.R’ ‘tcplVarMat.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  targetDiagram.Rd: xyplot, panel.xyplot, simpleTheme, ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  split_choices.Rd: choices_selected
  template_coxreg_m.Rd: control_coxreg
  template_coxreg_u.Rd: control_coxreg
  tm_t_tte.Rd: data_extract_spec, coxph_pairwise, surv_timepoint,
    surv_time
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running examples in ‘teal.modules.general-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tm_a_pca
> ### Title: 'teal' module: Principal component analysis
> ### Aliases: tm_a_pca
> 
> ### ** Examples
> 
> library(teal.widgets)
> 
> # general data example
> data <- teal_data()
> data <- within(data, {
+   require(nestcolor)
+   USArrests <- USArrests
+ })
> 
> datanames(data) <- "USArrests"
Warning: `datanames<-()` was deprecated in teal.data 0.7.0.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
  `teal_data`. See ?names.teal_data
> 
> app <- init(
+   data = data,
+   modules = modules(
+     tm_a_pca(
+       "PCA",
+       dat = data_extract_spec(
+         dataname = "USArrests",
+         select = select_spec(
+           choices = variable_choices(
+             data = data[["USArrests"]], c("Murder", "Assault", "UrbanPop", "Rape")
+           ),
+           selected = c("Murder", "Assault"),
+           multiple = TRUE
+         ),
+         filter = NULL
+       ),
+       ggplot2_args = ggplot2_args(
+         labs = list(subtitle = "Plot generated by PCA Module")
+       )
+     )
+   )
+ )
[INFO] 2025-02-21 06:29:44.7362 pid:492421 token:[] teal.modules.general Initializing tm_a_pca
Error in as.list(data@env) : 
  no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
add_facet_labels 4.191  0.173   5.502
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  TealReportCard.Rd: ReportCard
  init.Rd: teal_data
  module_teal_with_splash.Rd: teal_data
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running examples in ‘teal-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: example_module
> ### Title: An example 'teal' module
> ### Aliases: example_module
> 
> ### ** Examples
> 
> app <- init(
+   data = teal_data(IRIS = iris, MTCARS = mtcars),
+   modules = example_module()
+ )
Error in as.list(data@env) : 
  no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘adding-support-for-reporting.Rmd’ using rmarkdown

Quitting from lines 106-112 [unnamed-chunk-4] (adding-support-for-reporting.Rmd)
Error: processing vignette 'adding-support-for-reporting.Rmd' failed with diagnostics:
no slot of name "env" for this object of class "teal_data"
--- failed re-building ‘adding-support-for-reporting.Rmd’

--- re-building ‘bootstrap-themes-in-teal.Rmd’ using rmarkdown
--- finished re-building ‘bootstrap-themes-in-teal.Rmd’

--- re-building ‘creating-custom-modules.Rmd’ using rmarkdown

Quitting from lines 174-183 [unnamed-chunk-4] (creating-custom-modules.Rmd)
Error: processing vignette 'creating-custom-modules.Rmd' failed with diagnostics:
no slot of name "env" for this object of class "teal_data"
--- failed re-building ‘creating-custom-modules.Rmd’

--- re-building ‘data-as-shiny-module.Rmd’ using rmarkdown
--- finished re-building ‘data-as-shiny-module.Rmd’

--- re-building ‘filter-panel.Rmd’ using rmarkdown
--- finished re-building ‘filter-panel.Rmd’

--- re-building ‘getting-started-with-teal.Rmd’ using rmarkdown

Quitting from lines 33-52 [unnamed-chunk-1] (getting-started-with-teal.Rmd)
Error: processing vignette 'getting-started-with-teal.Rmd' failed with diagnostics:
no slot of name "env" for this object of class "teal_data"
--- failed re-building ‘getting-started-with-teal.Rmd’

--- re-building ‘including-data-in-teal-applications.Rmd’ using rmarkdown
--- finished re-building ‘including-data-in-teal-applications.Rmd’

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

SUMMARY: processing the following files failed:
  ‘adding-support-for-reporting.Rmd’ ‘creating-custom-modules.Rmd’
  ‘getting-started-with-teal.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  action_card.Rd: R6Class
  card_section.Rd: R6Class
  connector_card.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Bot.Rd: R6Class
  CallbackQueryHandler.Rd: R6Class
  CommandHandler.Rd: R6Class
  Dispatcher.Rd: R6Class
  ErrorHandler.Rd: R6Class
  Handler.Rd: R6Class
  MessageHandler.Rd: R6Class
  TelegramObject.Rd: R6Class
  Update.Rd: R6Class
  Updater.Rd: R6Class
  Webhook.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  TGBot.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Tendril.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  parse_arguments.Rd: yaml.load
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Error(s) in re-building vignettes:
  ...
--- re-building ‘tern-rbmi.Rmd’ using rmarkdown
0,248,Js_of_ocaml__Js.Error,18,TypeError: not a function

Quitting from lines 164-172 [unnamed-chunk-7] (tern-rbmi.Rmd)
Error: processing vignette 'tern-rbmi.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘tern-rbmi.Rmd’

SUMMARY: processing the following file failed:
  ‘tern-rbmi.Rmd’

Error: Vignette re-building failed.
Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘incidence_rate.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tcolour.Rd: dichromat
  tpalette.Rd: dichromat
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘georeference_overlay.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_spatial_rgb.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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])}}
       |                                                                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cettiidae.Rd: read.tree, ape
  conifers.Rd: read.tree, ape
  mammalia.Rd: read.tree, ape
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) lognormConstCVCI.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lognormConstCVCI.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lognormConstCVCI.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  chk-defunct.Rd: dplyr_tidy_select
  expect-defunct.Rd: dplyr_tidy_select
  output_results_excel.Rd: test_dir, test_file
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘testthat/libs/testthat.so’:
  Found non-API calls to R: ‘SET_BODY’, ‘SET_CLOENV’, ‘SET_FORMALS’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
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.}
       |  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  TExPosition-package.Rd: ExPosition
  tepBADA.Rd: expo.scale, epGPCA, corePCA, epPCA, epMDS
  tepDICA.Rd: epCA, coreCA, epMCA
  tepGPLS.Rd: epPCA, epGPCA, expo.scale, corePCA
  tepGraphs.Rd: prettyGraphs, createColorVectorsByDesign, prettyPlot
  tepPLS.Rd: expo.scale, epGPCA, corePCA, epPCA
  tepPLSCA.Rd: epCA, coreCA, epMCA
  texpoDesignCheck.Rd: designCheck
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘utils-perm.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_sdg.Rd: color
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tts_speak_engine.Rd: knit_engines
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BNS.Rd: R6Class
  Collocations.Rd: R6Class
  LatentDirichletAllocation.Rd: R6Class
  LatentSemanticAnalysis.Rd: R6Class
  RelaxedWordMoversDistance.Rd: R6Class
  TfIdf.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}.}
       |                                              ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘nlp_build_chunks.R’ ‘sem_search_corpus.R’
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘textra.R’
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}{
       |                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  feature_columns.Rd: tidyselect
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addDate.Rd: tfExpand
  tfplot.Rd: tfprint, tframe, tframed
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
       |                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  initializer_blockwise.Rd: initializer_constant
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘mock_tbl.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  flags.Rd: yaml.load
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) predict.tfunHDDC.Rd:31-39: Lost braces
    31 | The teigen family. Stat Comput 22:1021{1029. <doi.org/10.1007/
       |                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tfunHDDC.Rd: tkmeans
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tggd.Rd: gamma_inc
  tggd_ln.Rd: gamma_inc
  tggd_log.Rd: gamma_inc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  thaipdf_document.Rd: pdf_document
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
'library' or 'require' calls not declared from:
  ‘dplyr’ ‘openxlsx’ ‘plyr’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ego.Rd: cluster_fast_greedy
  graphjs.Rd: igraph, layout_with_fr, igraph.plotting
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3dimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Reaper-class.Rd: distanceMatrix, PCDimension
  SimThresher-class.Rd: AuerGervini
  Thresher-class.Rd: distanceMatrix, AuerGervini, PCDimension,
    AuerGervini-class
  matchLabels.Rd: distanceMatrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  TBinaryProtocol.Rd: R6Class
  TBinaryProtocolFactory.Rd: R6Class
  TBufferedTransport.Rd: R6Class
  TBufferedTransportFactory.Rd: R6Class
  TClient.Rd: R6Class
  TMemoryBuffer.Rd: R6Class
  TPayload.Rd: R6Class
  TServerSocket.Rd: R6Class
  TSocket.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  deprecated.Rd: quasiquotation
  formatting.Rd: tbl_format_setup
  frame_matrix.Rd: !!, !!!, quasiquotation
  lst.Rd: !!, !!!, .data, .env
  subsetting.Rd: vec_slice
  tibble.Rd: !!, !!!, .data, .env, quasiquotation
  tribble.Rd: !!, !!!, quasiquotation
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘tibble/libs/tibble.so’:
  Found non-API call to R: ‘SET_S4_OBJECT’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  guess_tspec.Rd: abort
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘tibblify/libs/tibblify.so’:
  Found non-API calls to R: ‘FRAME’, ‘HASHTAB’, ‘PRENV’, ‘PRVALUE’,
    ‘R_PromiseExpr’, ‘Rf_findVarInFrame3’, ‘SETLENGTH’, ‘SET_BODY’,
    ‘SET_CLOENV’, ‘SET_FORMALS’, ‘SET_GROWABLE_BIT’, ‘SET_TRUELENGTH’,
    ‘STRING_PTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  design_gray.Rd: ggplot2
  design_grey.Rd: ggplot2
  design_lmu.Rd: ggplot2
  new_tdcmm.Rd: tibble
  visualize.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tidy_inverse_normal.Rd: rinvgauss
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘explain_methods.R’ ‘fit.gets.R’ ‘fit.group_lasso.R’ ‘m.R’
    ‘post_process.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘import_fst_chunked.R’ ‘pkg_load.R’ ‘round0.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘functions_chr_int.R’ ‘gate_app.R’ ‘methods.R’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  predict.SL.glmnet.interaction.Rd: SL.glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘checks.R’ ‘compute-indexes.R’ ‘dimension-reduction.R’
    ‘distribution-fit.R’ ‘drought-indexes.R’ ‘init.R’ ‘normalise.R’
    ‘rescaling.R’ ‘swap-values.R’ ‘temporal-aggregation.R’
    ‘variable-transformation.R’
'::' or ':::' imports not declared from:
  ‘here’ ‘janitor’ ‘ozmaps’ ‘readxl’ ‘rmapshaper’ ‘sf’ ‘tibble’
'library' or 'require' calls not declared from:
  ‘GGally’ ‘ozmaps’ ‘tidyverse’
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                    ^
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                           ^
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                                          ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
checkRd: (-1) single_imputation.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) single_imputation.Rd:23-27: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.mc.Rd: ggplot2
  plot.summary.mc.Rd: ggplot2
  tidy_mc_latex.Rd: kableExtra
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘tidymodl.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘tidy_plate.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘answer_as_key_value.R’ ‘answer_as_named_list.R’ ‘answer_as_text.R’
    ‘answer_using_sql.R’ ‘answer_using_tools.R’ ‘chat_history.R’
    ‘internal_extraction.R’ ‘internal_request_llm_provider.R’
    ‘internal_test_helpers.R’ ‘llm_providers.R’ ‘misc_llm_verify.R’
    ‘persistent_chat.R’ ‘send_prompt.R’ ‘tidyprompt.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘import_instruments.R’ ‘make_choose_all_table.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  group_by.Rd: group_by_drop_default
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  add_paths.Rd: lavaan
  mixture_starts.Rd: mxData
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘describe_data.r’ ‘helper_functions.r’ ‘tidy_stats.R’
    ‘tidy_stats.afex.r’ ‘tidy_stats.brmsfit.r’ ‘tidy_stats.emmeans.R’
    ‘tidy_stats.irr.r’ ‘tidy_stats.lavaan.r’ ‘tidy_stats.lmerMod.r’
    ‘tidy_stats.nlme.r’ ‘tidy_stats.psych.r’ ‘tidy_stats.tidystats.r’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cast_sparse.Rd: sparseMatrix
  document_term_casters.Rd: sparseMatrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  are_true.Rd: as_logical
  categorical_test_by.Rd: map_dfr
  count_by.Rd: count
  first_non_nas_at.Rd: select
  first_which_non_na_at.Rd: select
  format_numbers_at.Rd: mutate_at
  format_p_values_at.Rd: mutate_at
  lump_rows.Rd: summarise
  order_factor_by.Rd: fct_reorder
  pluck_vector.Rd: pluck, simplify
  rename_factor.Rd: fct_recode, fct_relevel
  rename_reorder_factor.Rd: fct_recode, fct_relevel
  with_name.Rd: pluck, str_detect
  with_value_containing.Rd: pluck, str_detect
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘tw_search.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  barchartGC.Rd: barchart
  theme.rpres.Rd: trellis.par.set, show.settings
  themerpres.Rd: trellis.par.set, show.settings
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
possible bashism in configure.ac line 138 (test -a/-o):
  if test ! -z "${with_tiledb}" -a x"${enable_building}" = x"yes"; then
  possible bashism in configure.ac line 151 (test -a/-o):
  if test ! -z "${with_tiledb}" -a x"${with_download}" = x"yes"; then
  possible bashism in configure.ac line 257 (test -a/-o):
          if test x"${machine}" = x"x86_64" && test x"${uname}" = x"Linux" -o x"${uname}" = x"Darwin"; then
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
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}
       |                ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘geom_weekly_timeslots.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_weekly_timeslots.Rd: layer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  parse_date2.Rd: anytime, anydate
  step_box_cox.Rd: selections
  step_diff.Rd: step_naomit, selections
  step_log_interval.Rd: selections
  step_ts_clean.Rd: selections
  step_ts_impute.Rd: selections
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}.
       |                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tintHtml.Rd: pdf_document, html_document
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘base-lenses.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  theme_ipsum_rc.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.}
       |                                           ^
checkRd: (-1) tierChart.Rd:332: Lost braces
   332 |   If the input argument code{boxes} is \code{F}, the \code{lBox},
       |                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_taxa_ridges.Rd: scale_fill_gradient, theme_ridges,
    geom_density_ridges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Unknown package ‘RClickhouse’ in Rd xrefs
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.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Tlasso.fit.Rd: huge
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) pmvn.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvn.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvn.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:25: Lost braces in \itemize; meant \describe ?
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.
       |                                                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tmle.Sl.dbarts2.Rd: SuperLearner
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AlcesteSource.Rd: meta, getSources
  readAlceste.Rd: getReaders
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EuropresseSource.Rd: getSources
  readEuropresse.Rd: getReaders
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FactivaSource.Rd: getSources
  readFactiva.Rd: getReaders
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LexisNexisSource.Rd: getSources
  readLexisNexis.Rd: getReaders
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gmm.tmvnorm.Rd: gmm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' call not declared from: ‘rgl’
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘position_diverge.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘Get_time_entries.R’
checkRd: (-1) jsonStr.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Format data as a JSON object (like this: {"x": "120"}).}
       |                                                 ^
checkRd: (-1) jsonStr.Rd:18: Lost braces; missing escapes or markup?
    18 | Format data as a JSON object (like this: {"x": "120"}).
       |                                          ^
checkRd: (-1) fixed_width_no_modeling.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:17: Lost braces in \itemize; meant \describe ?
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 required but not available: ‘qpgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘dat_checks.R’ ‘setters_and_getters.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LDAprep.Rd: lda
  plotTopic.Rd: top.topic.words
  plotTopicWord.Rd: top.topic.words
  plotWordSub.Rd: top.topic.words
  plotWordpt.Rd: top.topic.words
  readWiki.Rd: WikipediR, pages_in_category
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘response_builder.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  TPACForCancer.Rd: hpa.data
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘replace_leading_whitespace.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  heartTP.Rd: heart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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{
       |         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Wprime.Rd: foreach
  read_directory.Rd: foreach
  smoother_control.trackeRdata.Rd: foreach
  zones.Rd: foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  printLabelledValues.Rd: setOutputLevel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Sim-Functions.Rd:99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:100-102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:109-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:111-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:114-116: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Sim-Functions.Rd: Logit-class, CES-class
  cournot_tariff.Rd: Cournot-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘predict.R’ ‘train.R’ ‘variables.R’
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
'::' or ':::' import not declared from: ‘devtools’
'library' or 'require' calls not declared from:
  ‘XML’ ‘devtools’ ‘jsonlite’ ‘ks’ ‘maps’
'::' or ':::' imports not declared from:
  ‘eha’ ‘flexsurv’ ‘frailtyEM’ ‘frailtypack’ ‘gamlss.cens’ ‘icenReg’
  ‘mpr’ ‘rms’ ‘rstpm2’ ‘timereg’
'library' or 'require' calls not declared from:
  ‘cotram’ ‘gamlss.cens’ ‘latex2exp’ ‘mpr’ ‘tramvs’
'data(package=)' calls not declared from:
  ‘AER’ ‘KONPsurv’ ‘gamlss.data’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  translate.logit.Rd: multinom
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) trtsel.Rd:69: Lost braces; missing escapes or markup?
    69 | numeric with two values {0,1} and gaussian(link = "identity") otherwise.
       |                         ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘tree_mesh.R’ ‘zzz.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rpart.predict.leaves.Rd: rpart
  treeClust.Rd: rpart.control
  treeClust.dist.Rd: daisy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘TreeMineR.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AdditionTree.Rd: ImposeConstraint
  AllSPR.Rd: phylo
  CharacterLength.Rd: phylo
  ConcordantInformation.Rd: phylo
  Consistency.Rd: phylo
  DoubleNNI.Rd: phylo
  JackLabels.Rd: phylo
  Jackknife.Rd: phylo
  MaximizeParsimony.Rd: phylo, ImposeConstraint
  MorphyTreeLength.Rd: RenumberTips, phylo
  NNI.Rd: phylo
  PlotCharacter.Rd: phylo
  Ratchet.Rd: phylo
  RearrangeEdges.Rd: phylo
  SPR.Rd: phylo
  SiteConcordance.Rd: phylo
  StopUnlessBifurcating.Rd: phylo
  SuccessiveApproximations.Rd: phylo
  TBR.Rd: phylo
  TBRWarning.Rd: phylo
  TaxonInfluence.Rd: ClusteringInfoDistance, write.nexus, path_sanitize
  TreeSearch.Rd: phylo
  cSPR.Rd: phylo
  dot-NonDuplicateRoot.Rd: phylo
  inapplicable.datasets.Rd: read.nexus.data
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotGroves.Rd: s.class
  plotGrovesD3.Rd: scatterD3
  plotTreeDiff.Rd: plot.phylo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calculate_mae.Rd: trending_model
  calculate_rmse.Rd: trending_model
  calculate_rsq.Rd: trending_model
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  check.decomp.Rd: Rssa
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Triact.Rd: fread, floor_date
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.
       |             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  TriDimRegression-package.Rd: loo, waic
  waic.tridim_transformation.Rd: loo-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  balance.plot.Rd: theme
  covariateBalance.Rd: cv.bal.psa
  loess3.plot.Rd: geom_point, geom_jitter, scale_colour_brewer,
    geom_smooth, stat_smooth
  multibalance.plot.Rd: cv.bal.psa
  summary.triangle.matches.Rd: ezANOVA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘get_troopdata.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘get_item_metadata.R’ ‘get_subscribed_metadata.R’
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{" "}}
       |                                                                                            ^
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [128s/40s]
Running R code in ‘testthat.R’ had CPU time 3.2 times elapsed time
checkRd: (-1) tsBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diss.AR.LPC.CEPS.Rd:39: Lost braces; missing escapes or markup?
    39 | If \code{order.x} or {order.y} are \code{NULL}, their respective series will be fitted automatically using a AR model.
       |                      ^
checkRd: (-1) diss.AR.PIC.Rd:31: Lost braces; missing escapes or markup?
    31 | If \code{order.x} or {order.y} are \code{NULL}, their respective series will be fitted automatically using a AR model. If \code{permissive} is \code{TRUE} and no AR order is found automatically, an AR order of 1 will be imposed, if this case fails, then no order can be found and the function produces an error.
       |                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  diss.DTWARP.Rd: pdc
  diss.FRECHET.Rd: longitudinalData
  diss.PDC.Rd: pdc
  diss.Rd: pdc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘calc_distance.R’ ‘reason_dataleaks.R’ ‘viz_dataleaks.R’
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘benchmark.R’ ‘print.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  density.Rd: networkDynamic
  durations.Rd: net.obs.period, as.data.frame.networkDynamic,
    get.vertex.activity
  incidence.Rd: networkDynamic
  plotpath.Rd: plot.network
  tDegree.Rd: networkDynamic
  tErgmStats.Rd: networkDynamic, network.collapse
  tSnaStats.Rd: network.collapse
  tiedDuration.Rd: networkDynamic
  timeProjectedNetwork.Rd: networkDynamic, network.collapse,
    get.networks, network
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘centrality.R’ ‘compare_gvar.R’ ‘posterior_plot.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ts_maintune.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  arimapar-deprecated.Rd: auto.arima
  arimapred.Rd: auto.arima
  fittestArima.Rd: auto.arima, forecast
  fittestArimaKF.Rd: predict.SSModel, SSMarima, KFAS, auto.arima,
    SSModel, AICc
  fittestEMD.Rd: AICc
  fittestLM.Rd: AICc
  fittestMAS.Rd: ets, stlf, AICc
  fittestPolyR.Rd: dredge, AICc
  fittestPolyRKF.Rd: SSModel, KFAS, fitSSM, AICc
  fittestWavelet.Rd: ets, AICc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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.
       |                                                          ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘berkowitz.R’ ‘dac.R’ ‘gmm.R’ ‘hongli.R’ ‘minzar.R’ ‘nyblom.R’
    ‘shortfall_de.R’ ‘signbias.R’ ‘var.R’ ‘var_cp.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FULLoption.Rd: impute, local.trend, mannKen, seasonTrend, seaKen
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotmatch.Rd: ppp
  sumppdist.Rd: ppp, solist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  treetable.Rd: datatable, data.tree
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ttScreening-package.Rd: sva
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  yt_oauth.Rd: oauth2.0_token
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  list_captions.Rd: GET
  upload_caption.Rd: POST
  upload_video.Rd: POST
  yt_oauth.Rd: oauth2.0_token
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tufte_handout.Rd: pdf_document, html_document
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  xtable.TukeyC.Rd: xtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running examples in ‘TukeyC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TukeyC
> ### Title: The TukeyC Test for Single Experiments
> ### Aliases: TukeyC TukeyC.default TukeyC.lm TukeyC.formula TukeyC.aovlist
> ###   TukeyC.lmerMod
> ### Keywords: package
> 
> ### ** Examples
> 
> ##
> ## Examples:Randomized Complete Block Design (RCBD)
> ## More details: demo(package='TukeyC')
> ##
> 
> ## The parameters can be: formula, aov, lm, aovlist and lmerMod
> 
> data(RCBD)
> 
> ## From: formula
> tk1 <- with(RCBD,
+             TukeyC(y ~ blk + tra,
+                    data=dfm,
+                    which='tra'))
Error in data.frame(means = aux_mt1, reps = reps) : 
  arguments imply differing number of rows: 0, 5
Calls: with ... TukeyC.formula -> TukeyC -> TukeyC.lm -> data.frame
Execution halted
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  TukeyRegion-package.Rd: depth.halfspace, ddalpha
  depth.wm.Rd: depth.halfspace, ddalpha
  plot.TukeyRegion.Rd: rgl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  turboSim.Rd: foreach
  turboem.Rd: foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘show_parliament.R’ ‘show_province_and_party.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coef.mtvgarch.Rd: zoo, garchx
  coef.tvgarch.Rd: zoo
  coef.tvgarchTest.Rd: zoo
  mtvgarch.Rd: zoo, garchx
  mtvgarchSim.Rd: zoo, garchx
  tvgarch.Rd: zoo, garchx
  tvgarchObj.Rd: zoo
  tvgarchSim.Rd: zoo, garchx
  tvgarchTest.Rd: zoo, garchx
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dx.wts.mediation.Rd: ps
  wgtmed.Rd: gbm, ps, twang
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.ps.xgb.Rd: ggplot
  ps.xgb.Rd: xgboost
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) tweedie-internal.Rd:74: Lost braces
    74 |         doi{10.1093/biomet/74.2.221}
       |            ^
checkRd: (-1) fit_stm.Rd:25: Lost braces
    25 | \item{xcov}{Either a \[stats]{formula} with an empty left-hand side specifying external covariates
       |                              ^
checkRd: (-1) twosigmag.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Ts.estim.Rd: coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |     ^
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |                                  ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |  ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |               ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |                                ^
File ‘typetracer/libs/typetracer.so’:
  Found non-API call to R: ‘SET_BODY’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
possible bashism in configure.ac line 34 (should be 'b = a'):
  dnl if test "${ac_cv_lib_expat_XML_ParserCreate}" == yes; then
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  associationsDiamondPlot.Rd: ggplot
  basicDiamondplotFunctions.Rd: geom_polygon, geom_jitter, ggplot
  biAxisDiamondPlot.Rd: ggplot
  comparisonDiamondPlots.Rd: gtable
  diamondPlot.Rd: ggplot
  ggBoxplot.Rd: ggplot, geom_boxplot
  ggEasyPlots.Rd: ggplot, geom_ridgeline, geom_bar
  ggProportionPlot.Rd: linetype, ggplot2
  ggqq.Rd: ggplot
  knitFig.Rd: ggplot, knit_expand, knit
  meanSDtoDiamondPlot.Rd: ggplot
  meansDiamondPlot.Rd: ggplot
  pwr.omegasq.Rd: pwr.anova.test, pwr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  html_imetropolis.Rd: html_document
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    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.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘readtextgrid.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘annotate_mf.R’ ‘annotate_mf_all.R’
checkRd: (-1) reg_1d.Rd:42: Lost braces; missing escapes or markup?
    42 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
checkRd: (-1) reg_2d.Rd:33: Lost braces; missing escapes or markup?
    33 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
checkRd: (-1) simRedCard.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simRedCard.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  all_eq.Rd: diffObj
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
possible bashism in configure.ac line 48 (should be 'b = a'):
  if test "${ac_cv_lib_expat_XML_ParserCreate}" == yes; then
'library' or 'require' call not declared from: ‘rvest’
checkRd: (-1) mllogitnorm.Rd:45: Lost braces
    45 | link[dlogitnorm]{dlogitnorm}for the normal density.
       |                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mlpower.Rd: Pareto
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘unm_summary.R’
checkRd: (-1) UNPaC_Copula.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}
       |                                  ^
checkRd: (-1) UNPaC_Copula.Rd:60: Lost braces; missing escapes or markup?
    60 | \item{\code{sim_CI}}: {vector containing the cluster indices for each generated unimodal reference distribution}
       |                       ^
checkRd: (-1) UNPaC_Copula.Rd:61-62: Lost braces
    61 | \item{\code{pvalue_emp}}: {the empirical p-value:  the proportion of times the cluster index from the reference
       |                           ^
checkRd: (-1) UNPaC_Copula.Rd:63: Lost braces; missing escapes or markup?
    63 | \item{\code{pvalue_norm}}: {the normalized p-value: the simulated p-value based on comparison to a standard normal distribution }
       |                            ^
checkRd: (-1) UNPaC_num_clust.Rd:58-62: Lost braces
    58 | \item{\code{BestK}}: {A matrix with 1 row and 4 columns named: "Max_CI","Max_CI_wi_1SE","Max_scaled_CI" and "Max_logWCSS_wi_1SE".
       |                      ^
checkRd: (-1) UNPaC_num_clust.Rd:63-65: Lost braces
    63 | \item{\code{full_process}}: {A matrix containing the number of clusters, K, evaluated, the CI from the data, the average CI from the null
       |                             ^
checkRd: (-1) UNPaC_num_clust.Rd:66: Lost braces; missing escapes or markup?
    66 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}}
       |                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  unsys.station.test.Rd: foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘available_version.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  UpDown.Rd: normalmixEM, mclust
  UpDownApp.Rd: shiny, ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  barplot_hp.Rd: rdacca.hp
  upset_vp.Rd: rdacca.hp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) encoder.Rd:32-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) encoder.Rd:38-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) encoder.Rd:45-48: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘intersection_powerset.R’ ‘pr.R’
checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) arctic.oscillations.Rd:19: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) arctic.oscillations.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) babies.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:43: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) exec.pay.Rd:5: Escaped LaTeX specials: \$
checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) sp500.excess.Rd:6: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  usl.Rd: nlxb, nlsr
  usl.solve.nlxb.Rd: nlxb
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘paste.R’
checkRd: (-1) partition_fold.Rd:21-22: Lost braces
    21 |    \code{train}{The mldr dataset with train examples, that includes all
       |                ^
checkRd: (-1) partition_fold.Rd:23-24: Lost braces
    23 |    \code{test}{The mldr dataset with test examples, defined by the
       |               ^
checkRd: (-1) partition_fold.Rd:25-26: Lost braces
    25 |    \code{validation}{Optionally, only if \code{has.validation = TRUE}.
       |                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  utiml.Rd: mldr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate_accuracy.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘benchmark_event.R’ ‘benchmark_score.R’ ‘benchmark_time.R’
    ‘compare_means_between_groups.R’ ‘compare_means_within_groups.R’
    ‘compare_rates_between_groups.R’ ‘compare_rates_within_groups.R’
    ‘get_concordant_discordant_pairs.R’
    ‘get_confidence_intervals_within_groups.R’
    ‘table_observed_expected.R’ ‘test_chisq_one.R’ ‘test_mcnemar.R’
    ‘test_n_1_prop.R’ ‘test_t.R’ ‘test_t_paired.R’
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  detect_boundary_cat.Rd: validator
  detect_boundary_num.Rd: validator
  detect_fixed_variables.Rd: validator
  detect_infeasible_rules.Rd: validator
  detect_redundancy.Rd: validator
  is_contradicted_by.Rd: validator
  is_implied_by.Rd: validator
  is_linear.Rd: validator
  make_feasible.Rd: validator
  remove_redundancy.Rd: validator
  simplify_conditional.Rd: validator
  simplify_fixed_variables.Rd: validator
  simplify_rules.Rd: validator
  validatetools.Rd: validate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  valorate.risk.Rd: coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ControlResponseBias.Rd: lavaan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘datasets.R’
possible bashism in configure.ac line 72 (test -a/-o):
      if test [$RVER_MAJOR -lt 3] -o [$RVER_MAJOR -eq 3 -a $RVER_MINOR -lt 3]; then
checkRd: (-1) sample_gen.Rd:18: Lost braces; missing escapes or markup?
    18 | Generate \code{n} random samples from multivariate Gaussian distribution N(0, (L^TL)^{-1})
       |                                                                                      ^
checkRd: (-1) vardannual.Rd:97: Lost braces
    97 | \item{ID_level2}{Optional}{variable for unit ID codes. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                           ^
checkRd: (-1) vardannual.Rd:99: Lost braces
    99 | \item{dataset}{Optional}{survey data object convertible to \code{data.table}.}
       |                         ^
checkRd: (-1) vardcrospoor.Rd:122: Lost braces
   122 | \item{ind_gr}{Optional}{variable by which divided independently X matrix of the auxiliary variables for the calibration. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                        ^
checkRd: (-1) vardcrospoor.Rd:124: Lost braces
   124 | \item{use.estVar}{Logical}{value. If value is \code{TRUE}, then \code{R} function \code{estVar} is used for the  estimation of covariance matrix of the residuals. If value is \code{FALSE}, then \code{R} function \code{estVar} is not used for the estimation of covariance matrix of the residuals.}
       |                           ^
checkRd: (-1) vardom_othstr.Rd:69: Lost braces
    69 | \item{percentratio}{Positive}{numeric value. All linearized variables are multiplied with \code{percentratio} value, by default - 1.}
       |                              ^
checkRd: (-1) varpoord.Rd:121: Lost braces
   121 | \item{month_at_work}{Variable}{for total number of month at work (sum of the number of months spent at full-time work as employee, number of months spent at part-time work as employee, number of months spent at full-time work as self-employed (including family worker), number of months spent at part-time work as self-employed (including family worker)).  One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                               ^
checkRd: (-1) betaburr.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Burr distribution due to Parana\'{i}ba et al. (2011) given by
       |                                                                                                                        ^
checkRd: (-1) betafrechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Fr\'{e}chet distribution due to Barreto-Souza et al. (2011) given by
       |                                                                                           ^
checkRd: (-1) frechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                      ^
checkRd: (-1) frechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                                                      ^
checkRd: (-1) kumburr7.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Kumaraswamy Burr XII distribution due to Parana\'{i}ba et al. (2013) given by
       |                                                                                                                                   ^
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.}
       |                                                                                             ^
checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) Acoef_sh.Rd:23: Lost braces; missing escapes or markup?
    23 | The function returns the K-by-K matrices {A_1, ..., A_p} as a list object.
       |                                          ^
checkRd: (-1) VARshrink.Rd:58: Lost braces; missing escapes or markup?
    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                    ^
checkRd: (-1) VARshrink.Rd:58: Lost braces; missing escapes or markup?
    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                                        ^
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
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘vineCopulas.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BB1Copula-class.Rd: VineCopula-package, joeCopula-class
  BB1Copula.Rd: joeCopula, VineCopula-package
  BB6Copula-class.Rd: VineCopula-package, joeCopula-class
  BB6Copula.Rd: joeCopula, VineCopula-package
  BB7Copula-class.Rd: VineCopula-package, joeCopula-class
  BB7Copula.Rd: joeCopula, VineCopula-package
  BB8Copula-class.Rd: VineCopula-package, joeCopula-class
  BB8Copula.Rd: joeCopula, VineCopula-package
  BiCop2copula.Rd: copula-class, VineCopula-package, BiCop
  ddCopula.Rd: dCopula, pCopula
  joeBiCopula-class.Rd: VineCopula-package, copula-package,
    joeCopula-class
  joeBiCopula.Rd: copula-package, joeCopula-class, VineCopula-package
  surClaytonCopula-class.Rd: VineCopula-package
  surClaytonCopula.Rd: VineCopula-package
  surGumbelCopula-class.Rd: VineCopula-package
  surGumbelCopula.Rd: VineCopula-package
  tawnT1Copula-class.Rd: VineCopula-package
  tawnT1Copula.Rd: VineCopula-package
  tawnT2Copula-class.Rd: VineCopula-package
  tawnT2Copula.Rd: VineCopula-package
  vineCopula-class.Rd: VineCopula-package, RVineMatrix
  vineCopula.Rd: RVineMatrix, VineCopula-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lmerMatrices.Rd: lmer
  lmerSummary.Rd: lmer
  remlMM.Rd: lmer
  remlVCA.Rd: lmer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) datasets.Rd:15: Lost braces
    15 | and dimension information (\code{dim} or code{length}) of each item,
       |                                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mcaplot.Rd: multilines
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘vctrs/libs/vctrs.so’:
  Found non-API calls to R: ‘FRAME’, ‘HASHTAB’, ‘LEVELS’, ‘PRENV’,
    ‘PRVALUE’, ‘R_PromiseExpr’, ‘Rf_findVarInFrame3’, ‘SETLENGTH’,
    ‘SET_BODY’, ‘SET_CLOENV’, ‘SET_ENCLOS’, ‘SET_FORMALS’,
    ‘SET_GROWABLE_BIT’, ‘SET_S4_OBJECT’, ‘SET_TRUELENGTH’,
    ‘STDVEC_DATAPTR’, ‘STRING_PTR’, ‘TRUELENGTH’, ‘UNSET_S4_OBJECT’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.spv.Rd: stat_binhex, grid.arrange, ggplot
  vdg-package.Rd: theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  applyTransformation.Rd: sp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ordiplot3d.Rd: envfit, ordiplot
  ordirgl.Rd: scores, envfit, cca, decorana
  vegan3d-package.Rd: rgl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  count_taxa.Rd: taxlist-class
  make_cocktail.Rd: taxlist-class
  subset.Rd: taxlist-class
  summary.Rd: taxlist-class
  tv2vegtable.Rd: taxlist-class, read.dbf
  used_synonyms.Rd: get_children, get_parents, taxlist-class,
    accepted_name
  vegtable-class.Rd: taxlist-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'::' or ':::' import not declared from: ‘eixport’
'library' or 'require' calls not declared from:
  ‘ggplot2’ ‘sp’
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 ?
File ‘versus/libs/versus.so’:
  Found non-API call to R: ‘STRING_PTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  blobness3D.Rd: nifti
  gradient3D.Rd: nifti
  hessian3D.Rd: nifti
  vesselness3D.Rd: nifti
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex125.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
File ‘vetr/libs/vetr.so’:
  Found non-API call to R: ‘SET_TYPEOF’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) VirtualArray-single-bracket-method.Rd:6: Lost braces
     6 | \title{Indexing to extract subsets of a 'code{\link[via:XArray-class]{VirtualArray}}'-class object}
       |                                              ^
checkRd: (-1) subset.Rd:20: Lost braces
    20 | \item{drop}{\code{logical} in case the result of subsetting is a single element, should the \\code{\link[via:XArray-class]{VirtualArray}} wrapper be dropped?}
       |                                                                                                   ^
checkRd: (-1) vic_param.Rd:311: Lost braces
   311 | albedo must be supplied in code{forcing_veg}. Default = 1.}
       |                                ^
checkRd: (-1) vic_param.Rd:323: Lost braces
   323 | supplied in code{forcing_veg}. Default = 1.}
       |                 ^
checkRd: (-1) vic_param.Rd:341: Lost braces
   341 | be supplied in code{forcing_veg} Default = 0.}
       |                    ^
checkRd: (-1) show_query.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) show_query.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) show_query.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:16: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘functions_upload.R’ ‘mod_hidecan.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bootstrap_se.Rd: boot
  cv_vim.Rd: boot
  vim.Rd: boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  regressionImp.Rd: lmrob, glmrob
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘knn_domain_score.R’ ‘mars_domain_score.R’ ‘nn_domain_score.R’
    ‘normalized_domain_plot.R’ ‘rf_domain_score.R’ ‘simple_domain_plot.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘glob_cub_vis.R’ ‘glob_knn_vis.R’ ‘glob_nn_vis.R’ ‘viralx_knn.R’
    ‘viralx_knn_glob.R’ ‘viralx_knn_shap.R’ ‘viralx_knn_vis.R’
    ‘viralx_mars.R’ ‘viralx_mars_shap.R’ ‘viralx_mars_vis.R’
    ‘viralx_nn.R’ ‘viralx_nn_glob.R’ ‘viralx_nn_shap.R’ ‘viralx_nn_vis.R’
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 ?
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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 ?
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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.
       |                                                                                                                                                                                                                                                                                                                                                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  parametersCheck.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  virtualspecies-package.Rd: terra, ade4, rnaturalearth
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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) 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
checkRd: (-1) ViSiElse.Rd:101-107: Lost braces in \itemize; meant \describe ?
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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 ?
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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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  visSave.Rd: saveWidget
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘customiseText.R’ ‘datatableInternal.R’ ‘formatEstimateName.R’
    ‘formatEstimateValue.R’ ‘formatHeader.R’ ‘formatTable.R’ ‘fxTable.R’
    ‘gtTable.R’ ‘helperFunctions.R’ ‘mockResults.R’ ‘plot.R’ ‘tidy.R’
    ‘utilities.R’ ‘visOmopTable.R’ ‘visTable.R’
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.}
       |                                   ^
checkRd: (-1) getTurnType.Rd:38: Lost braces; missing escapes or markup?
    38 | Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
       |               ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ctd_cast.Rd: ctdFindProfiles
  vpr_manual_classification.Rd: image_scale
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘vroom/libs/vroom.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’,
    ‘STDVEC_DATAPTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  vscc.Rd: teigen, Mclust
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  vsd.Rd: ggplot2, Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  VSOLassoBag.Rd: coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  VSURF.Rd: randomForest
  VSURF_interp.Rd: randomForest
  VSURF_pred.Rd: randomForest
  VSURF_thres.Rd: randomForest
  predict.VSURF.Rd: randomForest, predict.randomForest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘walkscore.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  warn.Rd: kde2d, width.SJ
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘warp/libs/warp.so’:
  Found non-API calls to R: ‘Rf_findVarInFrame3’, ‘STRING_PTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘flextable.R’
'::' or ':::' import not declared from: ‘NPRED’
'library' or 'require' call not declared from: ‘NPRED’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotParam.Rd: xyplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  waterfallchart.Rd: barchart, bwplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 Rd file(s) with Rd \link{} targets missing package
anchors:
  loess_auto.Rd: loess.as
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  02-util.Rd: xmlParseDoc, igraph
  03-main.Rd: igraph, plot.igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  wcep.Rd: coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  WCE.Rd: coxph.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_wis_raster_layer.Rd: get_map_layer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
       |       ^
checkRd: (-1) busTrace.Rd:15: Lost braces
    15 | /href{https://crawdad.org/coppe-ufrj/RioBuses/20180319/}
       |      ^
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
       |                         ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘WeightIt.Rmd’ using rmarkdown_notangle
--- finished re-building ‘WeightIt.Rmd’

--- re-building ‘estimating-effects.Rmd’ using rmarkdown_notangle

Quitting from lines 398-410 [unnamed-chunk-16] (estimating-effects.Rmd)
Error: processing vignette 'estimating-effects.Rmd' failed with diagnostics:
Assertion failed. One of the following must apply:
 * checkmate::check_character(hypothesis): Must comply to pattern '='
 * checkmate::check_numeric(hypothesis): Must be of type 'numeric', not 'character'
 * checkmate::check_formula(hypothesis): Must be a formula, not character
 * checkmate::check_matrix(hypothesis): Must be of type 'matrix', not 'character'
 * checkmate::check_function(hypothesis): Must be a function, not 'character'
 * checkmate::check_null(hypothesis): Must be NULL
--- failed re-building ‘estimating-effects.Rmd’

--- re-building ‘installing-packages.Rmd’ using rmarkdown_notangle
--- finished re-building ‘installing-packages.Rmd’

SUMMARY: processing the following file failed:
  ‘estimating-effects.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotwtdinteraction.Rd: mice, gam, bam
  wpct.Rd: wtd.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘plot_network.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘coords_from_words.R’ ‘get_available_languages.R’
    ‘words_from_coords.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘export.R’ ‘week.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  download_img_data.Rd: img_data
  smooth_hist.Rd: gam
  whitestripe_ind_to_mask.Rd: writeNIfTI
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Hals.fastcv.snow.Rd: snowfall
  Hals.snow.Rd: snowfall
  fun.load.Rd: snowfall
  widals.snow.Rd: snowfall
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘Cs.r’ ‘DI.R’ ‘GetTO.r’ ‘HAI.R’ ‘Lixn.R’ ‘conProcess.R’
    ‘ltraj_move2.R’ ‘move2_ltraj.R’
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘general_gd.R’ ‘plot_gd.R’ ‘window_gd.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotComb.Rd: hdi
  plot_Bwiqid.Rd: postPlot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  wkt_plot.Rd: wkt, wkb
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  WoodburyMatrix-class.Rd: Matrix-class, symmetricMatrix-class
  solve-methods.Rd: Matrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_transform_names.Rd: is_primitive
  simbase_covar.Rd: group_by, tibble
  simbase_list.Rd: group_by, tibble
  simulate_conditionally.simbase_list.Rd: nest, unnest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) word2vec_similarity.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) word2vec_similarity.Rd:31: Lost braces in \itemize; meant \describe ?
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [30s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > require(testthat)
  Loading required package: testthat
  > test_check("wordmap")
  Loading required package: wordmap
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 115 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-textplot.R:14:5'): textplot_terms works with dictionary ──────
  `print(textplot_terms(wmp1, data_dictionary_LSD2015, max_highlighted = 10))` produced warnings.
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 115 ]
  Error: Test failures
  Execution halted
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DSM_TermContextMatrix.Rd: dgCMatrix-class
  as_distmat.Rd: sparseMatrix
  dsm.Rd: sparseMatrix-class, dMatrix-class
  dsm_canonical_matrix.Rd: dgTMatrix-class, dgCMatrix-class,
    denseMatrix-class
  dsm_projection.Rd: sparsesvd
  rsvd.Rd: sparsesvd
  signcount.Rd: Matrix, dgeMatrix-class, dgCMatrix-class,
    dgRMatrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  wflow_build.Rd: rmarkdown
  wflow_git_commit.Rd: git2r
  wflow_git_config.Rd: git2r
  wflow_git_pull.Rd: git2r
  wflow_git_push.Rd: git2r
  wflow_post_knit.Rd: rmarkdown
  wflow_pre_knit.Rd: rmarkdown
  wflow_pre_processor.Rd: rmarkdown
  wflow_remove.Rd: git2r
  wflow_rename.Rd: git2r
  wflow_start.Rd: git2r
  wflow_status.Rd: git2r
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}}.}
       |                                                                                                                                                                                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  countChildrenParent.Rd: countSameStartEnd, contribToContigPerFrag
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) wtest.Rd:61-64: Lost braces
    61 | {When \code{w.order} =2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
checkRd: (-1) wtest.high.Rd:61-64: Lost braces
    61 | {When \code{w.order} > 2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
checkRd: (-1) batch_modwt_wvar_cpp.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) batch_modwt_wvar_cpp.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) batch_modwt_wvar_cpp.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3_robust.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3_robust.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3_robust.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_wave_variance.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_wave_variance.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_wave_variance.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modwt_wvar_cpp.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modwt_wvar_cpp.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modwt_wvar_cpp.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wvar_cpp.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wvar_cpp.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wvar_cpp.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:67-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateData.Rd:47: Lost braces
    47 | \bold{code{data}} \tab the generated data \cr
       |           ^
checkRd: (-1) generateData.Rd:53: Lost braces
    53 | Refer to \bold{\emph{code{\link{retrieveDataFactory}}}} and to
       |                          ^
checkRd: (-1) qualifyFunctionArguments.Rd:14: Lost braces
    14 | A emph{\code{list}} with following names
       |       ^
checkRd: (-1) qualifyFunctionArguments.Rd:26: Lost braces
    26 | \item{code{arguments}}{a \code{pairList} of argument names and values.
       |           ^
checkRd: (-1) completeManualPage.Rd:12: Lost braces
    12 | See \emph{\bold{code{\link{ProcessingContext}}}}. Only
       |                     ^
checkRd: (-1) produceAllManualPagesFromObject.Rd:14: Lost braces
    14 | See \emph{\bold{\\code{\link{ProcessingContext}}}}.}
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  inf_mr.Rd: httw
  moon_reader.Rd: html_document
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  xtest.Rd: compareGrowthCurves
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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 ?
Found the following files/directories:
  ‘xgb.txt’
possible bashism in configure.ac line 65 (unsafe echo with backslash):
      echo '         To use all CPU cores for training jobs, you should install OpenMP by running\n'
'::' or ':::' import not declared from: ‘devtools’
'library' or 'require' calls not declared from:
  ‘caret’ ‘cplm’ ‘e1071’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fit_XCI_E_model.Rd: coxph
  fit_XCI_model.Rd: coxph
  fit_all_models.Rd: coxph
  xlink_fit.Rd: coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  XML2Obs.Rd: getNodeSet
  XML2R.Rd: xmlParse, getNodeSet
  docsToNodes.Rd: getNodeSet
  nodesToList.Rd: xmlToList
  re_name.Rd: collapse
  urlsToDocs.Rd: xmlParse
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}
       |         ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘add_frag.R’ ‘data_frag.R’ ‘list_as_xml_document.R’ ‘read_fragment.R’
    ‘tag.R’ ‘write_xml.R’ ‘xml_fragment.R’ ‘xmlbuilder.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  xpose.VPC.categorical.Rd: xyplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  imDisplay.Rd: cimg
  imRead.Rd: load.image, imager, cimg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RJulia.Rd: getInterface
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  estimateVariance.Rd: selectiveInference
  xtune.Rd: glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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
       |                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.yaConsensus.Rd: pheatmap
  yaConsensus.Rd: doParallel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ycevo.Rd: dplyr_tidy_select
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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}.
       |                                                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  boot.yhat.Rd: boot
  booteval.yhat.rd: boot
  plotCI.yhat.rd: boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' calls not declared from:
  ‘plyr’ ‘randomForest’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cce.factor.Rd: glassoFast
  cogarch.est.incr.rd: zoo
  llag.Rd: zoo
  llag.test.Rd: boot
  setData.Rd: zoo
  wllag.Rd: zoo
  yuima-class.Rd: zoo
  yuima.carma.qmle-class.Rd: zoo
  yuima.data-class.Rd: zoo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘yyjsonr/libs/yyjsonr.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘zcta.R’
'library' or 'require' calls not declared from:
  ‘coda’ ‘dlm’ ‘maps’ ‘mgcv’ ‘mnormt’ ‘mvtnorm’ ‘randomForest’ ‘rpart’
  ‘rpart.plot’ ‘sensitivity’ ‘sp’ ‘spatial’ ‘tseries’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  periodogram.Rd: behavr
  periodogram_methods.Rd: data.table
  spectrogram.Rd: behavr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ZenodoManager.Rd: R6Class
  ZenodoRecord.Rd: R6Class, DCEntry
  ZenodoRequest.Rd: R6Class
  zen4RLogger.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘cache_report.R’ ‘list_deposit.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  graph_pairs.Rd: graphNEL
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' calls not declared from:
  ‘crop’ ‘mvtnorm’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘deposit_stats.R’ ‘scrap_stats.R’
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.}
       |                                                                                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  glm.cons.Rd: glm2
  glm.fit.cons.Rd: glm.fit2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘convert-jyear-legacy.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘notate.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  zoib.Rd: Formula
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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"}.
       |                                          ^
Package required but not available: ‘Rgraphviz’

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘Ch-Basics.R’ [2s/2s]
  Comparing ‘Ch-Basics.Rout’ to ‘Ch-Basics.Rout.save’ ... OK
  Running ‘Ch-Intro.R’ [2s/3s]
  Comparing ‘Ch-Intro.Rout’ to ‘Ch-Intro.Rout.save’ ... OK
  Running ‘Ch-LinearRegression.R’ [4s/5s]
  Comparing ‘Ch-LinearRegression.Rout’ to ‘Ch-LinearRegression.Rout.save’ ...46,51c46,51
<  Min.   :   2   Min.   :  20   Min.   : 0.00522  
<  1st Qu.:  52   1st Qu.: 134   1st Qu.: 0.46449  
<  Median : 122   Median : 282   Median : 1.32051  
<  Mean   : 197   Mean   : 418   Mean   : 2.54846  
<  3rd Qu.: 268   3rd Qu.: 541   3rd Qu.: 3.44017  
<  Max.   :1098   Max.   :2120   Max.   :24.45946  
---
>  Min.   :   2   Min.   :  20   Min.   : 0.005  
>  1st Qu.:  52   1st Qu.: 134   1st Qu.: 0.464  
>  Median : 122   Median : 282   Median : 1.321  
>  Mean   : 197   Mean   : 418   Mean   : 2.548  
>  3rd Qu.: 268   3rd Qu.: 541   3rd Qu.: 3.440  
>  Max.   :1098   Max.   :2120   Max.   :24.459  
886c886
< -0.619068 -0.025568  0.000000 -0.000134  0.033201  0.641027 
---
> -0.6191 -0.0256  0.0000 -0.0001  0.0332  0.6410 
  Running ‘Ch-Microeconometrics.R’ [2s/3s]
  Comparing ‘Ch-Microeconometrics.Rout’ to ‘Ch-Microeconometrics.Rout.save’ ... OK
  Running ‘Ch-Programming.R’ [17s/19s]
  Comparing ‘Ch-Programming.Rout’ to ‘Ch-Programming.Rout.save’ ... OK
  Running ‘Ch-TimeSeries.R’ [3s/4s]
  Comparing ‘Ch-TimeSeries.Rout’ to ‘Ch-TimeSeries.Rout.save’ ... OK
  Running ‘Ch-Validation.R’ [62s/71s]
  Comparing ‘Ch-Validation.Rout’ to ‘Ch-Validation.Rout.save’ ... OK
Package required but not available: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/akc.Rcheck/00install.out’ for details.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
Package required but not available: ‘BiDAG’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘BRugs.R’ [3s/4s]
  Comparing ‘BRugs.Rout’ to ‘BRugs.Rout.save’ ...65c65
< Welcome to BRugs connected to OpenBUGS version 3.2.2
---
> Welcome to BRugs connected to OpenBUGS version 3.2.3
  Running ‘examples.R’ [18s/27s]
  Comparing ‘examples.Rout’ to ‘examples.Rout.save’ ...55c55
< Welcome to BRugs connected to OpenBUGS version 3.2.2
---
> Welcome to BRugs connected to OpenBUGS version 3.2.3
106c106
< 20000 updates took 1 s
---
> 20000 updates took 2 s
205c205
< 20000 updates took 1 s
---
> 20000 updates took 3 s
218c218
< 20000 updates took 1 s
---
> 20000 updates took 2 s
  Running ‘examples.stats.R’ [0s/0s]
  Running ‘functions.R’ [8s/15s]
  Comparing ‘functions.Rout’ to ‘functions.Rout.save’ ...138c138
< Welcome to BRugs connected to OpenBUGS version 3.2.2
---
> Welcome to BRugs connected to OpenBUGS version 3.2.3
  Running ‘local.R’ [0s/0s]
Running ‘testthat.R’ [25s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > 
  > test_check("btergm")
  Loading required package: btergm
  Registered S3 methods overwritten by 'btergm':
    method    from
    plot.gof  ergm
    print.gof ergm
  Package:  btergm
  Version:  1.10.12
  Date:     2024-03-31
  Authors:  Philip Leifeld (University of Manchester)
            Skyler J. Cranmer (The Ohio State University)
            Bruce A. Desmarais (Pennsylvania State University)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test-btergm.R:82:3', 'test-btergm.R:180:3',
    'test-btergm.R:197:3', 'test-data.R:4:3', 'test-interpret.R:4:3',
    'test-interpret.R:32:3', 'test-interpret.R:59:3', 'test-interpret.R:87:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-btergm.R:73:3'): offset argument in btergm works without composition change ──
  Error in `ergm::ergm.pl(nw, Clist.miss, model, theta.offset = c(rep(FALSE, 
      length(l$rhs.terms) - 1), TRUE), verbose = FALSE, control = control.ergm)`: VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-btergm.R:73:3
   2. │ └─base::withCallingHandlers(...)
   3. └─btergm::btergm(...)
   4.   └─ergm::ergm.pl(...)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  Error: Test failures
  Execution halted
Running examples in ‘CAESAR.Suite-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CoUMAP
> ### Title: Co-embedding UMAP for Genes and Cells in a Seurat Object
> ### Aliases: CoUMAP
> 
> ### ** Examples
> 
> data(toydata)
> 
> seu <- toydata$seu
> 
> seu <- CoUMAP(seu, gene.set = rownames(seu))
Error in min(nrow(X), na.rm = col(X)) : 
  'length = 40100' in coercion to 'logical(1)'
Calls: CoUMAP ... <Anonymous> -> .local -> do.call -> <Anonymous> -> uwot
Execution halted
Running ‘exprSet-example.R’ [4s/5s]
  Comparing ‘exprSet-example.Rout’ to ‘exprSet-example.Rout.save’ ... OK
  Running ‘test00-color.R’ [0s/1s]
  Comparing ‘test00-color.Rout’ to ‘test00-color.Rout.save’ ... OK
  Running ‘test01-distance.R’ [0s/1s]
  Comparing ‘test01-distance.Rout’ to ‘test01-distance.Rout.save’ ... OK
  Running ‘test02-cluster.R’ [1s/1s]
  Comparing ‘test02-cluster.Rout’ to ‘test02-cluster.Rout.save’ ...28c28
< 3.674e-05 6.434e-02 3.529e-01 2.976e-01 5.154e-01 6.698e-01 
---
> 0.0000367 0.0643374 0.3528907 0.2975618 0.5153581 0.6697706 
  Running ‘test02.1-just.R’ [0s/1s]
  Comparing ‘test02.1-just.Rout’ to ‘test02.1-just.Rout.save’ ... OK
  Running ‘test03-boot.R’ [1s/2s]
  Comparing ‘test03-boot.Rout’ to ‘test03-boot.Rout.save’ ... OK
  Running ‘test04-perturb.R’ [1s/2s]
  Comparing ‘test04-perturb.Rout’ to ‘test04-perturb.Rout.save’ ... OK
  Running ‘test04.1-gpca.R’ [0s/1s]
  Comparing ‘test04.1-gpca.Rout’ to ‘test04.1-gpca.Rout.save’ ... OK
  Running ‘test05-spca.R’ [0s/1s]
  Comparing ‘test05-spca.Rout’ to ‘test05-spca.Rout.save’ ... OK
  Running ‘test06-mosaic.R’ [1s/1s]
  Comparing ‘test06-mosaic.Rout’ to ‘test06-mosaic.Rout.save’ ... OK
  Running ‘test07-pcanova.R’ [0s/1s]
  Comparing ‘test07-pcanova.Rout’ to ‘test07-pcanova.Rout.save’ ... OK
Running ‘test01-Simplex.R’ [1s/2s]
  Comparing ‘test01-Simplex.Rout’ to ‘test01-Simplex.Rout.save’ ... OK
  Running ‘test02-WV.R’ [1s/2s]
  Comparing ‘test02-WV.Rout’ to ‘test02-WV.Rout.save’ ... OK
  Running ‘test03-simulate.R’ [21s/27s]
  Comparing ‘test03-simulate.Rout’ to ‘test03-simulate.Rout.save’ ...213c213
<  3rd Qu.:14.000   3rd Qu.:265.75   3rd Qu.: 0.0029188   3rd Qu.:0.5005  
---
>  3rd Qu.:14.000   3rd Qu.:265.75   3rd Qu.: 0.0029187   3rd Qu.:0.5005  
  Running ‘test04-algorithm.R’ [53s/74s]
  Comparing ‘test04-algorithm.Rout’ to ‘test04-algorithm.Rout.save’ ...177c177
<  Max.   :2.002   Max.   :0.9989221   Max.   :2747  
---
>  Max.   :2.002   Max.   :0.9989222   Max.   :2747  
238c238
<  Mean   : 7.286   Mean   :184.3   Mean   : 0.03329   Mean   :0.5902  
---
>  Mean   : 7.286   Mean   :184.3   Mean   : 0.03329   Mean   :0.5903  
244c244
<  Median :1.0415   Median :1.0144845   Median :1352  
---
>  Median :1.0415   Median :1.0144844   Median :1352
Running examples in ‘clusterMI-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cluster.intern
> ### Title: Apply clustering method after multiple imputation
> ### Aliases: cluster.intern
> ### Keywords: internal
> 
> ### ** Examples
> 
> data(wine)
> 
> require(parallel)
Loading required package: parallel
> set.seed(123456)
> ref <- wine$cult
> nb.clust <- 3
> m <- 5 # number of imputed data sets. Should be larger in practice
> wine.na <- wine
> wine.na$cult <- NULL
> wine.na <- prodna(wine.na)
> 
> #imputation
> res.imp <- imputedata(data.na = wine.na, nb.clust = nb.clust, m = m)
JM-GL 
1...Error in islistfactor(x, recursive) : NA in coercion to Rboolean
Calls: imputedata -> unlist
Execution halted
Running ‘draw.R’ [1s/1s]
  Running ‘inputs.R’ [1s/1s]
  Running ‘thread.R’ [2s/2s]
  Running ‘varDeps.R’ [1s/1s]
Running the tests in ‘tests/draw.R’ failed.
Complete output:
  > library(CodeDepends)
  > library(Rgraphviz)
  Error in library(Rgraphviz) : there is no package called 'Rgraphviz'
  Execution halted
Missing or unexported object: ‘CDMConnector::cdm_from_con’
Running examples in ‘CohortCharacteristics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: availablePlotColumns
> ### Title: Available columns to use in 'facet' and 'colour' arguments in
> ###   plot functions.
> ### Aliases: availablePlotColumns
> 
> ### ** Examples
> 
> {
+ cdm <- mockCohortCharacteristics()
+ 
+ result <- summariseCharacteristics(cdm$cohort1)
+ 
+ availablePlotColumns(result)
+ 
+ mockDisconnect(cdm)
+ }
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Execution halted
Running ‘testthat.R’ [20s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(correlation)
  > 
  > test_check("correlation")
  
  For i = 2 j = 1  A cell entry of 0 was replaced with correct =  0.5.  Check your data!
  For i = 2 j = 1  A cell entry of 0 was replaced with correct =  0.5.  Check your data!
  [ FAIL 2 | WARN 1 | SKIP 11 | PASS 124 ]
  
  ══ Skipped tests (11) ══════════════════════════════════════════════════════════
  • On CRAN (11): 'test-as.list.R:7:3', 'test-correlation.R:172:3',
    'test-correlation.R:195:3', 'test-display_print_dataframe.R:2:3',
    'test-display_print_dataframe.R:14:3', 'test-display_print_matrix.R:4:3',
    'test-display_print_matrix.R:13:3', 'test-display_print_matrix.R:31:3',
    'test-methods.R:9:3', 'test-renaming.R:9:3',
    'test-selecting_variables.R:28:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cormatrix_to_excel.R:3:3'): cormatrix_to_excel select ──────────
  Error: x must be class wbColour
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-cormatrix_to_excel.R:3:3
   2.   └─rlang::cnd_signal(state$error)
  ── Error ('test-cormatrix_to_excel.R:16:3'): cormatrix_to_excel p_adjust ───────
  Error: x must be class wbColour
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-cormatrix_to_excel.R:16:3
   2.   └─rlang::cnd_signal(state$error)
  
  [ FAIL 2 | WARN 1 | SKIP 11 | PASS 124 ]
  Error: Test failures
  Execution halted
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gl.diagnostics.sim.Rd: gl.filter.callrate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gl.spatial.autoCorr.Rd: gl.propShared, gl.dist.ind
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mockery)
  > library(DataFakeR)
  > 
  > test_check("DataFakeR")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-lint_check.R:3:3'): Linting package ────────────────────────────
  Error: Function with_defaults was deprecated in lintr version 3.0.0. Use linters_with_defaults or modify_defaults instead.
  Backtrace:
      ▆
   1. └─lintr::with_defaults(...) at test-lint_check.R:3:3
   2.   └─lintr:::lintr_deprecated(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ]
  Error: Test failures
  Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [102s/128s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DataPackageR)
  > # Test only if pandoc is available.
  > if (rmarkdown::pandoc_available()) {
  +   test_check("DataPackageR")
  + }
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 247 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-r-processing.R:20:5'): R file processing works and creates vignettes ──
  Error in `abs_path(output_file)`: The file '/tmp/Rtmpsc3vIr/file35d9f534bc07e7/rfiletest/inst/extdata/Logfiles/rfileTest.pdf' does not exist.
  Backtrace:
       ▆
    1. └─base::eval(...)
    2.   └─base::eval(...)
    3.     ├─testthat::expect_equal(...) at test-r-processing.R:20:5
    4.     │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    5.     │   └─rlang::eval_bare(expr, quo_get_env(quo))
    6.     ├─base::basename(...)
    7.     └─DataPackageR::package_build(...)
    8.       └─DataPackageR:::DataPackageR(arg = package_path, deps = deps)
    9.         └─rmarkdown::render(...)
   10.           └─rmarkdown:::abs_path(output_file)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 247 ]
  Error: Test failures
  Execution halted
File ‘data.table/libs/data_table.so’:
  Found non-API calls to R: ‘LEVELS’, ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’, ‘TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Running examples in ‘easycsv-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fread_zip
> ### Title: read multiple csv files into named data frames
> ### Aliases: fread_zip
> ### Keywords: ~utilities ~misc
> 
> ### ** Examples
> 
> 
>   require(easycsv)
>   filezip <- system.file("exampleZips", "example_tables.zip", package="easycsv")
>   fread_zip(filezip)
Error in data.table::fread(input = tbl, sep = sep, nrows = nrows, header = header,  : 
  'autostart' is deprecated. Consider skip='string' or skip=n. This argument will be removed in the next release.
Calls: fread_zip -> <Anonymous> -> stopf -> raise_condition -> signal
Execution halted
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’ ‘table3.txt’ ‘table4.txt’
checkRd: (-1) Emas.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EMAS.manhattan.Rd: manhattan
  Emas.parallel.Rd: sem, lavaan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running ‘EpiILM.network.R’ [4s/5s]
  Comparing ‘EpiILM.network.Rout’ to ‘EpiILM.network.Rout.save’ ...9817c9817
<  [ reached 'max' / getOption("max.print") -- omitted 301 rows ]
---
>  [ reached getOption("max.print") -- omitted 301 rows ]
19695c19695
<  [ reached 'max' / getOption("max.print") -- omitted 301 rows ]
---
>  [ reached getOption("max.print") -- omitted 301 rows ]
  Running ‘EpiILM.spatial.R’ [2s/3s]
  Comparing ‘EpiILM.spatial.Rout’ to ‘EpiILM.spatial.Rout.save’ ... OK
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
Running examples in ‘flowTraceR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert_all_levels
> ### Title: Conversion of software specific levels
> ### Aliases: convert_all_levels
> 
> ### ** Examples
> 
> # Load libraries
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(stringr)
> library(tidyr)
> library(comprehenr)
> library(tibble)
> 
> # MaxQuant example data
> evidence <- tibble::tibble(
+   "Modified sequence" = c("_AACLLPK_",
+    "_ALTDM(Oxidation (M))PQM(Oxidation (M))R_",
+    "ALTDM(Dummy_Modification)PQMK"),
+   Charge = c(2,2,3),
+   "Protein group IDs" = c("26", "86;17", "86;17")
+ )
> 
> proteingroups <- tibble::tibble(
+ "Protein IDs" = c("A0A075B6P5;P01615;A0A087WW87;P01614;A0A075B6S6", "P02671", "P02672"),
+ id = c(26, 86, 17)
+ )
> 
> # Conversion
> convert_all_levels(
+  input_df = evidence,
+  input_MQ_pg = proteingroups,
+  software = "MaxQuant"
+ )
Error in islistfactor(x, recursive) : NA in coercion to Rboolean
Calls: convert_all_levels -> sort_string_pg -> %>% -> unlist
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Example_RT_distribution.Rmd’ using rmarkdown

Quitting from lines 51-55 [all levels] (Example_RT_distribution.Rmd)
Error: processing vignette 'Example_RT_distribution.Rmd' failed with diagnostics:
NA in coercion to Rboolean
--- failed re-building ‘Example_RT_distribution.Rmd’

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

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

Quitting from lines 97-101 [proteinGroup] (Workflow.Rmd)
Error: processing vignette 'Workflow.Rmd' failed with diagnostics:
NA in coercion to Rboolean
--- failed re-building ‘Workflow.Rmd’

SUMMARY: processing the following files failed:
  ‘Example_RT_distribution.Rmd’ ‘Workflow.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ftsa-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fplsr
> ### Title: Functional partial least squares regression
> ### Aliases: fplsr
> ### Keywords: models
> 
> ### ** Examples
> 
> # When weight = FALSE, all observations are assigned equally.
> # When weight = TRUE, all observations are assigned geometrically decaying weights.
> fplsr(data = ElNino_ERSST_region_1and2, order = 6, type = "nipals")
Error in sum(abs((t - t.old)/t), na.rm = T) : 
  'length = 408' in coercion to 'logical(1)'
Calls: fplsr -> nipals
Execution halted
Running ‘bsch.R’ [1s/1s]
  Comparing ‘bsch.Rout’ to ‘bsch.Rout.save’ ...3a4
> 
  Running ‘penInf.R’ [3s/4s]
  Comparing ‘penInf.Rout’ to ‘penInf.Rout.save’ ...5a6
> 
  Running ‘sh9.2012.R’ [2s/3s]
  Comparing ‘sh9.2012.Rout’ to ‘sh9.2012.Rout.save’ ...3a4
> 
  Running ‘shPUR.R’ [2s/2s]
  Comparing ‘shPUR.Rout’ to ‘shPUR.Rout.save’ ...3a4
> 
  Running ‘test1Fast.R’ [3s/3s]
  Comparing ‘test1Fast.Rout’ to ‘test1Fast.Rout.save’ ...3a4
> 
  Running ‘test1QE.R’ [2s/2s]
  Comparing ‘test1QE.Rout’ to ‘test1QE.Rout.save’ ...3a4
> 
  Running ‘test2Fast.R’ [3s/3s]
  Comparing ‘test2Fast.Rout’ to ‘test2Fast.Rout.save’ ...3a4
> 
  Running ‘test2QE.R’ [1s/2s]
  Comparing ‘test2QE.Rout’ to ‘test2QE.Rout.save’ ...3a4
> 
  Running ‘test3Fast.R’ [3s/3s]
  Comparing ‘test3Fast.Rout’ to ‘test3Fast.Rout.save’ ...3a4
> 
  Running ‘test3QE.R’ [1s/2s]
  Comparing ‘test3QE.Rout’ to ‘test3QE.Rout.save’ ...3a4
> 
  Running ‘test5Fast.R’ [3s/4s]
  Comparing ‘test5Fast.Rout’ to ‘test5Fast.Rout.save’ ...3a4
> 
  Running ‘test7Fast.R’ [3s/3s]
  Comparing ‘test7Fast.Rout’ to ‘test7Fast.Rout.save’ ...3a4
> 
  Running ‘testMyFam.R’ [1s/1s]
  Comparing ‘testMyFam.Rout’ to ‘testMyFam.Rout.save’ ...3a4
>
Error(s) in re-building vignettes:
  ...
--- re-building ‘kmeans_vignette.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gmfd.Rcheck/vign_test/gmfd/vignettes/kmeans_vignette_files/figure-html/unnamed-chunk-2-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26405 bytes
Input file size = 26519 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 20099
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 20099

Output IDAT size = 20099 bytes (6306 bytes decrease)
Output file size = 20177 bytes (6342 bytes = 23.91% decrease)


Quitting from lines 143-153 [unnamed-chunk-5] (kmeans_vignette.Rmd)
Error: processing vignette 'kmeans_vignette.Rmd' failed with diagnostics:
'x' must be an array of at least two dimensions
--- failed re-building ‘kmeans_vignette.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘gsDesign-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as_rtf
> ### Title: Save a summary table object as an RTF file
> ### Aliases: as_rtf as_rtf.gsBinomialExactTable as_rtf.gsBoundSummary
> 
> ### ** Examples
> 
> # as_rtf for gsBinomialExact
> zz <- gsBinomialExact(
+   k = 3, theta = seq(0.1, 0.9, 0.1), n.I = c(12, 24, 36),
+   a = c(-1, 0, 11), b = c(5, 9, 12)
+ )
> zz %>%
+   as_table() %>%
+   as_rtf(
+     file = tempfile(fileext = ".rtf"),
+     title = "Power/Type I Error and Expected Sample Size for a Group Sequential Design"
+   )
> 
> safety_design <- binomialSPRT(
+   p0 = .04, p1 = .1, alpha = .04, beta = .2, minn = 4, maxn = 75
+ )
> safety_power <- gsBinomialExact(
+   k = length(safety_design$n.I),
+   theta = seq(.02, .16, .02),
+   n.I = safety_design$n.I,
+   a = safety_design$lower$bound,
+   b = safety_design$upper$bound
+ )
> safety_power %>%
+   as_table() %>%
+   as_rtf(
+     file = tempfile(fileext = ".rtf"),
+     theta_label = "Underlying\nAE Rate",
+     prob_decimals = 3,
+     bound_label = c("Low Rate", "High Rate")
+   )
> # as_rtf for gsBoundSummary
> xgs <- gsSurv(lambdaC = .2, hr = .5, eta = .1, T = 2, minfup = 1.5)
> gsBoundSummary(xgs, timename = "Year", tdigits = 1) %>% as_rtf(file = tempfile(fileext = ".rtf"))
Error in unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"),  : 
  'recursive' must be of length 1
Calls: %>% ... rtf_encode_table -> paste -> as_rtf_footnote -> unlist
Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘plot.R’
Running examples in ‘hddplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: accTrainTest
> ### Title: Two subsets of data each take in turn the role of test set
> ### Aliases: accTrainTest
> ### Keywords: htest
> 
> ### ** Examples
> 
> mat <- matrix(rnorm(1000), ncol=20)
> cl <- factor(rep(1:3, c(7,9,4)))
> gp.id <- divideUp(cl, nset=2)
Error in islistfactor(x, recursive) : NA in coercion to Rboolean
Calls: divideUp -> unlist
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘QUICKhddplot.Rnw’ using knitr

Quitting from lines 195-204 [selection-4lda] (QUICKhddplot.Rnw)
Error: processing vignette 'QUICKhddplot.Rnw' failed with diagnostics:
NA in coercion to Rboolean
--- failed re-building ‘QUICKhddplot.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘hilldiv-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: div_profile_plot
> ### Title: Diversity profile plot
> ### Aliases: div_profile_plot
> ### Keywords: alpha beta gamma hill
> 
> ### ** Examples
> 
> data(bat.diet.otutable)
> data(bat.diet.hierarchy)
> #One sample example
> bat.diet.sample <- bat.diet.otutable[,1]
> profile.onesample <- div_profile(count=bat.diet.sample,qvalues=seq(from = 0, to = 5, by = (0.1)))
> div_profile_plot(profile.onesample)
> #Multiple samples
> profile.multiplesamples <- div_profile(bat.diet.otutable)
> div_profile_plot(profile.multiplesamples)
Error in melt.default(profile) : 
  The melt generic in data.table has been passed a matrix and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. To continue using melt methods from reshape2 while both packages are attached, e.g. melt.list, you can prepend the namespace, i.e. reshape2::melt(profile). In the next version, this warning will become an error.
Calls: div_profile_plot ... melt -> melt.default -> stopf -> raise_condition -> signal
Execution halted
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AnnotateDBSVCF.Rd: BSgenome
  AnnotateSBSVCF.Rd: BSgenome
  GeneExpressionData.Rd: data.table
  ICAMS.Rd: BSgenome
  MutectVCFFilesToCatalog.Rd: BSgenome
  MutectVCFFilesToCatalogAndPlotToPdf.Rd: BSgenome
  MutectVCFFilesToZipFile.Rd: BSgenome
  NormalizeGenomeArg.Rd: BSgenome
  PlotTransBiasGeneExp.Rd: data.table
  PlotTransBiasGeneExpToPdf.Rd: data.table
  StrelkaSBSVCFFilesToCatalog.Rd: BSgenome
  StrelkaSBSVCFFilesToCatalogAndPlotToPdf.Rd: BSgenome
  StrelkaSBSVCFFilesToZipFile.Rd: BSgenome
  VCFsToCatalogs.Rd: BSgenome
  VCFsToCatalogsAndPlotToPdf.Rd: BSgenome
  VCFsToDBSCatalogs.Rd: BSgenome
  VCFsToSBSCatalogs.Rd: BSgenome
  VCFsToZipFile.Rd: BSgenome
  revc.Rd: reverseComplement
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package required but not available: ‘KEGGgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘blm.R’ ‘checkBaseline.R’ ‘cleaning.R’ ‘countMissing.R’
    ‘getStanParameter.R’ ‘logit.R’ ‘negativeBionomial.R’
Running ‘allexercises.R’ [3s/4s]
  Comparing ‘allexercises.Rout’ to ‘allexercises.Rout.save’ ... OK
  Running ‘allscripts.R’ [3s/4s]
  Comparing ‘allscripts.Rout’ to ‘allscripts.Rout.save’ ...1821,1822c1821,1822
<    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
<     0.0     8.0    28.0   225.7   268.5  1836.0     338 
---
>   Length    Class     Mode 
>      829 difftime  numeric 
2844c2844
<  Mean   :1.373   Mean   :164325   Mean   :23.00  
---
>  Mean   :1.373   Mean   :164326   Mean   :23.00  
2853c2853
<           Mean   :164325   Mean   :23.00  
---
>           Mean   :164326   Mean   :23.00
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/iTOP.Rcheck/vign_test/iTOP/vignettes/vignette_files/figure-html/unnamed-chunk-3-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 6912 bytes
Input file size = 6990 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 6050
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 6050

Output IDAT size = 6050 bytes (862 bytes decrease)
Output file size = 6128 bytes (862 bytes = 12.33% decrease)

Failed with error:  'there is no package called 'Rgraphviz''

Quitting from lines 94-99 [unnamed-chunk-8] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
Package 'Rgraphviz' (from Bioconductor) must be installed for plotting graphs!
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’
File ‘JavaGD/libs/JavaGD.so’:
  Found non-API call to R: ‘Rf_gsetVar’

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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Running ‘testthat.R’ [7s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #This file runs all unit tests on every R CMD check.
  > #Comment this out to disable.
  > 
  > library(testthat)
  > 
  > #filter is to disable tests that rely on external servers
  > test_check("jsonlite", filter="toJSON|fromJSON|libjson|serializeJSON")
  Loading required package: jsonlite
  Failed with error:  'there is no package called 'nopackage''
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1534 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-fromJSON-datasets.R:15:5'): fromJSON datasets ────────────────
  names(object) not identical to names(newobject).
  3/17 mismatches
  x[15]: "Delta 15 N (o/oo)"
  y[15]: "Comments"
  
  x[16]: "Delta 13 C (o/oo)"
  y[16]: "Delta 15 N (o/oo)"
  
  x[17]: "Comments"
  y[17]: "Delta 13 C (o/oo)"
  Backtrace:
      ▆
   1. └─base::lapply(...) at test-fromJSON-datasets.R:12:3
   2.   └─jsonlite (local) FUN(X[[i]], ...)
   3.     └─testthat::expect_identical(names(object), names(newobject)) at test-fromJSON-datasets.R:15:5
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1534 ]
  Error: Test failures
  Execution halted
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kibior.Rd: R6Class, count
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running examples in ‘kmeRs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kmeRs_heatmap
> ### Title: K-mer similarity score heatmap
> ### Aliases: kmeRs_heatmap
> 
> ### ** Examples
> 
> # Use RColorBrewer to generate a figure similar to publication
> library(RColorBrewer)
> h.palette <- rev(brewer.pal(9, "YlGnBu"))
> q0 <- c("GATTACA", "ACAGATT", "GAATTAC", "GAAATCT", "CTATAGA", "GTACATA", "AACGATT")
> example <- kmeRs_similarity_matrix(q0, submat = "BLOSUM62")
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
Calls: kmeRs_similarity_matrix ... mpi.XStringSet.pairwiseAlignment -> XStringSet.pairwiseAlignment -> array -> unlist
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_kmeRs_package.Rmd’ using rmarkdown

Quitting from lines 40-44 [unnamed-chunk-2] (Introduction_to_kmeRs_package.Rmd)
Error: processing vignette 'Introduction_to_kmeRs_package.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
--- failed re-building ‘Introduction_to_kmeRs_package.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘kpcalg_tutorial.Rnw’ using knitr

Quitting from lines 61-65 [unnamed-chunk-2] (kpcalg_tutorial.Rnw)
Error: processing vignette 'kpcalg_tutorial.Rnw' failed with diagnostics:
package required but not installed: 'Rgraphviz'
--- failed re-building ‘kpcalg_tutorial.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘kst.Rnw’ using Sweave
Loading required package: proxy

Attaching package: ‘proxy’

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

    as.dist, dist

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

    as.matrix

Loading required package: relations
Loading required package: sets
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Error: processing vignette 'kst.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'kst.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ks
t.Rcheck/vign_test/kst/vignettes/kst-012.pdf): PDF inclusion: required page doe
s not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘kst.Rnw’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘mapping-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mapping
> ### Title: Static maps
> ### Aliases: mapping
> 
> ### ** Examples
> 
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(sf)
Linking to GEOS 3.13.0, GDAL 3.10.2, PROJ 9.5.1; sf_use_s2() is TRUE
> 
> data("popIT")
> popIT <- popIT
> coords <- loadCoordIT(unit = "provincia", year = '2019')
> cr <- left_join(coords, popIT, by = c( "provincia" = "ID"))
> 
> ###############
> #   Statics   #
> ###############
> 
> mapping(cr)

── tmap v3 code detected ───────────────────────────────────────────────────────
[v3->v4] `tm_borders()`: use 'fill' for the fill color of polygons/symbols
(instead of 'col'), and 'col' for the outlines (instead of 'border.col').
This message is displayed once every 8 hours.
[v3->v4] `tm_borders()`: use `fill_alpha` instead of `alpha`.
Error in `<current-expression>` : node stack overflow
Calls: <Anonymous> ... as.data.table -> as.data.table.data.frame -> as.data.table
Execution halted
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Mega2gdsfmt.Rd: gdsfmt
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running examples in ‘memisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: html
> ### Title: Building Blocks for HTML Code
> ### Aliases: html print.html_elem as.character.html_elem c.html_elem
> ###   html_group as.html_group as.character.html_group print.html_group
> ###   [.html_group [<-.html_group c.html_group content content<- setContent
> ###   attribs attribs<- setAttribs setAttribs.character
> ###   setAttribs.html_elem setAttribs.html_group [<-.html_attributes css
> ###   as.css style style<- setStyle setStyle.character setStyle.html_elem
> ###   setStyle.html_group as.character.css print.css [<-.css
> 
> ### ** Examples
> 
> 
> html("img")
<img> 
> html("img",src="test.png")
<img src="test.png"> 
> html("div",class="element",id="first","Sisyphus")
Error in islistfactor(x, recursive) : NA in coercion to Rboolean
Calls: <Anonymous> ... cat -> as.character -> as.character.html_elem -> unlist
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘anes48.Rmd’ using rmarkdown

Quitting from lines 122-123 [unnamed-chunk-6] (anes48.Rmd)
Error: processing vignette 'anes48.Rmd' failed with diagnostics:
NA in coercion to Rboolean
--- failed re-building ‘anes48.Rmd’

--- re-building ‘ftable-matrix.Rmd’ using rmarkdown

Quitting from lines 53-54 [unnamed-chunk-7] (ftable-matrix.Rmd)
Error: processing vignette 'ftable-matrix.Rmd' failed with diagnostics:
NA in coercion to Rboolean
--- failed re-building ‘ftable-matrix.Rmd’

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

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

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

Quitting from lines 380-381 [unnamed-chunk-25] (items.Rmd)
Error: processing vignette 'items.Rmd' failed with diagnostics:
NA in coercion to Rboolean
--- failed re-building ‘items.Rmd’

--- re-building ‘mtable-html.Rmd’ using rmarkdown

Quitting from lines 42-43 [unnamed-chunk-5] (mtable-html.Rmd)
Error: processing vignette 'mtable-html.Rmd' failed with diagnostics:
NA in coercion to Rboolean
--- failed re-building ‘mtable-html.Rmd’

SUMMARY: processing the following files failed:
  ‘anes48.Rmd’ ‘ftable-matrix.Rmd’ ‘items.Rmd’ ‘mtable-html.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘metalite.ae-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tlf_ae_specific
> ### Title: Specific adverse events table
> ### Aliases: tlf_ae_specific
> 
> ### ** Examples
> 
> meta <- meta_ae_example()
> 
> meta |>
+   prepare_ae_specific(
+     population = "apat",
+     observation = "wk12",
+     parameter = "rel"
+   ) |>
+   format_ae_specific() |>
+   tlf_ae_specific(
+     source = "Source:  [CDISCpilot: adam-adsl; adae]",
+     meddra_version = "24.0",
+     path_outdata = tempfile(fileext = ".Rdata"),
+     path_outtable = tempfile(fileext = ".rtf")
+   )
The outdata is saved in/tmp/Rtmpxbp7U7/file3bd51c4d93abb8.Rdata
Error in unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"),  : 
  'recursive' must be of length 1
Calls: tlf_ae_specific ... rtf_encode_table -> paste -> as_rtf_footnote -> unlist
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
extend_ae_specific_inference 5.923  0.047   8.155
Error(s) in re-building vignettes:
  ...
--- re-building ‘ae-listing.Rmd’ using rmarkdown

Quitting from lines 100-107 [unnamed-chunk-10] (ae-listing.Rmd)
Error: processing vignette 'ae-listing.Rmd' failed with diagnostics:
'recursive' must be of length 1
--- failed re-building ‘ae-listing.Rmd’

--- re-building ‘ae-specific-subgroup.Rmd’ using rmarkdown

Quitting from lines 159-166 [unnamed-chunk-17] (ae-specific-subgroup.Rmd)
Error: processing vignette 'ae-specific-subgroup.Rmd' failed with diagnostics:
'recursive' must be of length 1
--- failed re-building ‘ae-specific-subgroup.Rmd’

--- re-building ‘ae-specific.Rmd’ using rmarkdown

Quitting from lines 253-260 [unnamed-chunk-22] (ae-specific.Rmd)
Error: processing vignette 'ae-specific.Rmd' failed with diagnostics:
'recursive' must be of length 1
--- failed re-building ‘ae-specific.Rmd’

--- re-building ‘ae-summary.Rmd’ using rmarkdown
--- finished re-building ‘ae-summary.Rmd’

--- re-building ‘exposure-adjusted-event-rate.Rmd’ using rmarkdown
--- finished re-building ‘exposure-adjusted-event-rate.Rmd’

--- re-building ‘metalite-ae.Rmd’ using rmarkdown
--- finished re-building ‘metalite-ae.Rmd’

--- re-building ‘rate-compare.Rmd’ using rmarkdown
--- finished re-building ‘rate-compare.Rmd’

SUMMARY: processing the following files failed:
  ‘ae-listing.Rmd’ ‘ae-specific-subgroup.Rmd’ ‘ae-specific.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘metalite.sl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rtf_exp_duration
> ### Title: Exposure duration table
> ### Aliases: rtf_exp_duration
> 
> ### ** Examples
> 
> meta <- meta_sl_exposure_example()
> 
> meta |>
+   prepare_exp_duration(population = "apat", parameter = "expdur") |>
+   format_exp_duration(display_col = c("n", "prop", "total")) |>
+   rtf_exp_duration(
+     source = "Source: [CDISCpilot: adam-adsl; adex]",
+     path_outdata = tempfile(fileext = ".Rdata"),
+     path_outtable = tempfile(fileext = ".rtf")
+   )
The outdata is saved in/tmp/Rtmp6zl7di/file3c0ba379db4d07.Rdata
Error in unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"),  : 
  'recursive' must be of length 1
Calls: rtf_exp_duration ... rtf_encode_table -> paste -> as_rtf_footnote -> unlist
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘baseline-character.Rmd’ using rmarkdown
--- finished re-building ‘baseline-character.Rmd’

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

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

Quitting from lines 149-155 [unnamed-chunk-11] (exp_duration.Rmd)
Error: processing vignette 'exp_duration.Rmd' failed with diagnostics:
'recursive' must be of length 1
--- failed re-building ‘exp_duration.Rmd’

--- re-building ‘interactive-baseline.Rmd’ using rmarkdown
--- finished re-building ‘interactive-baseline.Rmd’

--- re-building ‘metalite.sl.Rmd’ using rmarkdown
--- finished re-building ‘metalite.sl.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Note: skipping ‘TwoModeNetworks.Rnw’ due to unavailable dependencies:
  'Rgraphviz'
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ncdf4.helpers)
  > 
  > test_check("ncdf4.helpers")
  Error in Rsx_nc4_put_vara_double: NetCDF: Not a valid data type or _FillValue type mismatch
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 43 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-file-functions.R:58:2'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-file-functions.R:155:2'): data can be written to a netCDF file ──
  Error in `ncdf4::ncvar_put(f, v, dat, start = starts, count = counts)`: C function Rsx_nc4_put_vara_double returned error
  Backtrace:
      ▆
   1. └─ncdf4.helpers::nc.put.var.subset.by.axes(...) at test-file-functions.R:155:9
   2.   └─ncdf4.helpers:::nc.put.subset.recursive(...)
   3.     └─ncdf4::ncvar_put(f, v, dat, start = starts, count = counts)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 43 ]
  Error: Test failures
  Execution halted
Running examples in ‘ohtadstats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dheatmap
> ### Title: Heatmap Plot
> ### Aliases: dheatmap
> 
> ### ** Examples
> 
> data(miyashita_langley_data)
> miyashita_langley_subset <- miyashita_langley_data[,1:15]
> ml_results <- dwrapper(miyashita_langley_subset)
Error in sum(geno[, 1], na.rm = T) : NA in coercion to Rboolean
Calls: dwrapper ... structure -> eval -> eval -> tapply -> lapply -> FUN -> FUN
Execution halted
checkRd: (-1) summary.blrm_trial.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:34: Lost braces in \itemize; meant \describe ?
Running ‘buffer.R’ [0s/1s]
  Comparing ‘buffer.Rout’ to ‘buffer.Rout.save’ ...5,10d4
< > 
< > if (!length(oclPlatforms())) {
< +     cat("== Cannot run tests as there is no platform")
< +     q("no")
< + }
< > 
  Running ‘kernel.R’ [2s/4s]
  Comparing ‘kernel.Rout’ to ‘kernel.Rout.save’ ...5,10d4
< > 
< > if (!length(oclPlatforms())) {
< +     cat("== Cannot run tests as there is no platform")
< +     q("no")
< + }
< >
Error(s) in re-building vignettes:
  ...
--- re-building ‘cohort-intersect.Rmd’ using rmarkdown

Quitting from lines 23-38 [unnamed-chunk-1] (cohort-intersect.Rmd)
Error: processing vignette 'cohort-intersect.Rmd' failed with diagnostics:
'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
--- failed re-building ‘cohort-intersect.Rmd’

--- re-building ‘concept-intersect.Rmd’ using rmarkdown

Quitting from lines 36-40 [unnamed-chunk-2] (concept-intersect.Rmd)
Error: processing vignette 'concept-intersect.Rmd' failed with diagnostics:
could not find function "eunomia_is_available"
--- failed re-building ‘concept-intersect.Rmd’

--- re-building ‘demographics.rmd’ using rmarkdown

Quitting from lines 20-28 [unnamed-chunk-1] (demographics.rmd)
Error: processing vignette 'demographics.rmd' failed with diagnostics:
'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
--- failed re-building ‘demographics.rmd’

--- re-building ‘summarise.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB


Quitting from lines 85-138 [unnamed-chunk-4] (summarise.Rmd)
Error: processing vignette 'summarise.Rmd' failed with diagnostics:
error in evaluating the argument 'dbObj' in selecting a method for function 'dbIsValid': could not find function "eunomia_dir"
--- failed re-building ‘summarise.Rmd’

--- re-building ‘table-intersect.Rmd’ using rmarkdown

Quitting from lines 35-39 [unnamed-chunk-3] (table-intersect.Rmd)
Error: processing vignette 'table-intersect.Rmd' failed with diagnostics:
could not find function "eunomia_is_available"
--- failed re-building ‘table-intersect.Rmd’

SUMMARY: processing the following files failed:
  ‘cohort-intersect.Rmd’ ‘concept-intersect.Rmd’ ‘demographics.rmd’
  ‘summarise.Rmd’ ‘table-intersect.Rmd’

Error: Vignette re-building failed.
Execution halted
Note: skipping ‘vignette2018.Rnw’ due to unavailable dependencies:
  'Rgraphviz'
Running ‘testthat.R’ [41s/57s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(poems)
  > 
  > test_check("poems")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1093 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_results_manager.R:385:5'): calculate summary weighted averages ──
  Error in `FUN(newX[, i], ...)`: NA in coercion to Rboolean
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(results_manager$calculate_summary_weighted_averages(na_replacements = list(abundance = na_function))) at test_results_manager.R:388:3
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. └─results_manager$calculate_summary_weighted_averages(na_replacements = list(abundance = na_function))
   10.   └─na_replacements[[param]](summary_matrix_list[[param]])
   11.     └─base::apply(a, 2, min, na.rm = NA) at test_results_manager.R:385:5
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1093 ]
  Error: Test failures
  Execution halted
Running ‘test01-utility.R’ [1s/1s]
  Comparing ‘test01-utility.Rout’ to ‘test01-utility.Rout.save’ ... OK
  Running ‘test03-channel-type.R’ [0s/1s]
  Comparing ‘test03-channel-type.Rout’ to ‘test03-channel-type.Rout.save’ ... OK
  Running ‘test04-channel.R’ [1s/1s]
  Comparing ‘test04-channel.Rout’ to ‘test04-channel.Rout.save’ ...42c42
<    0.2436  280.0141  675.7335  987.6435 1355.5114 9630.5918 
---
>    0.244  280.014  675.734  987.643 1355.511 9630.592 
  Running ‘test05-processor.R’ [1s/1s]
  Comparing ‘test05-processor.Rout’ to ‘test05-processor.Rout.save’ ... OK
  Running ‘test06-pipeline.R’ [1s/1s]
  Comparing ‘test06-pipeline.Rout’ to ‘test06-pipeline.Rout.save’ ... OK
  Running ‘test07-complete-channel.R’ [1s/1s]
  Comparing ‘test07-complete-channel.Rout’ to ‘test07-complete-channel.Rout.save’ ...22,27c22,27
<  Min.   :6.560e-02   Min.   :33.61   Min.   :    0.0  
<  1st Qu.:2.855e+02   1st Qu.:55.95   1st Qu.:  225.7  
<  Median :6.874e+02   Median :60.01   Median :  626.7  
<  Mean   :1.003e+03   Mean   :59.99   Mean   :  944.6  
<  3rd Qu.:1.396e+03   3rd Qu.:64.07   3rd Qu.: 1336.5  
<  Max.   :1.178e+04   Max.   :85.24   Max.   :11718.9  
---
>  Min.   :    0.066   Min.   :33.61   Min.   :    0.0  
>  1st Qu.:  285.474   1st Qu.:55.95   1st Qu.:  225.7  
>  Median :  687.351   Median :60.01   Median :  626.7  
>  Mean   : 1002.718   Mean   :59.99   Mean   :  944.6  
>  3rd Qu.: 1395.736   3rd Qu.:64.07   3rd Qu.: 1336.5  
>  Max.   :11776.787   Max.   :85.24   Max.   :11718.9
Running examples in ‘proftools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: filterProfileData
> ### Title: Filter Profile Data
> ### Aliases: filterProfileData
> ### Keywords: programming utilities
> 
> ### ** Examples
> 
> pd <- readProfileData(system.file("samples", "glmEx.out", package="proftools"))
> plotProfileCallGraph(pd)
Error in loadNamespace(x) : there is no package called ‘Rgraphviz’
Calls: plotProfileCallGraph ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘proftools.Rnw’ using knitr

Quitting from lines 231-232 [fullCallGraph] (proftools.Rnw)
Error: processing vignette 'proftools.Rnw' failed with diagnostics:
there is no package called 'Rgraphviz'
--- failed re-building ‘proftools.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Running ‘basic.R’ [20s/23s]
  Comparing ‘basic.Rout’ to ‘basic.Rout.save’ ...294,307c294,307
<       YYYY         MM          DD      timestamp           Qobs   deseaonalized
<  Min.   :0   Min.   :0   Min.   :0   Min.   :0 secs   Min.   :0   Min.   :0    
<  1st Qu.:0   1st Qu.:0   1st Qu.:0   1st Qu.:0 secs   1st Qu.:0   1st Qu.:0    
<  Median :0   Median :0   Median :0   Median :0 secs   Median :0   Median :0    
<  Mean   :0   Mean   :0   Mean   :0   Mean   :0 secs   Mean   :0   Mean   :0    
<  3rd Qu.:0   3rd Qu.:0   3rd Qu.:0   3rd Qu.:0 secs   3rd Qu.:0   3rd Qu.:0    
<  Max.   :0   Max.   :0   Max.   :0   Max.   :0 secs   Max.   :0   Max.   :0    
<        r1   
<  Min.   :0  
<  1st Qu.:0  
<  Median :0  
<  Mean   :0  
<  3rd Qu.:0  
<  Max.   :0  
---
>       YYYY         MM          DD     timestamp             Qobs  
>  Min.   :0   Min.   :0   Min.   :0   Length:1825       Min.   :0  
>  1st Qu.:0   1st Qu.:0   1st Qu.:0   Class :difftime   1st Qu.:0  
>  Median :0   Median :0   Median :0   Mode  :numeric    Median :0  
>  Mean   :0   Mean   :0   Mean   :0                     Mean   :0  
>  3rd Qu.:0   3rd Qu.:0   3rd Qu.:0                     3rd Qu.:0  
>  Max.   :0   Max.   :0   Max.   :0                     Max.   :0  
>  deseaonalized       r1   
>  Min.   :0     Min.   :0  
>  1st Qu.:0     1st Qu.:0  
>  Median :0     Median :0  
>  Mean   :0     Mean   :0  
>  3rd Qu.:0     3rd Qu.:0  
>  Max.   :0     Max.   :0
Running examples in ‘qdapRegex-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cheat
> ### Title: A Cheat Sheet of Common Regex Task Chunks
> ### Aliases: cheat
> 
> ### ** Examples
> 
> cheat()
Error in islistfactor(x, recursive) : NA in coercion to Rboolean
Calls: cheat -> sapply -> lapply -> FUN -> unlist
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("qdapRegex")
  > 
  > 
  > test_check("qdapRegex")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 177 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cheat.R:28:5'): cheat returns as expected ──────────────────────
  Error in `islistfactor(x, recursive)`: NA in coercion to Rboolean
  Backtrace:
      ▆
   1. └─qdapRegex::cheat(print = FALSE) at test-cheat.R:28:5
   2.   └─base::sapply(...)
   3.     └─base::lapply(X = X, FUN = FUN, ...)
   4.       └─qdapRegex (local) FUN(X[[i]], ...)
   5.         └─base::unlist(dictionary[[i]], colnames(dictionary)[i])
  ── Error ('test-cheat.R:63:5'): cheat prints as expected ───────────────────────
  Error in `islistfactor(x, recursive)`: NA in coercion to Rboolean
  Backtrace:
       ▆
    1. ├─testthat::expect_equivalent(capture.output(cheat()), out2) at test-cheat.R:63:5
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─utils::capture.output(cheat())
    5. │ └─base::withVisible(...elt(i))
    6. └─qdapRegex::cheat()
    7.   └─base::sapply(...)
    8.     └─base::lapply(X = X, FUN = FUN, ...)
    9.       └─qdapRegex (local) FUN(X[[i]], ...)
   10.         └─base::unlist(dictionary[[i]], colnames(dictionary)[i])
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 177 ]
  Error: Test failures
  Execution halted
Running examples in ‘qMRI-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estimateIRfluid
> ### Title: Estimate parameters in Inversion Recovery MRI experiments model
> ###   for CSF voxel
> ### Aliases: estimateIRfluid
> ### Keywords: models regression
> 
> ### ** Examples
> 
> dataDir0 <- system.file("extdataIR", package = "qMRI")
> dataDir <- tempdir("IRdata")
Error in tempdir(check) : NA in coercion to Rboolean
Execution halted
Running ‘testthat.R’ [51s/62s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rearrr)
  > 
  > if (require("xpectr")) {
  +   test_check("rearrr")
  + }
  Loading required package: xpectr
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 7341 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_n_fn.R:842:3'): testing quantile_index() ─────────────────────
  xpectr::strip(side_effects_19148[["error"]]) does not match "probs outside 01".
  Actual value: "ℹ In index 1Caused by error in quantiledefault type must be an integer in 19"
  Backtrace:
      ▆
   1. └─testthat::expect_match(...) at test_n_fn.R:842:3
   2.   └─testthat:::expect_match_(...)
  ── Failure ('test_n_fn.R:859:3'): testing quantile_index() ─────────────────────
  xpectr::strip(side_effects_19148[["error"]]) does not match "object a not found".
  Actual value: "ℹ In index 1Caused by error in quantiledefault type must be an integer in 19"
  Backtrace:
      ▆
   1. └─testthat::expect_match(...) at test_n_fn.R:859:3
   2.   └─testthat:::expect_match_(...)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 7341 ]
  Error: Test failures
  Execution halted
Note: skipping ‘relations.Rnw’ due to unavailable dependencies: 'Rgraphviz'
Running ‘testthat.R’ [12s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rempsyc)
  Suggested APA citation: Thériault, R. (2023). rempsyc: Convenience functions for psychology. 
  Journal of Open Source Software, 8(87), 5466. https://doi.org/10.21105/joss.05466
  > 
  > test_check("rempsyc")
  [ FAIL 1 | WARN 0 | SKIP 19 | PASS 46 ]
  
  ══ Skipped tests (19) ══════════════════════════════════════════════════════════
  • On CRAN (19): 'test-best_duplicate.R:8:3', 'test-extract_duplicates.R:8:3',
    'test-find_mad.R:2:3', 'test-format_value.R:2:3',
    'test-nice_assumptions.R:9:3', 'test-nice_contrasts.R:7:3',
    'test-nice_lm.R:5:3', 'test-nice_lm_contrasts.R:12:3',
    'test-nice_lm_slopes.R:5:3', 'test-nice_mod.R:4:3', 'test-nice_na.R:2:3',
    'test-nice_randomize.R:5:3', 'test-nice_reverse.R:3:3',
    'test-nice_slopes.R:4:3', 'test-nice_t_test.R:5:3', 'test-nice_table.R:13:3',
    'test-nice_var.R:2:3', 'test-scale_mad.R:2:3', 'test-winsorize_mad.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cormatrix_excel.R:5:3'): cormatrix_excel ───────────────────────
  Error: x must be class wbColour
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-cormatrix_excel.R:5:3
   2.   └─rlang::cnd_signal(state$error)
  
  [ FAIL 1 | WARN 0 | SKIP 19 | PASS 46 ]
  Error: Test failures
  Execution halted
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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Running examples in ‘rock-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: qna_to_tlm
> ### Title: Convert a QNA network to Linear Topic Map format
> ### Aliases: qna_to_tlm
> 
> ### ** Examples
> 
> ### Get path to example source
> examplePath <-
+   system.file("extdata", package="rock");
> 
> ### Read a souce coded with the Qualitative Network Approach
> qnaExample <-
+   rock::parse_source(
+     file.path(
+       examplePath,
+       "network-example-1.rock"
+     )
+   );
> 
> ### Convert and show the topic map
> cat(
+   rock::qna_to_tlm(
+     qnaExample
+   ),
+   sep="\n"
+ );
Error in unlist(df$from, df$to) : 'recursive' must be of length 1
Calls: cat -> <Anonymous> -> lapply -> FUN -> unique -> unlist
Execution halted
Running ‘testthat.R’ [80s/93s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(ROCsurf)
  > 
  > test_check("ROCsurf")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 516 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('testfunction.R:3754:3'): function return a double or list ───────────
  Error in `r.tc_index(x, y, z, init_param = c(alpha1 = alpha1, beta1 = beta1, 
      alpha2 = alpha2, beta2 = beta2, alpha3 = alpha3, beta3 = beta3), 
      init_index = c(median(x), median(y)), model = c("LLL"), method = c("MLE"))`: Optimization did not converge.Please check your initial parameters.
  Backtrace:
      ▆
   1. ├─testthat::expect_type(...) at testfunction.R:3754:3
   2. │ └─testthat::quasi_label(enquo(object), arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─ROCsurf::r.tc_index(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 516 ]
  Error: Test failures
  Execution halted
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_Outputfile’,
    ‘R_TempDir’, ‘R_Visible’, ‘R_curErrorBuf’, ‘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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  launch_shinystan.stanreg.Rd: shinystan-package
  loo.stanreg.Rd: loo-package
  plot.stanreg.Rd: bayesplot
  pp_check.stanreg.Rd: bayesplot
  stan_betareg.Rd: stanfit-class
  stan_glm.Rd: stanfit-class
  stan_lm.Rd: stanfit-class
  stan_polr.Rd: stanfit-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(sasr)
  > 
  > test_check("sasr")
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 16 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test-run_sas.R:4:3', 'test-run_sas.R:9:3',
    'test-run_sas.R:15:3', 'test-utils.R:58:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-rmarkdown.R:4:3'): rmarkdown engine works ──────────────────────
  Error in `file(con, "w")`: cannot open the connection
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-rmarkdown.R:4:3
   2.   └─rlang::cnd_signal(state$error)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 16 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘ontologyPlot’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shinyCLT)
  > 
  > test_check("shinyCLT")
  Loading required package: shiny
  Loading required package: gamlss
  Loading required package: splines
  Loading required package: gamlss.data
  
  Attaching package: 'gamlss.data'
  
  The following object is masked from 'package:datasets':
  
      sleep
  
  Loading required package: gamlss.dist
  Loading required package: nlme
  Loading required package: parallel
   **********   GAMLSS Version 5.4-22  ********** 
  For more on GAMLSS look at https://www.gamlss.com/
  Type gamlssNews() to see new features/changes/bug fixes.
  
  Loading required package: plotly
  Loading required package: ggplot2
  
  Attaching package: 'plotly'
  
  The following object is masked from 'package:ggplot2':
  
      last_plot
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following object is masked from 'package:graphics':
  
      layout
  
  Loading required package: future
  Loading required package: shinycssloaders
  Loading required package: waiter
  Loading required package: shinythemes
  Loading required package: shinyWidgets
  Loading required package: cachem
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-plot.R:99:3'): plot_compare_density_qq works correctly ─────────
  Error in `unlist(d.x1, d.x2)`: 'recursive' must be of length 1
  Backtrace:
      ▆
   1. └─global plot_compare_density_qq(group1, group2, input) at test-plot.R:99:3
   2.   └─base::unlist(d.x1, d.x2)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shiny.info)
  > 
  > test_check("shiny.info")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 24 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-lintr.R:1:1'): (code run outside of `test_that()`) ─────────────
  Error: Function with_defaults was deprecated in lintr version 3.0.0. Use linters_with_defaults or modify_defaults instead.
  Backtrace:
      ▆
   1. └─lintr::with_defaults(...) at test-lintr.R:1:1
   2.   └─lintr:::lintr_deprecated(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 24 ]
  Error: Test failures
  Execution halted
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  simSBS.Rd: BSgenome
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
Running ‘testthat.R’ [69s/80s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("smurf")
  > 
  > test_check("smurf")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 591 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_output.R:323:3'): Test n.par.cov in output ─────────────────────
  Error in `islistfactor(x, recursive)`: NA in coercion to Rboolean
  Backtrace:
      ▆
   1. ├─testthat::expect_true(...) at test_output.R:323:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::unlist(munich.fit$n.par.cov, length)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 591 ]
  Error: Test failures
  Execution halted
Running examples in ‘spectralGraphTopology-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: learn_k_component_graph
> ### Title: Learn the Laplacian matrix of a k-component graph Learns a
> ###   k-component graph on the basis of an observed data matrix. Check out
> ###   https://mirca.github.io/spectralGraphTopology for code examples.
> ### Aliases: learn_k_component_graph
> 
> ### ** Examples
> 
> # design true Laplacian
> Laplacian <- rbind(c(1, -1, 0, 0),
+                    c(-1, 1, 0, 0),
+                    c(0, 0, 1, -1),
+                    c(0, 0, -1, 1))
> n <- ncol(Laplacian)
> # sample data from multivariate Gaussian
> Y <- MASS::mvrnorm(n * 500, rep(0, n), MASS::ginv(Laplacian))
> # estimate graph on the basis of sampled data
> graph <- learn_k_component_graph(cov(Y), k = 2, beta = 10)
Error in max(werr/(w + w0), na.rm = "ignore") : 
  NA in coercion to Rboolean
Calls: learn_k_component_graph ... <Anonymous> -> pb_tick -> assert_named_or_empty_list -> stopifnot
Execution halted
Running examples in ‘STRMPS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: findStutter,stringCoverageGenotypeList-method
> ### Title: Find stutters
> ### Aliases: findStutter,stringCoverageGenotypeList-method
> 
> ### ** Examples
> 
> # The object returned by merging a stringCoverageList-Object
> # and a genotypeList-Object.
> data("stringCoverageGenotypeList")
> 
> stutterList <- findStutter(stringCoverageGenotypeList)
Error in unlist(substitutionMatrix, substitutionMatrix) : 
  'recursive' must be of length 1
Calls: findStutter ... mpi.XStringSet.pairwiseAlignment -> XStringSet.pairwiseAlignment -> array -> unlist
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘STRMPSworkflow.Rmd’ using rmarkdown

Quitting from lines 169-174 [unnamed-chunk-14] (STRMPSworkflow.Rmd)
Error: processing vignette 'STRMPSworkflow.Rmd' failed with diagnostics:
'recursive' must be of length 1
--- failed re-building ‘STRMPSworkflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘teal.modules.general-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tm_a_pca
> ### Title: 'teal' module: Principal component analysis
> ### Aliases: tm_a_pca
> 
> ### ** Examples
> 
> library(teal.widgets)
> 
> # general data example
> data <- teal_data()
> data <- within(data, {
+   require(nestcolor)
+   USArrests <- USArrests
+ })
> 
> datanames(data) <- "USArrests"
Warning: `datanames<-()` was deprecated in teal.data 0.7.0.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
  `teal_data`. See ?names.teal_data
> 
> app <- init(
+   data = data,
+   modules = modules(
+     tm_a_pca(
+       "PCA",
+       dat = data_extract_spec(
+         dataname = "USArrests",
+         select = select_spec(
+           choices = variable_choices(
+             data = data[["USArrests"]], c("Murder", "Assault", "UrbanPop", "Rape")
+           ),
+           selected = c("Murder", "Assault"),
+           multiple = TRUE
+         ),
+         filter = NULL
+       ),
+       ggplot2_args = ggplot2_args(
+         labs = list(subtitle = "Plot generated by PCA Module")
+       )
+     )
+   )
+ )
[INFO] 2025-02-22 18:05:07.1792 pid:3938913 token:[] teal.modules.general Initializing tm_a_pca
Error in as.list(data@env) : 
  no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
Running examples in ‘TEAM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TEAM
> ### Title: Testing on an Aggregation Tree Method
> ### Aliases: TEAM
> 
> ### ** Examples
> 
> set.seed(1)
> # Simulate local shift difference for each population from mixture of normals
> N1 <- N2 <- 1e6
> require(ks) #loads rnorm.mixt function
Loading required package: ks
> #Controls
> x1 <- rnorm.mixt(N1,mus=c(0.2,0.89),sigmas=c(0.04,0.01),props=c(0.97,0.03))
> #Cases
> x2 <- rnorm.mixt(N2,mus=c(0.2,0.88),sigmas=c(0.04,0.01),props=c(0.97,0.03))
> res <- TEAM(x1,x2,K=14,alpha=0.05,L=3)
Error in islistfactor(x, recursive) : NA in coercion to Rboolean
Calls: TEAM -> unique -> unlist
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TestGenerator.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(tidyformula)
  > 
  > test_check("tidyformula")
  [ FAIL 1 | WARN 39 | SKIP 0 | PASS 19 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-tidyformula.R:65:3'): tidyformula handles weird data frames ──
  `tidyformula(~everything(), df_empty)` did not throw the expected error.
  
  [ FAIL 1 | WARN 39 | SKIP 0 | PASS 19 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘qpgraph’

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘TT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: treetable
> ### Title: Display tree structured data using 'datatable' widget
> ### Aliases: treetable
> 
> ### ** Examples
> 
> data("org")
> data("col_order")
> colnames <- factor(c("org",org$attributesAll),
+                    levels =  col_order)
> treetable(org, color="#FFFFFF", colnames=colnames)
Warning: Automatic coercion from double to character was deprecated in purrr 1.0.0.
ℹ Please use an explicit call to `as.character()` within `map_chr()` instead.
ℹ The deprecated feature was likely used in the TT package.
  Please report the issue to the authors.
Error in unlist(x, recursive, use.names) : 
  'length = 517' in coercion to 'logical(1)'
Calls: treetable -> %>% -> <Anonymous> -> list2 -> unlist
Execution halted
Running ‘testthat.R’ [86s/114s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(uwot)
  Loading required package: Matrix
  > 
  > test_check("uwot")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 705 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_errors.R:28:1'): (code run outside of `test_that()`) ─────────
  `umap(iris10, pca = 500)` threw an error with unexpected message.
  Expected match: "'pca' must be <="
  Actual message: "'length = 40' in coercion to 'logical(1)'"
  Backtrace:
      ▆
   1. ├─testthat::expect_error(umap(iris10, pca = 500), "'pca' must be <=") at test_errors.R:28:1
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─uwot::umap(iris10, pca = 500)
   7.   └─uwot:::uwot(...)
  ── Error ('test_output.R:395:1'): (code run outside of `test_that()`) ──────────
  Error in `min(nrow(X), na.rm = col(X))`: 'length = 40' in coercion to 'logical(1)'
  Backtrace:
      ▆
   1. └─uwot::umap(...) at test_output.R:395:1
   2.   └─uwot:::uwot(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 705 ]
  Error: Test failures
  Execution halted
Running examples in ‘vioplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_labels
> ### Title: Annotated Violin Plot
> ### Aliases: add_labels
> ### Keywords: annotation. graphics plot violin
> 
> ### ** Examples
> 
> 
> # box- vs violin-plot
> par(mfrow=c(2,1))
> mu<-2
> si<-0.6
> bimodal<-c(rnorm(1000,-mu,si),rnorm(1000,mu,si))
> uniform<-runif(2000,-4,4)
> normal<-rnorm(2000,0,3)
> 
> # annotate a violin plot
> group <- rep(c("bimodal", "uniform", "normal"),
+              sapply(list(bimodal, uniform, normal), length))
> table(group)
group
bimodal  normal uniform 
   2000    2000    2000 
> vioplot(bimodal,uniform,normal)
> add_labels(unlist(bimodal,uniform,normal), group, height = 3, cex = 0.8)
Error in unlist(bimodal, uniform, normal) : 
  'recursive' must be of length 1
Calls: add_labels -> text -> text.default -> unlist
Execution halted
Running examples in ‘zenplots-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: graph_pairs
> ### Title: Turn pairs or paths into a graph
> ### Aliases: graph_pairs
> 
> ### ** Examples
> 
> ## To display the graphs constructed the packages
> ## graph and Rgraphviz packages need to be loaded
> library(graph)
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: ‘BiocGenerics’

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

> library(Rgraphviz)
Error in library(Rgraphviz) : there is no package called ‘Rgraphviz’
Execution halted
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
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.
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.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘hunspell’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppProgress’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/adfExplorer.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespace in Imports field not imported from: ‘cli’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
Running ‘Ch-Basics.R’
  Comparing ‘Ch-Basics.Rout’ to ‘Ch-Basics.Rout.save’ ... OK
  Running ‘Ch-Intro.R’ [4s/10s]
  Comparing ‘Ch-Intro.Rout’ to ‘Ch-Intro.Rout.save’ ... OK
  Running ‘Ch-LinearRegression.R’ [9s/28s]
  Comparing ‘Ch-LinearRegression.Rout’ to ‘Ch-LinearRegression.Rout.save’ ...46,51c46,51
<  Min.   :   2   Min.   :  20   Min.   : 0.00522  
<  1st Qu.:  52   1st Qu.: 134   1st Qu.: 0.46449  
<  Median : 122   Median : 282   Median : 1.32051  
<  Mean   : 197   Mean   : 418   Mean   : 2.54846  
<  3rd Qu.: 268   3rd Qu.: 541   3rd Qu.: 3.44017  
<  Max.   :1098   Max.   :2120   Max.   :24.45946  
---
>  Min.   :   2   Min.   :  20   Min.   : 0.005  
>  1st Qu.:  52   1st Qu.: 134   1st Qu.: 0.464  
>  Median : 122   Median : 282   Median : 1.321  
>  Mean   : 197   Mean   : 418   Mean   : 2.548  
>  3rd Qu.: 268   3rd Qu.: 541   3rd Qu.: 3.440  
>  Max.   :1098   Max.   :2120   Max.   :24.459  
886c886
< -0.619068 -0.025568  0.000000 -0.000134  0.033201  0.641027 
---
> -0.6191 -0.0256  0.0000 -0.0001  0.0332  0.6410 
  Running ‘Ch-Microeconometrics.R’ [6s/20s]
  Comparing ‘Ch-Microeconometrics.Rout’ to ‘Ch-Microeconometrics.Rout.save’ ... OK
  Running ‘Ch-Programming.R’ [50s/131s]
  Comparing ‘Ch-Programming.Rout’ to ‘Ch-Programming.Rout.save’ ... OK
  Running ‘Ch-TimeSeries.R’ [9s/16s]
  Comparing ‘Ch-TimeSeries.Rout’ to ‘Ch-TimeSeries.Rout.save’ ... OK
  Running ‘Ch-Validation.R’ [84s/160s]
  Comparing ‘Ch-Validation.Rout’ to ‘Ch-Validation.Rout.save’ ... OK
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mFilter’ ‘regclass’ ‘writexl’
  All declared Imports should be used.
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.
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.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘randomNames’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rsolnp’ ‘SuperLearner’ ‘future.apply’ ‘ggplot2’ ‘progressr’ ‘stats’
  ‘utils’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/akc.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
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.
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.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/ambient.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘devtools’ ‘dplyr’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘class’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
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.
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.
Found the following significant warnings:
  cpp11/include/cpp11/R.hpp:47:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/archive.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/area.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/packages/tests-clang/arrow/libarrow/arrow-18.1.0/include/arrow/vendored/datetime/date.h:966:34: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/packages/tests-clang/arrow/libarrow/arrow-18.1.0/include/arrow/vendored/datetime/date.h:967:34: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/packages/tests-clang/arrow/libarrow/arrow-18.1.0/include/arrow/vendored/datetime/date.h:1975:13: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/packages/tests-clang/arrow/libarrow/arrow-18.1.0/include/arrow/vendored/datetime/date.h:1983:13: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  filesystem.cpp:261:37: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/arrow.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R.rsp’
  All declared Imports should be used.
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: ‘abind’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Ckmeans.1d.dp’ ‘broom.mixed’ ‘igraph’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinycssloaders’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘crosstalk’ ‘plotly’
  All declared Imports should be used.
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.
File ‘base64enc/libs/base64enc.so’:
  Found non-API call to R: ‘SETLENGTH’
File ‘base64enc/libs/base64enc.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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Namespace in Imports field not imported from: ‘splines’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘circlize’ ‘hexbin’ ‘scales’ ‘sna’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘vtable’
  All declared Imports should be used.
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.
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.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/bayesdfa.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘StanHeaders’ ‘astsa’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘FastGP’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘HDInterval’ ‘MCMCpack’ ‘R2WinBUGS’ ‘R2jags’ ‘carData’ ‘rjags’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘matrixcalc’ ‘stats’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘coda’ ‘knitr’ ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
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.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/Bernadette.Rcheck/00install.out’ for details.
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.
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.
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.
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.
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.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/bignum.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/bigrquery.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 20.1.0-rc2’
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
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.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/binpackr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
Running examples in ‘blackbox-Ex.R’ failed
The error most likely occurred in:

> ### Name: bboptim
> ### Title: Black-box function optimization
> ### Aliases: bboptim rbb
> ### Keywords: optimize
> 
> ### ** Examples
> 
> # Classical toy example with optional noise
> fr <- function(v,sd) {   ## Rosenbrock Banana function 
+   10 * (v["y"] - v["x"]^2)^2 + (1 - v["x"])^2 + rnorm(1,sd=sd)
+ }
> set.seed(123)
> 
> # Initial parameter values, including duplicates. See ?init_grid.
> parsp <- init_grid(lower=c(x=0,y=0),upper=c(x=2,y=2),nUnique=25)
> 
> #### Without noise
> # add function values
> simuls <- cbind(parsp,bb=apply(parsp,1,"fr",sd=0))
> 
> # optimization
> bbresu <- bboptim(simuls)
    Only 25 unique coordinates selected for cross-validation.
Warning in spaMM.options(spaMM_glm_conv_silent = TRUE) :
  'spaMM_glm_conv_silent' not previously in spaMM.options. Check such name(s)?

Execution halted
Namespaces in Imports field not imported from:
  ‘knitr’ ‘markdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Running ‘test-all.R’ [40s/59s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > if (require(testthat, quietly = TRUE)) {
  +   test_check("blme")
  + } else {
  +   cat("package 'testthat' not available; cannot run unit tests\n")
  + }
  Loading required package: blme
  Loading required package: lme4
  Loading required package: Matrix
  [ FAIL 2 | WARN 15 | SKIP 0 | PASS 109 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-06-lmm_resid.R:20:3'): blmer fits the eight schools example correctly ──
  eightSchools@theta not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  ── Error ('test-07-lmm_fixef.R:120:3'): blmer fits sleep study example in documentation ──
  Error in `optwrap(optimizer, devfun, startingValues, lower = lowerBounds, 
      control = control, adj = FALSE, verbose = verbose, ...)`: (converted from warning) convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
  Backtrace:
      ▆
   1. └─blme::blmer(...) at test-07-lmm_fixef.R:120:3
   2.   └─blme:::optimizeLmer(...)
   3.     └─lme4:::optwrap(...)
  
  [ FAIL 2 | WARN 15 | SKIP 0 | PASS 109 ]
  Error: Test failures
  Execution halted
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.
Namespaces in Imports field not imported from:
  ‘BH’ ‘RcppEigen’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘fastDummies’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘HSAUR3’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
Running ‘BRugs.R’ [5s/11s]
  Comparing ‘BRugs.Rout’ to ‘BRugs.Rout.save’ ... OK
  Running ‘examples.R’ [32s/94s]
  Comparing ‘examples.Rout’ to ‘examples.Rout.save’ ...165c165
< 20000 updates took 1 s
---
> 20000 updates took 0 s
218c218
< 20000 updates took 1 s
---
> 20000 updates took 2 s
  Running ‘examples.stats.R’
  Running ‘functions.R’ [15s/40s]
  Comparing ‘functions.Rout’ to ‘functions.Rout.save’ ... OK
  Running ‘local.R’
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘grDevices’ ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mvtnorm’ ‘ssmn’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘RcppParallel’ ‘purrr’ ‘rstantools’ ‘scales’ ‘vizdraws’
  All declared Imports should be used.
Running ‘testthat.R’ [60s/104s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > 
  > test_check("btergm")
  Loading required package: btergm
  Registered S3 methods overwritten by 'btergm':
    method    from
    plot.gof  ergm
    print.gof ergm
  Package:  btergm
  Version:  1.10.12
  Date:     2024-03-31
  Authors:  Philip Leifeld (University of Manchester)
            Skyler J. Cranmer (The Ohio State University)
            Bruce A. Desmarais (Pennsylvania State University)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test-btergm.R:82:3', 'test-btergm.R:180:3',
    'test-btergm.R:197:3', 'test-data.R:4:3', 'test-interpret.R:4:3',
    'test-interpret.R:32:3', 'test-interpret.R:59:3', 'test-interpret.R:87:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-btergm.R:73:3'): offset argument in btergm works without composition change ──
  Error in `ergm::ergm.pl(nw, Clist.miss, model, theta.offset = c(rep(FALSE, 
      length(l$rhs.terms) - 1), TRUE), verbose = FALSE, control = control.ergm)`: VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-btergm.R:73:3
   2. │ └─base::withCallingHandlers(...)
   3. └─btergm::btergm(...)
   4.   └─ergm::ergm.pl(...)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘magrittr’ ‘rmarkdown’
  All declared Imports should be used.
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.
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.
Running examples in ‘CAESAR.Suite-Ex.R’ failed
The error most likely occurred in:

> ### Name: CoUMAP
> ### Title: Co-embedding UMAP for Genes and Cells in a Seurat Object
> ### Aliases: CoUMAP
> 
> ### ** Examples
> 
> data(toydata)
> 
> seu <- toydata$seu
> 
> seu <- CoUMAP(seu, gene.set = rownames(seu))
Error in min(nrow(X), na.rm = col(X)) : 
  'length = 40100' in coercion to 'logical(1)'
Calls: CoUMAP ... <Anonymous> -> .local -> do.call -> <Anonymous> -> uwot
Execution halted
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/carbondate.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘sp’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘broom’ ‘epitools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘epitools’ ‘forcats’ ‘purrr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘CBPS’ ‘spelling’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/cbq.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘GeneNet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
Running examples in ‘cellKey-Ex.R’ failed
The error most likely occurred in:

> ### Name: ck_params_nums
> ### Title: Set perturbation parameters for continuous variables
> ### Aliases: ck_params_nums
> 
> ### ** Examples
> 
> # create a perturbation table using
> # functionality from ptable-pkg; see help(pa = "ptable")
> # this returns an extra ptable for very small cells
> ptab <- ptable::pt_ex_nums(separation = TRUE)
Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
Error: The ptable can't be calculated without a violation of the constraints. The combination of the input parameters you set (e.g. D=5, V=1, js=0 or pstay) doesn't work. Please try another specification: either change the arguments 'mono=' or 'optim=' or try to use a different combination of input parameters (hint: changing the variance is sufficient in most cases).
Execution halted
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Running ‘testthat.R’ [8s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(centr)
  > 
  > test_check("centr")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-median_center.R:15:3'): median_center ────────────────────────
  sf::st_coordinates(...) (`actual`) not equal to as.matrix(data.frame(X = -96.0135231, Y = 28.6822725)) (`expected`).
  
  actual vs expected
                       [,1]     [,2]
  - actual[1, ]   -96.01353 28.68227
  + expected[1, ] -96.01352 28.68227
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
  Error: Test failures
  Execution halted
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.
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.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘AER’ ‘graphics’ ‘lmtest’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/cheapr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
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: ‘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.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘circlize’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
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.
Running ‘exprSet-example.R’ [9s/17s]
  Comparing ‘exprSet-example.Rout’ to ‘exprSet-example.Rout.save’ ... OK
  Running ‘test00-color.R’
  Comparing ‘test00-color.Rout’ to ‘test00-color.Rout.save’ ... OK
  Running ‘test01-distance.R’
  Comparing ‘test01-distance.Rout’ to ‘test01-distance.Rout.save’ ... OK
  Running ‘test02-cluster.R’
  Comparing ‘test02-cluster.Rout’ to ‘test02-cluster.Rout.save’ ...28c28
< 3.674e-05 6.434e-02 3.529e-01 2.976e-01 5.154e-01 6.698e-01 
---
> 0.0000367 0.0643374 0.3528907 0.2975618 0.5153581 0.6697706 
  Running ‘test02.1-just.R’
  Comparing ‘test02.1-just.Rout’ to ‘test02.1-just.Rout.save’ ... OK
  Running ‘test03-boot.R’
  Comparing ‘test03-boot.Rout’ to ‘test03-boot.Rout.save’ ... OK
  Running ‘test04-perturb.R’
  Comparing ‘test04-perturb.Rout’ to ‘test04-perturb.Rout.save’ ... OK
  Running ‘test04.1-gpca.R’
  Comparing ‘test04.1-gpca.Rout’ to ‘test04.1-gpca.Rout.save’ ... OK
  Running ‘test05-spca.R’
  Comparing ‘test05-spca.Rout’ to ‘test05-spca.Rout.save’ ... OK
  Running ‘test06-mosaic.R’
  Comparing ‘test06-mosaic.Rout’ to ‘test06-mosaic.Rout.save’ ... OK
  Running ‘test07-pcanova.R’
  Comparing ‘test07-pcanova.Rout’ to ‘test07-pcanova.Rout.save’ ... OK
Running examples in ‘CleanBSequences-Ex.R’ failed
The error most likely occurred in:

> ### Name: DNAStringSetOPR
> ### Title: Curing of biological sequences
> ### Aliases: DNAStringSetOPR
> 
> ### ** Examples
> 
> SEQs = readDNAStringSet(system.file("sequences","SeqInputOPR.fasta", package = "CleanBSequences"))
> PrimerR= DNAString ("GACTGCGTACCATGC")
> DNAStringSetOPR (SEQs,PrimerR)
DNAStringSet object of length 2:
    width seq                                               names               
[1]   116 GCCTCGCCTCCCTCTTTGATCAG...CCTTTGCAATCTTCACAAGGTGG 170522-033_K03_11...
[2]   113 GTCTACTCGATCGTGATCCGGTA...CCTTTGCAATCTTCACAAGGTGG 170522-033_C05_15...
Local PairwiseAlignmentsSingleSubject (1 of 2)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'table' in selecting a method for function 'match': object 'DNA_AND_RNA_COLORED_LETTERS' not found
Calls: DNAStringSetOPR ... add_colors.DNA -> vapply -> FUN -> match -> .handleSimpleError -> h
Execution halted
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.
Namespace in Imports field not imported from: ‘xfun’
  All declared Imports should be used.
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.
Running ‘test01-Simplex.R’
  Comparing ‘test01-Simplex.Rout’ to ‘test01-Simplex.Rout.save’ ... OK
  Running ‘test02-WV.R’
  Comparing ‘test02-WV.Rout’ to ‘test02-WV.Rout.save’ ... OK
  Running ‘test03-simulate.R’ [57s/96s]
  Comparing ‘test03-simulate.Rout’ to ‘test03-simulate.Rout.save’ ...213c213
<  3rd Qu.:14.000   3rd Qu.:265.75   3rd Qu.: 0.0029188   3rd Qu.:0.5005  
---
>  3rd Qu.:14.000   3rd Qu.:265.75   3rd Qu.: 0.0029187   3rd Qu.:0.5005  
  Running ‘test04-algorithm.R’ [161s/235s]
  Comparing ‘test04-algorithm.Rout’ to ‘test04-algorithm.Rout.save’ ...177c177
<  Max.   :2.002   Max.   :0.9989221   Max.   :2747  
---
>  Max.   :2.002   Max.   :0.9989222   Max.   :2747  
238c238
<  Mean   : 7.286   Mean   :184.3   Mean   : 0.03329   Mean   :0.5902  
---
>  Mean   : 7.286   Mean   :184.3   Mean   : 0.03329   Mean   :0.5903  
244c244
<  Median :1.0415   Median :1.0144845   Median :1352  
---
>  Median :1.0415   Median :1.0144844   Median :1352
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
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.
Running examples in ‘clusterMI-Ex.R’ failed
The error most likely occurred in:

> ### Name: cluster.intern
> ### Title: Apply clustering method after multiple imputation
> ### Aliases: cluster.intern
> ### Keywords: internal
> 
> ### ** Examples
> 
> data(wine)
> 
> require(parallel)
Loading required package: parallel
> set.seed(123456)
> ref <- wine$cult
> nb.clust <- 3
> m <- 5 # number of imputed data sets. Should be larger in practice
> wine.na <- wine
> wine.na$cult <- NULL
> wine.na <- prodna(wine.na)
> 
> #imputation
> res.imp <- imputedata(data.na = wine.na, nb.clust = nb.clust, m = m)
JM-GL 
1...Warning in is.na(recursive) :
  is.na() applied to non-(list or vector) of type 'builtin'
Error in islistfactor(x, recursive) : NA in coercion to Rboolean
Calls: imputedata -> unlist
Execution halted
Found the following significant warnings:
  cppzmq/zmq.hpp:1366:35: warning: identifier '_zbuf' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  cppzmq/zmq.hpp:1370:35: warning: identifier '_zbuf' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  cppzmq/zmq.hpp:1374:35: warning: identifier '_zbuf' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  cppzmq/zmq.hpp:1378:35: warning: identifier '_zbuf' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/clustermq.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
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.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘datasets’ ‘dplyr’ ‘klaR’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘MPV’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/CMF.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
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.
Namespace in Imports field not imported from: 'Hmisc'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nnet’
  All declared Imports should be used.
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.
Running examples in ‘CohensdpLibrary-Ex.R’ failed
The error most likely occurred in:

> ### Name: Cohensdp
> ### Title: Cohen's standardized mean difference.
> ### Aliases: Cohensdp
> 
> ### ** Examples
> 
> 
> # example in which the means are 114 vs. 101 with sds of 14.3 and 12.5 respectively
> Cohensdp( statistics = list( m1= 101, m2= 114, s1= 12.5, s2= 14.3, n1= 12, n2= 12 ), 
+           design     = "between")
Error: segfault from C stack overflow
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("CohensdpLibrary")
  Loading required package: CohensdpLibrary
  Error: segfault from C stack overflow
  Execution halted
Running examples in ‘CohortCharacteristics-Ex.R’ failed
The error most likely occurred in:

> ### Name: availablePlotColumns
> ### Title: Available columns to use in 'facet' and 'colour' arguments in
> ###   plot functions.
> ### Aliases: availablePlotColumns
> 
> ### ** Examples
> 
> {
+ cdm <- mockCohortCharacteristics()
+ 
+ result <- summariseCharacteristics(cdm$cohort1)
+ 
+ availablePlotColumns(result)
+ 
+ mockDisconnect(cdm)
+ }
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Execution halted
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘qpdf’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘chi’ ‘dplyr’ ‘spatstat.utils’ ‘utils’
  All declared Imports should be used.
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:
  ./Jaro.h:7:32: warning: identifier '_sz' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/comparator.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
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.
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  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:
  ‘kernlab’ ‘purrr’ ‘survminer’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘scales’ ‘sna’
  All declared Imports should be used.
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.
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.
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.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘re2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
Running examples in ‘correlation-Ex.R’ failed
The error most likely occurred in:

> ### Name: cormatrix_to_excel
> ### Title: Easy export of correlation matrix to Excel
> ### Aliases: cormatrix_to_excel
> ### Keywords: Excel correlation matrix
> 
> ### ** Examples
> 
> ## Don't show: 
> if (requireNamespace("openxlsx2", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ ## Don't show: 
+ .old_wd <- setwd(tempdir())
+ ## End(Don't show)
+ # Basic example
+ suppressWarnings(cormatrix_to_excel(mtcars,
+   select = c("mpg", "cyl", "disp", "hp", "carb"), filename = "cormatrix1"
+ ))
+ suppressWarnings(cormatrix_to_excel(iris,
+   p_adjust = "none",
+   filename = "cormatrix2"
+ ))
+ suppressWarnings(cormatrix_to_excel(airquality,
+   method = "spearman",
+   filename = "cormatrix3"
+ ))
+ ## Don't show: 
+ setwd(.old_wd)
+ ## End(Don't show)
+ ## Don't show: 
+ }) # examplesIf
> .old_wd <- setwd(tempdir())
> suppressWarnings(cormatrix_to_excel(mtcars, select = c("mpg", "cyl", "disp", 
+     "hp", "carb"), filename = "cormatrix1"))
# Correlation Matrix (pearson-method)

Parameter |      mpg |      cyl |     disp |       hp |    carb
---------------------------------------------------------------
mpg       |          | -0.85*** | -0.85*** | -0.78*** | -0.55**
cyl       | -0.85*** |          |  0.90*** |  0.83*** |  0.53**
disp      | -0.85*** |  0.90*** |          |  0.79*** |   0.39*
hp        | -0.78*** |  0.83*** |  0.79*** |          | 0.75***
carb      |  -0.55** |   0.53** |    0.39* |  0.75*** |        

p-value adjustment method: Holm (1979)
Error: x must be class wbColour
Execution halted
Running ‘testthat.R’ [49s/80s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(correlation)
  > 
  > test_check("correlation")
  
  For i = 2 j = 1  A cell entry of 0 was replaced with correct =  0.5.  Check your data!
  For i = 2 j = 1  A cell entry of 0 was replaced with correct =  0.5.  Check your data!
  [ FAIL 2 | WARN 125 | SKIP 11 | PASS 124 ]
  
  ══ Skipped tests (11) ══════════════════════════════════════════════════════════
  • On CRAN (11): 'test-as.list.R:7:3', 'test-correlation.R:172:3',
    'test-correlation.R:195:3', 'test-display_print_dataframe.R:2:3',
    'test-display_print_dataframe.R:14:3', 'test-display_print_matrix.R:4:3',
    'test-display_print_matrix.R:13:3', 'test-display_print_matrix.R:31:3',
    'test-methods.R:9:3', 'test-renaming.R:9:3',
    'test-selecting_variables.R:28:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cormatrix_to_excel.R:3:3'): cormatrix_to_excel select ──────────
  Error: x must be class wbColour
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-cormatrix_to_excel.R:3:3
   2.   └─rlang::cnd_signal(state$error)
  ── Error ('test-cormatrix_to_excel.R:16:3'): cormatrix_to_excel p_adjust ───────
  Error: x must be class wbColour
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-cormatrix_to_excel.R:16:3
   2.   └─rlang::cnd_signal(state$error)
  
  [ FAIL 2 | WARN 125 | SKIP 11 | PASS 124 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘cosa_tutorial.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/cosa.Rcheck/vign_test/cosa/vignettes/cosa_tutorial_files/figure-html/unnamed-chunk-2-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 45045 bytes
Input file size = 45183 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 35157
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 35157

Output IDAT size = 35157 bytes (9888 bytes decrease)
Output file size = 35235 bytes (9948 bytes = 22.02% decrease)


Quitting from lines 90-114 [unnamed-chunk-3] (cosa_tutorial.Rmd)
Error: processing vignette 'cosa_tutorial.Rmd' failed with diagnostics:
Solution is not feasible. Change default settings
--- failed re-building ‘cosa_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
Running examples in ‘cpmBigData-Ex.R’ failed
The error most likely occurred in:

> ### Name: ormBD
> ### Title: Cumulative Probability Model for Big Data
> ### Aliases: ormBD
> 
> ### ** Examples
> 
> ## generate a small example data and run one of the three methods 
> set.seed(1)
> n <- 200
> x1 = rnorm(n); x2 = rnorm(n)
> tmpdata = data.frame(x1 = x1, x2 = x2, y = rnorm(n) + x1 + 2*x2)
> modbinning <- ormBD(y ~ x1 + x2, data = tmpdata, family = loglog,
+                      approach = "binning", target_num = 100)
Error: object 'loglog' not found
Execution halted
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.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/cpp11armadillo.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/cpp11bigwig.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/cpp11qpdf.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/cppdoubles.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
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.
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.
Namespaces in Imports field not imported from:
  ‘DT’ ‘gbm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘geosphere’ ‘mapdata’ ‘maps’ ‘marmap’ ‘shinydashboard’
  ‘shinyjs’ ‘stringr’ ‘swfscDAS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘future’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rstantools’ ‘statmod’
  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.
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘TCGAbiolinks’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
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.
Running ‘testthat.R’ [8s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mockery)
  > library(DataFakeR)
  > 
  > test_check("DataFakeR")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-lint_check.R:3:3'): Linting package ────────────────────────────
  Error: Function with_defaults was deprecated in lintr version 3.0.0. Use linters_with_defaults or modify_defaults instead.
  Backtrace:
      ▆
   1. └─lintr::with_defaults(...) at test-lint_check.R:3:3
   2.   └─lintr:::lintr_deprecated(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ]
  Error: Test failures
  Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’ [169s/170s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DataPackageR)
  > # Test only if pandoc is available.
  > if (rmarkdown::pandoc_available()) {
  +   test_check("DataPackageR")
  + }
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 247 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-r-processing.R:20:5'): R file processing works and creates vignettes ──
  Error in `abs_path(output_file)`: The file '/tmp/Rtmp3ue0f8/working_dir/RtmpnAKVIi/file3d14a97f74718b/rfiletest/inst/extdata/Logfiles/rfileTest.pdf' does not exist.
  Backtrace:
       ▆
    1. └─base::eval(...)
    2.   └─base::eval(...)
    3.     ├─testthat::expect_equal(...) at test-r-processing.R:20:5
    4.     │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    5.     │   └─rlang::eval_bare(expr, quo_get_env(quo))
    6.     ├─base::basename(...)
    7.     └─DataPackageR::package_build(...)
    8.       └─DataPackageR:::DataPackageR(arg = package_path, deps = deps)
    9.         └─rmarkdown::render(...)
   10.           └─rmarkdown:::abs_path(output_file)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 247 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  simple_date/date.h:952:34: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  simple_date/date.h:953:34: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  simple_date/date.h:1871:13: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  simple_date/date.h:1879:13: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/datasailr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tidyverse’ ‘vctrs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘html5’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘qpdf’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinydisconnect’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘class’ ‘e1071’ ‘gam’ ‘gbm’ ‘glmnet’ ‘randomForest’ ‘weights’
  ‘xgboost’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘shinyBS’ ‘shinyMatrix’
  All declared Imports should be used.
Found the following significant warnings:
  ./json.h:25655:35: warning: identifier '_json' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./json.h:25674:49: warning: identifier '_json_pointer' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/denim.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/densityClust.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘purrr’
  All declared Imports should be used.
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.
62,63d61
< 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).
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘proxy’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rlang’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plotly’ ‘pryr’ ‘rpart’
  All declared Imports should be used.
Running ‘testthat.R’ [104s/117s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dmlalg)
  > 
  > test_check("dmlalg")
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 1150 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-methods_mm.R:197:5'): print.summary.mmdml outputs right formats ──
  `res` has length 23, not length 20.
  Backtrace:
      ▆
   1. └─dmlalg (local) do_tests(fit1, 20) at test-methods_mm.R:200:3
   2.   └─testthat::expect_length(res, len) at test-methods_mm.R:197:5
  ── Failure ('test-methods_mm.R:197:5'): print.summary.mmdml outputs right formats ──
  `res` has length 30, not length 25.
  Backtrace:
      ▆
   1. └─dmlalg (local) do_tests(fit2, 25) at test-methods_mm.R:201:3
   2.   └─testthat::expect_length(res, len) at test-methods_mm.R:197:5
  
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 1150 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [48s/85s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dominanceanalysis)
  > 
  > test_check("dominanceanalysis")
  [ FAIL 2 | WARN 162 | SKIP 0 | PASS 207 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-da-with-lmm.R:17:3'): contribution.average are correct ───────
  ca$rb.r2.1 not equal to c(N = 0.34, P = -0.03, K = 0.15).
  3/3 mismatches (average diff: 0.0293)
  [1]  0.2844 -  0.34 == -0.05558
  [2] -0.0233 - -0.03 ==  0.00666
  [3]  0.1243 -  0.15 == -0.02566
  ── Failure ('test-lmmR2-lme4.R:60:2'): Report correct values for lmer comparing both models ──
  lmmR2.1$sb.r2.2 not equal to 0.25.
  1/1 mismatches
  [1] 0.435 - 0.25 == 0.185
  
  [ FAIL 2 | WARN 162 | SKIP 0 | PASS 207 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘ggplot2’ ‘nloptr’
  All declared Imports should be used.
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.
Running examples in ‘dtmapi-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_idp_admin1_data
> ### Title: Fetch IDP Admin1 Data
> ### Aliases: get_idp_admin1_data
> 
> ### ** Examples
> 
> # Fetch IDP data at Admin Level 1
> idp_admin1_df <- get_idp_admin1_data(CountryName='Sudan', Admin1Name="Blue Nile")
Error in value[[3L]](cond) : 
  API request failed: HTTP 500 Internal Server Error.
Calls: get_idp_admin1_data ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 88-93 [get_idp_admin1] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
API request failed: HTTP 500 Internal Server Error.
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/RcppDate/include/date.h:966:34: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/RcppDate/include/date.h:967:34: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/RcppDate/include/date.h:1975:13: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/RcppDate/include/date.h:1983:13: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/dtts.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
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.
Found the following significant warnings:
  ../inst/include/cpp11/R.hpp:54:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/cpp11/named_arg.hpp:44:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  duckdb/third_party/fmt/include/fmt/format.h:551:33: warning: identifier '_u' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  duckdb/third_party/fmt/include/fmt/format.h:3345:56: warning: identifier '_format' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  duckdb/third_party/fmt/include/fmt/format.h:3349:59: warning: identifier '_format' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  duckdb/third_party/fmt/include/fmt/format.h:3365:50: warning: identifier '_a' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  duckdb/third_party/fmt/include/fmt/format.h:3369:53: warning: identifier '_a' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  duckdb/third_party/httplib/httplib.hpp:3422:43: warning: identifier '_t' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  duckdb/third_party/httplib/httplib.hpp:3437:26: warning: identifier '_t' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  duckdb/third_party/httplib/httplib.hpp:3495:26: warning: identifier '_t' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/duckdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Error(s) in re-building vignettes:
--- re-building ‘developers.Rmd’ using rmarkdown
--- finished re-building ‘developers.Rmd’

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

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

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

Quitting from lines 168-170 [unnamed-chunk-10] (large.Rmd)
Error: processing vignette 'large.Rmd' failed with diagnostics:
rapi_execute: Failed to run query
Error: Invalid Input Error: Initialization function "httpfs_init" from file "/data/gannet/ripley/.local/share/R/duckdb/extensions/v1.2.0/linux_amd64_gcc4/httpfs.duckdb_extension" threw an exception: "Attempted to dereference unique_ptr that is NULL!"
--- failed re-building ‘large.Rmd’

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘GenEst’ ‘expint’ ‘numDeriv’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
Running examples in ‘easycsv-Ex.R’ failed
The error most likely occurred in:

> ### Name: fread_zip
> ### Title: read multiple csv files into named data frames
> ### Aliases: fread_zip
> ### Keywords: ~utilities ~misc
> 
> ### ** Examples
> 
> 
>   require(easycsv)
>   filezip <- system.file("exampleZips", "example_tables.zip", package="easycsv")
>   fread_zip(filezip)
Error in data.table::fread(input = tbl, sep = sep, nrows = nrows, header = header,  : 
  'autostart' is deprecated. Consider skip='string' or skip=n. This argument will be removed in the next release.
Calls: fread_zip -> <Anonymous> -> stopf -> raise_condition -> signal
Execution halted
Namespace in Imports field not imported from: ‘rprojroot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qcr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/economiccomplexity.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘rlang’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘PCovR’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
Running ‘testthat.R’ [13s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(ellmer)
  > 
  > test_check("ellmer")
  Starting 2 test processes
  
  
  Error in `private$handle_error()`:
  ! testthat subprocess exited in file `test-content-image.R`
  Caused by error:
  ! R session closed the process connection, killed
  Backtrace:
       ▆
    1. └─testthat::test_check("ellmer")
    2.   └─testthat::test_dir(...)
    3.     └─testthat:::test_files(...)
    4.       └─testthat:::test_files_parallel(...)
    5.         ├─withr::with_dir(...)
    6.         │ └─base::force(code)
    7.         ├─testthat::with_reporter(...)
    8.         │ └─base::tryCatch(...)
    9.         │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   10.         │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   11.         │       └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   12.         └─testthat:::parallel_event_loop_chunky(queue, reporters, ".")
   13.           └─queue$poll(Inf)
   14.             └─base::lapply(...)
   15.               └─testthat (local) FUN(X[[i]], ...)
   16.                 └─private$handle_error(msg, i)
   17.                   └─rlang::abort(...)
  Execution halted
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.
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘DECIPHER’ ‘ggplot2’ ‘reshape2’ ‘usethis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tinytest’
  All declared Imports should be used.
Running ‘EpiILM.network.R’
  Comparing ‘EpiILM.network.Rout’ to ‘EpiILM.network.Rout.save’ ...9817c9817
<  [ reached 'max' / getOption("max.print") -- omitted 301 rows ]
---
>  [ reached getOption("max.print") -- omitted 301 rows ]
19695c19695
<  [ reached 'max' / getOption("max.print") -- omitted 301 rows ]
---
>  [ reached getOption("max.print") -- omitted 301 rows ]
  Running ‘EpiILM.spatial.R’
  Comparing ‘EpiILM.spatial.Rout’ to ‘EpiILM.spatial.Rout.save’ ... OK
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘knitr’ ‘plyr’ ‘tidyverse’ ‘xml2’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/epiworldR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespace in Imports field not imported from: ‘xts’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
Running examples in ‘eudract-Ex.R’ failed
The error most likely occurred in:

> ### Name: clintrials_gov_convert
> ### Title: applies a conversion using xslt from a simple xml file to a
> ###   ClinicalTrials.gov compatible file, and checks against the schema
> ### Aliases: clintrials_gov_convert
> 
> ### ** Examples
> 
> safety_statistics <- safety_summary(safety,
+                                     exposed=c("Experimental"=60,"Control"=67))
> simple <- tempfile(fileext = ".xml")
> eudract <- tempfile(fileext = ".xml")
> ct <- tempfile(fileext = ".xml")
> simple_safety_xml(safety_statistics, simple)
'/tmp/RtmpxG0XVM/working_dir/Rtmpa1gPHw/file2fa6b63ee5e3aa.xml' is created or modified

Warning in simple_safety_xml(safety_statistics, simple) :
  local complex type: The content model is not determinist.Element 'TABLE': No matching global declaration available for the validation root.
> eudract_convert(input=simple,
+                 output=eudract)
Error in eudract_convert(input = simple, output = eudract) : 
  local complex type: The content model is not determinist.Element 'TABLE': No matching global declaration available for the validation root.
Execution halted
Namespaces in Imports field not imported from:
  ‘forcats’ ‘rqPen’ ‘utils’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘KMsurv’ ‘MLEcens’ ‘lubridate’ ‘msm’ ‘perm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggpmisc’
  All declared Imports should be used.
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.
Running ‘testthat.R’ [133s/214s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(eyetrackingR)
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("eyetrackingR")
  Test Type:	 lmer 
  Predictor:	 (Intercept) 
  Formula:	 Prop ~ AOI + (1 | Trial) 
  Runs of Significant Time Bins: 
  Positive Run 1  ===== 
  	Time:		 15500 - 21000 Test Type:	 boot_splines 
  Predictor:	 Target 
  Formula:	 Prop ~ Target 
  Runs of Significant Time Bins: 
  Positive Run 1  ===== 
  	Time:		 15800 - 21000 [ FAIL 3 | WARN 16 | SKIP 0 | PASS 39 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_analyze_time_bins.R:105:3'): The function analyze_time_bins has correct data (interaction) ──
  Error in `compare_dfs(tb_interaction1_check, tb_interaction1)`: all(dim(df1) == dim(df2)) is not TRUE
  Backtrace:
      ▆
   1. └─eyetrackingR (local) compare_dfs(tb_interaction1_check, tb_interaction1) at test_analyze_time_bins.R:105:3
   2.   └─base::stopifnot(all(dim(df1) == dim(df2))) at test_analyze_time_bins.R:6:3
  ── Failure ('test_cluster_analysis.R:97:3'): The function make_time_cluster_data gives necessary eyetrackingR attributes with lmer ──
  nrow(attr(tclust_data_lmer, "eyetrackingR")$clusters) not equal to 2.
  1/1 mismatches
  [1] 0 - 2 == -2
  ── Failure ('test_cluster_analysis.R:98:3'): The function make_time_cluster_data gives necessary eyetrackingR attributes with lmer ──
  ncol(attr(tclust_data_lmer, "eyetrackingR")$clusters) not equal to 5.
  1/1 mismatches
  [1] 3 - 5 == -2
  
  [ FAIL 3 | WARN 16 | SKIP 0 | PASS 39 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tsibbledata’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘caTools’ ‘httr’ ‘jsonlite’ ‘rlang’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘base’ ‘data.table’
  All declared Imports should be used.
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.
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.
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.
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.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grDevices’ ‘utils’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/fastplyr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
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.
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘collapse’ ‘data.table’ ‘kit’ ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘agridat’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/fcirt.Rcheck/00install.out’ for details.
Running examples in ‘fdacluster-Ex.R’ failed
The error most likely occurred in:

> ### Name: fdadbscan
> ### Title: Performs density-based clustering for functional data with
> ###   amplitude and phase separation
> ### Aliases: fdadbscan
> 
> ### ** Examples
> 
> #----------------------------------
> # Extracts 15 out of the 30 simulated curves in `simulated30_sub` data set
> idx <- c(1:5, 11:15)
> x <- simulated30_sub$x[idx, ]
> y <- simulated30_sub$y[idx, , ]
> 
> #----------------------------------
> # Runs an HAC with affine alignment, searching for 2 clusters
> out <- fdadbscan(
+   x = x,
+   y = y,
+   warping_class = "affine",
+   metric = "normalized_l2"
+ )
Running ‘testthat.R’ [30m/30m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(fdacluster)
  > 
  > test_check("fdacluster")
Namespaces in Imports field not imported from:
  ‘FastGP’ ‘MASS’ ‘fdapace’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘ggplot2’ ‘randomcoloR’ ‘sqldf’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘lattice’ ‘randomForest’ ‘tibble’ ‘utils’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘panelView’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rclipboard’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
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.
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.
Running examples in ‘flowTraceR-Ex.R’ failed
The error most likely occurred in:

> ### Name: convert_all_levels
> ### Title: Conversion of software specific levels
> ### Aliases: convert_all_levels
> 
> ### ** Examples
> 
> # Load libraries
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(stringr)
> library(tidyr)
> library(comprehenr)
> library(tibble)
> 
> # MaxQuant example data
> evidence <- tibble::tibble(
+   "Modified sequence" = c("_AACLLPK_",
+    "_ALTDM(Oxidation (M))PQM(Oxidation (M))R_",
+    "ALTDM(Dummy_Modification)PQMK"),
+   Charge = c(2,2,3),
+   "Protein group IDs" = c("26", "86;17", "86;17")
+ )
> 
> proteingroups <- tibble::tibble(
+ "Protein IDs" = c("A0A075B6P5;P01615;A0A087WW87;P01614;A0A075B6S6", "P02671", "P02672"),
+ id = c(26, 86, 17)
+ )
> 
> # Conversion
> convert_all_levels(
+  input_df = evidence,
+  input_MQ_pg = proteingroups,
+  software = "MaxQuant"
+ )
Error in unlist(., .data, use.names = FALSE) : 
  'recursive' must be of length 1
Calls: convert_all_levels -> sort_string_pg -> %>% -> unlist
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Example_RT_distribution.Rmd’ using rmarkdown

Quitting from lines 51-55 [all levels] (Example_RT_distribution.Rmd)
Error: processing vignette 'Example_RT_distribution.Rmd' failed with diagnostics:
'recursive' must be of length 1
--- failed re-building ‘Example_RT_distribution.Rmd’

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

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

Quitting from lines 97-101 [proteinGroup] (Workflow.Rmd)
Error: processing vignette 'Workflow.Rmd' failed with diagnostics:
'recursive' must be of length 1
--- failed re-building ‘Workflow.Rmd’

SUMMARY: processing the following files failed:
  ‘Example_RT_distribution.Rmd’ ‘Workflow.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘decomposedPSF’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘forrel’ ‘pedtools’ ‘plotly’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘blockCV’ ‘patchwork’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘spatstat’ ‘spatstat.data’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘TreeSim’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘LaplacesDemon’
  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.
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.
Running examples in ‘FREEtree-Ex.R’ failed
The error most likely occurred in:

> ### Name: FREEtree
> ### Title: Initial FREEtree call which then calls actual FREEtree methods
> ###   depending on parameters being passed through.
> ### Aliases: FREEtree
> 
> ### ** Examples
> 
> #locate example data file
> dataf <- system.file("data/data.RData", package="FREEtree")
> mytree = FREEtree(data,fixed_regress=c("time","time2"), fixed_split=c("treatment"),
+                   var_select=paste("V",1:200,sep=""), minModuleSize = 5,
+                   cluster="patient", Fuzzy=TRUE, maxdepth_factor_select = 0.5,
+                   maxdepth_factor_screen = 0.04, minsize_multiplier = 5,
+                   alpha_screen = 0.2, alpha_select=0.2,alpha_predict=0.05)
Use FREEtree_time

Warning in optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower,  :
  convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  unable to evaluate scaled gradient
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
Error in if (continue & (abs(newloglik - oldloglik[2]) < abstol)) { : 
  missing value where TRUE/FALSE needed
Calls: FREEtree -> FREEtree_time -> lmertree
Execution halted
Running ‘testthat.R’ [44s/68s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FREEtree)
  
  > 
  > test_check("FREEtree")
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_FREEtree.R:113:3'): FREEtree_time a5 estimation ────────────────
  Error in `if (continue & (abs(newloglik - oldloglik[2]) < abstol)) {
      if (newloglik > oldloglik[1]) 
          continue <- FALSE
  }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. └─FREEtree::FREEtree(...) at test_FREEtree.R:113:3
   2.   └─FREEtree:::FREEtree_time(...)
   3.     └─glmertree::lmertree(...)
  ── Error ('test_FREEtree.R:230:3'): FREEtree_PC a0 estimation ──────────────────
  Error in `if (continue & (abs(newloglik - oldloglik[2]) < abstol)) {
      if (newloglik > oldloglik[1]) 
          continue <- FALSE
  }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. └─FREEtree::FREEtree(...) at test_FREEtree.R:230:3
   2.   └─FREEtree:::FREEtree_PC(...)
   3.     └─glmertree::lmertree(...)
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bigalgebra’ ‘biganalytics’
  All declared Imports should be used.
File ‘gafit/libs/gafit.so’:
  Found non-API calls to R: ‘FRAME’, ‘HASHTAB’
File ‘gafit/libs/gafit.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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
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:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
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.
Found the following significant warnings:
  gdalcubes/src/external/date.h:913:40: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  gdalcubes/src/external/date.h:914:41: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  gdalcubes/src/external/date.h:1705:20: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  gdalcubes/src/external/date.h:1711:20: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./gdalcubes/src/external/date.h:913:40: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./gdalcubes/src/external/date.h:914:41: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./gdalcubes/src/external/date.h:1705:20: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./gdalcubes/src/external/date.h:1711:20: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/gdalcubes.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/gdm.Rcheck/00install.out’ for details.
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.
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.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘pracma’ ‘rlang’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘R.utils’ ‘markdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘GGEBiplots’ ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’
  ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘luz’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’ ‘spData’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘pipeR’ ‘rlang’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘googlesheets4’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘gtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mathjaxr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rdpack’
  All declared Imports should be used.
Running ‘bsch.R’
  Comparing ‘bsch.Rout’ to ‘bsch.Rout.save’ ...3a4
> 
  Running ‘penInf.R’
  Comparing ‘penInf.Rout’ to ‘penInf.Rout.save’ ...5a6
> 
  Running ‘sh9.2012.R’
  Comparing ‘sh9.2012.Rout’ to ‘sh9.2012.Rout.save’ ...3a4
> 
  Running ‘shPUR.R’
  Comparing ‘shPUR.Rout’ to ‘shPUR.Rout.save’ ...3a4
> 
  Running ‘test1Fast.R’
  Comparing ‘test1Fast.Rout’ to ‘test1Fast.Rout.save’ ...3a4
> 
  Running ‘test1QE.R’
  Comparing ‘test1QE.Rout’ to ‘test1QE.Rout.save’ ...3a4
> 
  Running ‘test2Fast.R’
  Comparing ‘test2Fast.Rout’ to ‘test2Fast.Rout.save’ ...3a4
> 
  Running ‘test2QE.R’
  Comparing ‘test2QE.Rout’ to ‘test2QE.Rout.save’ ...3a4
> 
  Running ‘test3Fast.R’ [8s/10s]
  Comparing ‘test3Fast.Rout’ to ‘test3Fast.Rout.save’ ...3a4
> 
  Running ‘test3QE.R’
  Comparing ‘test3QE.Rout’ to ‘test3QE.Rout.save’ ...3a4
> 
  Running ‘test5Fast.R’
  Comparing ‘test5Fast.Rout’ to ‘test5Fast.Rout.save’ ...3a4
> 
  Running ‘test7Fast.R’ [8s/11s]
  Comparing ‘test7Fast.Rout’ to ‘test7Fast.Rout.save’ ...3a4
> 
  Running ‘testMyFam.R’
  Comparing ‘testMyFam.Rout’ to ‘testMyFam.Rout.save’ ...3a4
>
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.
Running ‘testthat.R’ [4s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggpath)
  > 
  > test_check("ggpath")
  free(): double free detected in tcache 2
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grDevices’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘RPostgres’ ‘colourpicker’ ‘ggpmisc’
  ‘ggpubr’ ‘glue’ ‘gridExtra’ ‘markdown’ ‘patchwork’ ‘plotly’
  ‘quantreg’ ‘shinyFiles’ ‘shinyjqui’ ‘shinyjs’ ‘table1’ ‘zoo’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/ggraph.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘nomogramFormula’ ‘survival’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘utils’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘mockery’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MCMCpack’ ‘ggplot2’ ‘moments’
  All declared Imports should be used.
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.
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.
Error(s) in re-building vignettes:
--- re-building ‘glmertree.Rnw’ using Sweave
Loading required package: lme4
Loading required package: Matrix
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Warning in optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower,  :
  convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.754457 (tol = 0.002, component 1)

Error: processing vignette 'glmertree.Rnw' failed with diagnostics:
 chunk 6 
Error in if (continue & (abs(newloglik - oldloglik[2]) < abstol)) { : 
  missing value where TRUE/FALSE needed

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

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘DiceKriging’ ‘rgenoud’
  All declared Imports should be used.
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.
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.
Namespaces in Imports field not imported from:
  ‘base’ ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rhandsontable’ ‘shiny’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘future’ ‘httr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘snpStats’
  All declared Imports should be used.
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.
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.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Undeclared package ‘glasso’ in Rd xrefs
Unknown package ‘edmcr’ in Rd xrefs
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘msm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘methods’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘rjags’
  All declared Imports should be used.
File ‘grove/libs/grove.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 ‘grr/libs/grr.so’:
  Found non-API call to R: ‘STRING_PTR’
File ‘grr/libs/grr.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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Running examples in ‘gsDesign-Ex.R’ failed
The error most likely occurred in:

> ### Name: as_rtf
> ### Title: Save a summary table object as an RTF file
> ### Aliases: as_rtf as_rtf.gsBinomialExactTable as_rtf.gsBoundSummary
> 
> ### ** Examples
> 
> # as_rtf for gsBinomialExact
> zz <- gsBinomialExact(
+   k = 3, theta = seq(0.1, 0.9, 0.1), n.I = c(12, 24, 36),
+   a = c(-1, 0, 11), b = c(5, 9, 12)
+ )
> zz %>%
+   as_table() %>%
+   as_rtf(
+     file = tempfile(fileext = ".rtf"),
+     title = "Power/Type I Error and Expected Sample Size for a Group Sequential Design"
+   )
> 
> safety_design <- binomialSPRT(
+   p0 = .04, p1 = .1, alpha = .04, beta = .2, minn = 4, maxn = 75
+ )
> safety_power <- gsBinomialExact(
+   k = length(safety_design$n.I),
+   theta = seq(.02, .16, .02),
+   n.I = safety_design$n.I,
+   a = safety_design$lower$bound,
+   b = safety_design$upper$bound
+ )
> safety_power %>%
+   as_table() %>%
+   as_rtf(
+     file = tempfile(fileext = ".rtf"),
+     theta_label = "Underlying\nAE Rate",
+     prob_decimals = 3,
+     bound_label = c("Low Rate", "High Rate")
+   )
> # as_rtf for gsBoundSummary
> xgs <- gsSurv(lambdaC = .2, hr = .5, eta = .1, T = 2, minfup = 1.5)
> gsBoundSummary(xgs, timename = "Year", tdigits = 1) %>% as_rtf(file = tempfile(fileext = ".rtf"))
Error in unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"),  : 
  'recursive' must be of length 1
Calls: %>% ... rtf_encode_table -> paste -> as_rtf_footnote -> unlist
Execution halted
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.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/gtfstools.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Running examples in ‘GUILDS-Ex.R’ failed
The error most likely occurred in:

> ### Name: maxLikelihood.Guilds.Conditional
> ### Title: Maximization of the loglikelihood under the Guilds Model,
> ###   conditioned on guild size.
> ### Aliases: maxLikelihood.Guilds.Conditional
> 
> ### ** Examples
> 
> theta = 20
> alpha = 0.1
> initParams <- c(theta, alpha)
> maxLikelihood.Guilds.Conditional(initParams,
+                                  model = "D0",
+                                  sadx  = 1:20,
+                                  sady  = 1:20,
+                                  verbose = TRUE)
Error in if (fnew <= fmin) { : missing value where TRUE/FALSE needed
Calls: maxLikelihood.Guilds.Conditional ... eval_f -> conditional.LogLik -> logLikguilds -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘GUILDS.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/GUILDS.Rcheck/vign_test/GUILDS/vignettes/GUILDS_files/figure-html/unnamed-chunk-1-1.png
576x288 pixels, 8 bits/pixel, 246 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 2947 bytes
Input file size = 3775 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 2454
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 2452
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 2452

Output IDAT size = 2452 bytes (495 bytes decrease)
Output file size = 2530 bytes (1245 bytes = 32.98% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/GUILDS.Rcheck/vign_test/GUILDS/vignettes/GUILDS_files/figure-html/unnamed-chunk-2-1.png
576x288 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4642 bytes
Input file size = 5497 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3998
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3970
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3970

Output IDAT size = 3970 bytes (672 bytes decrease)
Output file size = 4048 bytes (1449 bytes = 26.36% decrease)
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘spgwr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘attempt’ ‘corpcor’ ‘glue’ ‘htmltools’ ‘pkgload’ ‘processx’
  ‘tools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘gsubfn’ ‘stringr’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/haven.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 20.1.0-rc2’
* used C++ compiler: ‘clang version 20.1.0-rc2’
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.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/hBayesDM.Rcheck/00install.out’ for details.
Running examples in ‘hddplot-Ex.R’ failed
The error most likely occurred in:

> ### Name: accTrainTest
> ### Title: Two subsets of data each take in turn the role of test set
> ### Aliases: accTrainTest
> ### Keywords: htest
> 
> ### ** Examples
> 
> mat <- matrix(rnorm(1000), ncol=20)
> cl <- factor(rep(1:3, c(7,9,4)))
> gp.id <- divideUp(cl, nset=2)
Warning in is.na(recursive) :
  is.na() applied to non-(list or vector) of type 'closure'
Error in islistfactor(x, recursive) : NA in coercion to Rboolean
Calls: divideUp -> unlist
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘QUICKhddplot.Rnw’ using knitr

Quitting from lines 195-204 [selection-4lda] (QUICKhddplot.Rnw)
Error: processing vignette 'QUICKhddplot.Rnw' failed with diagnostics:
NA in coercion to Rboolean
--- failed re-building ‘QUICKhddplot.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘ggjoy’ ‘isotone’ ‘png’ ‘questionr’ ‘rprojroot’
  ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RandomWalker’ ‘TidyDensity’ ‘healthyR’ ‘healthyR.ai’ ‘healthyR.data’
  ‘healthyR.ts’ ‘tidyAML’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/heumilkr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/hilbert.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Running examples in ‘hilldiv-Ex.R’ failed
The error most likely occurred in:

> ### Name: div_profile_plot
> ### Title: Diversity profile plot
> ### Aliases: div_profile_plot
> ### Keywords: alpha beta gamma hill
> 
> ### ** Examples
> 
> data(bat.diet.otutable)
> data(bat.diet.hierarchy)
> #One sample example
> bat.diet.sample <- bat.diet.otutable[,1]
> profile.onesample <- div_profile(count=bat.diet.sample,qvalues=seq(from = 0, to = 5, by = (0.1)))
> div_profile_plot(profile.onesample)
> #Multiple samples
> profile.multiplesamples <- div_profile(bat.diet.otutable)
> div_profile_plot(profile.multiplesamples)
Error in melt.default(profile) : 
  The melt generic in data.table has been passed a matrix and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. To continue using melt methods from reshape2 while both packages are attached, e.g. melt.list, you can prepend the namespace, i.e. reshape2::melt(profile). In the next version, this warning will become an error.
Calls: div_profile_plot ... melt -> melt.default -> stopf -> raise_condition -> signal
Execution halted
Running ‘testthat.R’ [179s/215s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(HLMdiag)
  
  Attaching package: 'HLMdiag'
  
  The following object is masked from 'package:stats':
  
      covratio
  
  > library(lme4)
  Loading required package: Matrix
  > library(nlme)
  
  Attaching package: 'nlme'
  
  The following object is masked from 'package:lme4':
  
      lmList
  
  > 
  > data(sleepstudy, package = 'lme4')
  > 
  > sleepstudy2 <- sleepstudy
  > sleepstudy2[7,1] <- NA
  > sleepstudy2[2,2] <- NA
  > 
  > 
  > test_check("HLMdiag")
  [ FAIL 1 | WARN 970 | SKIP 6 | PASS 423 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (6): 'test-hlm_influence.R:32:3', 'test-hlm_influence.R:56:3',
    'test-hlm_resid.R:90:3', 'test-hlm_resid.R:111:3',
    'test-influence_functions.R:158:3', 'test-influence_functions.R:172:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-case_delete.R:545:3'): Dimenstions of variance components are correct for single case deletion for nlme models ──
  length(sleep.lme.caseD$varcomp.delete) not equal to length(varcomp.lme(sleep.lme)).
  1/1 mismatches
  [1] 3 - 4 == -1
  
  [ FAIL 1 | WARN 970 | SKIP 6 | PASS 423 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘RSpectra’ ‘ggrepel’ ‘markdown’ ‘matrixStats’ ‘reshape2’ ‘tidyr’
  ‘uuid’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘quantreg’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘recipes’ ‘tune’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shiny’ ‘wordcloud2’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘digest’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
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.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/igraph.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 20.1.0-rc2’
* used C++ compiler: ‘clang version 20.1.0-rc2’
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(imagefluency)
  > 
  > test_check("imagefluency")
  free(): double free detected in tcache 2
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘haven’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pscl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/imt.Rcheck/00install.out’ for details.
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.
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.
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.
Namespace in Imports field not imported from: ‘splines2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘broom’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘fdrtool’ ‘nimble’
  All declared Imports should be used.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘NAMED’, ‘R_GetConnection’,
    ‘R_ReadConnection’, ‘R_WriteConnection’, ‘SETLENGTH’, ‘SET_NAMED’
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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘expm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘glmnet’
  All declared Imports should be used.
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.
Running ‘local_tests.R’
  Running ‘spelling.R’
  Running ‘testthat.R’ [30m/37m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(IsoriX)
  
   IsoriX version 0.9.3 is now loaded
  
   Type:
     * `?IsoriX` for a very short description
     * `browseURL('https://bookdown.org/content/782/')` for a longer (online) documentation
     * `help(package = 'IsoriX', help_type = 'html')` for a list of the package objects and help files
     * `citation('IsoriX')` for how to cite IsoriX (i.e. the papers you should read)
     * `news(package = 'IsoriX')` for info on changed between versions of IsoriX
  
   Please join the mailing list 'https://groups.google.com/g/IsoriX'
   for help, news and discussions about IsoriX
  
  
  Attaching package: 'IsoriX'
  
  The following objects are masked from 'package:graphics':
  
      plot, points
  
  The following object is masked from 'package:base':
  
      plot
  
  > 
  > test_check("IsoriX")
Running ‘allexercises.R’
  Comparing ‘allexercises.Rout’ to ‘allexercises.Rout.save’ ... OK
  Running ‘allscripts.R’
  Comparing ‘allscripts.Rout’ to ‘allscripts.Rout.save’ ...1821,1822c1821,1822
<    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
<     0.0     8.0    28.0   225.7   268.5  1836.0     338 
---
>   Length    Class     Mode 
>      829 difftime  numeric 
2844c2844
<  Mean   :1.373   Mean   :164325   Mean   :23.00  
---
>  Mean   :1.373   Mean   :164326   Mean   :23.00  
2853c2853
<           Mean   :164325   Mean   :23.00  
---
>           Mean   :164326   Mean   :23.00
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fBasics’ ‘reshape’ ‘tidyr’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘DiagrammeR’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ids’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./inja/nlohmann/json.hpp:26390:35: warning: identifier '_json' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./inja/nlohmann/json.hpp:26409:49: warning: identifier '_json_pointer' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./inja/inja.hpp:208:39: warning: identifier '_sv' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./inja/inja.hpp:213:42: warning: identifier '_sv' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./inja/inja.hpp:218:42: warning: identifier '_sv' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./inja/inja.hpp:223:40: warning: identifier '_sv' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/jinjar.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
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.
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
Running ‘testthat.R’ [19s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #This file runs all unit tests on every R CMD check.
  > #Comment this out to disable.
  > 
  > library(testthat)
  > 
  > #filter is to disable tests that rely on external servers
  > test_check("jsonlite", filter="toJSON|fromJSON|libjson|serializeJSON")
  Loading required package: jsonlite
  Failed with error:  'there is no package called 'nopackage''
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1534 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-fromJSON-datasets.R:15:5'): fromJSON datasets ────────────────
  names(object) not identical to names(newobject).
  3/17 mismatches
  x[15]: "Delta 15 N (o/oo)"
  y[15]: "Comments"
  
  x[16]: "Delta 13 C (o/oo)"
  y[16]: "Delta 15 N (o/oo)"
  
  x[17]: "Comments"
  y[17]: "Delta 13 C (o/oo)"
  Backtrace:
      ▆
   1. └─base::lapply(...) at test-fromJSON-datasets.R:12:3
   2.   └─jsonlite (local) FUN(X[[i]], ...)
   3.     └─testthat::expect_identical(names(object), names(newobject)) at test-fromJSON-datasets.R:15:5
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1534 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  ./../inst/include/nlohmann/json_cran.h:25253:35: warning: identifier '_json' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./../inst/include/nlohmann/json_cran.h:25272:49: warning: identifier '_json_pointer' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/nlohmann/json_cran.h:25253:35: warning: identifier '_json' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/nlohmann/json_cran.h:25272:49: warning: identifier '_json_pointer' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/jsonStrings.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘Superpower’ ‘pwr’ ‘shinydashboard’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘gifski’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EQL’ ‘univariateML’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/kendallknight.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
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.
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.
Running examples in ‘kergp-Ex.R’ failed
The error most likely occurred in:

> ### Name: gp
> ### Title: Gaussian Process Model
> ### Aliases: gp
> 
> ### ** Examples
> 
> ## ==================================================================
> ## Example 1. Data sampled from a GP model with a known covTS object
> ## ==================================================================
> set.seed(1234)
> myCov <- covTS(inputs = c("Temp", "Humid"),
+                kernel = "k1Matern5_2",
+                dep = c(range = "input"),
+                value = c(range = 0.4))
> ## change coefficients (variances)
> coef(myCov) <- c(0.5, 0.8, 2, 16)
> d <- myCov@d; n <- 20
> ## design matrix
> X <- matrix(runif(n*d), nrow = n, ncol = d)
> colnames(X) <- inputNames(myCov)
> ## generate the GP realization
> myGp <- gp(formula = y ~ 1, data = data.frame(y = rep(0, n), X), 
+             cov = myCov, estim = FALSE,
+             beta = 10, varNoise = 0.05)
> y <- simulate(myGp, cond = FALSE)$sim
Loading required package: MASS
> 
> ## parIni: add noise to true parameters
> parCovIni <- coef(myCov)
> parCovIni[] <- 0.9 * parCovIni[] +  0.1 * runif(length(parCovIni))
> coefLower(myCov) <- rep(1e-2, 4)
> coefUpper(myCov) <- c(5, 5, 20, 20)
> est <- gp(y ~ 1, data = data.frame(y = y, X),
+           cov = myCov, 
+           noise = TRUE,
+           varNoiseLower = 1e-2,
+           varNoiseIni = 1.0,
+           parCovIni = parCovIni) 
Warning in nloptr.add.default.options(opts.user = opts, x0 = x0, num_constraints_ineq = num_constraints_ineq,  :
  No termination criterion specified, using default(relative x-tolerance = 1e-04)
Error in fitList[[bestIndex]] : 
  attempt to select less than one element in get1index
Error in gp(y ~ 1, data = data.frame(y = y, X), cov = myCov, noise = TRUE,  : 
  Maximum Likelihood error
Execution halted
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.
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘Rsamtools’ ‘rtracklayer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fitdistrplus’ ‘plotly’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘SnowballC’ ‘stringi’
  All declared Imports should be used.
Running examples in ‘kmeRs-Ex.R’ failed
The error most likely occurred in:

> ### Name: kmeRs_heatmap
> ### Title: K-mer similarity score heatmap
> ### Aliases: kmeRs_heatmap
> 
> ### ** Examples
> 
> # Use RColorBrewer to generate a figure similar to publication
> library(RColorBrewer)
> h.palette <- rev(brewer.pal(9, "YlGnBu"))
> q0 <- c("GATTACA", "ACAGATT", "GAATTAC", "GAAATCT", "CTATAGA", "GTACATA", "AACGATT")
> example <- kmeRs_similarity_matrix(q0, submat = "BLOSUM62")
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
Calls: kmeRs_similarity_matrix ... mpi.XStringSet.pairwiseAlignment -> XStringSet.pairwiseAlignment -> array -> unlist
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Introduction_to_kmeRs_package.Rmd’ using rmarkdown

Quitting from lines 40-44 [unnamed-chunk-2] (Introduction_to_kmeRs_package.Rmd)
Error: processing vignette 'Introduction_to_kmeRs_package.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
--- failed re-building ‘Introduction_to_kmeRs_package.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.
Running ‘testthat.R’ [31s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(konfound)
  Sensitivity analysis as described in Frank, 
  Maroulis, Duong, and Kelcey (2013) and in 
  Frank (2000).
  For more information visit http://konfound-it.com.
  > 
  > test_check("konfound")
  Dependent variable is mpg 
  Dependent variable is wt 
  Using the absolute value of the estimated effect, 
            results can be interpreted by symmetry.
  Using the absolute value of the estimated effect, 
            results can be interpreted by symmetry.
  Using the absolute value of the estimated effect, 
            results can be interpreted by symmetry.
  [ FAIL 1 | WARN 6 | SKIP 0 | PASS 181 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-konfound.R:15:5'): konfound works for lme4 model ─────────────
  output3$RIR_perc not equal to 84.826.
  1/1 mismatches
  [1] 84.3 - 84.8 == -0.517
  
  [ FAIL 1 | WARN 6 | SKIP 0 | PASS 181 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
Undeclared package ‘fso’ in Rd xrefs
Unknown package ‘optpart’ 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.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bslib’ ‘ggplot2’ ‘shinydashboard’
  All declared Imports should be used.
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.
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.
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.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘leaflet’
  All declared Imports should be used.
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.
Found the following significant warnings:
  ../src/geos_include/nlohmann_json.hpp:25253:35: warning: identifier '_json' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../src/geos_include/nlohmann_json.hpp:25272:49: warning: identifier '_json_pointer' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/libgeos.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 20.1.0-rc2’
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘data.table’ ‘e1071’ ‘fastmatch’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘itertools’ ‘knitr’ ‘utils’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/literanger.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
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.
Running examples in ‘lme4-Ex.R’ failed
The error most likely occurred in:

> ### Name: profile-methods
> ### Title: Profile method for merMod objects
> ### Aliases: as.data.frame.thpr log.thpr logProf varianceProf
> ###   profile-methods profile.merMod
> ### Keywords: methods
> 
> ### ** Examples
> 
> fm01ML <- lmer(Yield ~ 1|Batch, Dyestuff, REML = FALSE)
Warning in optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower,  :
  convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 1.01096 (tol = 0.002, component 1)
> system.time(
+   tpr  <- profile(fm01ML, optimizer="Nelder_Mead", which="beta_")
+ )## fast; as only *one* beta parameter is profiled over -> 0.09s (2022)
Error in profile.merMod(fm01ML, optimizer = "Nelder_Mead", which = "beta_") : 
  Profiling over both the residual variance and
fixed effects is not numerically consistent with
profiling over the fixed effects only (relative difference: 1);
consider adjusting devmatchtol
Calls: system.time -> profile -> profile.merMod
Timing stopped at: 0.039 0 0.041
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘lmerperf.Rmd’ using rmarkdown
--- finished re-building ‘lmerperf.Rmd’

--- re-building ‘Theory.Rnw’ using knitr
--- finished re-building ‘Theory.Rnw’

--- re-building ‘lmer.Rnw’ using knitr

Quitting from lines 2660-2661 [profile_zeta_plot] (lmer.Rnw)
Error: processing vignette 'lmer.Rnw' failed with diagnostics:
arguments imply differing number of rows: 18, 0
--- failed re-building ‘lmer.Rnw’

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

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

Error: Vignette re-building failed.
Execution halted
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.
Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘purrr’ ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘base’ ‘qpdf’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/lobstr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
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.
Namespace in Imports field not imported from: ‘lestat’
  All declared Imports should be used.
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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(longpower)
  Loading required package: lme4
  Loading required package: Matrix
  Loading required package: nlme
  
  Attaching package: 'nlme'
  
  The following object is masked from 'package:lme4':
  
      lmList
  
  > 
  > test_check("longpower")
  
   Converting negative delta to absolute value, you have specified:  -0.2560938 
  [ FAIL 4 | WARN 4 | SKIP 0 | PASS 43 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('tests.R:94:3'): lmmpower (diggle) ─────────────────────────────────
  lmmpower(fm1, pct.change = 0.3, t = seq(0, 9, 1), power = 0.8)$n[1] not equal to 68.4699286748582.
  1/1 mismatches
  [1] 956 - 68.5 == 888
  ── Failure ('tests.R:182:3'): lmmpower (liuliang) ──────────────────────────────
  ...[] not equal to 68.4699286748582.
  1/1 mismatches
  [1] 956 - 68.5 == 888
  ── Failure ('tests.R:211:3'): lmmpower (edland) ────────────────────────────────
  ...[] not equal to 68.4699286748582.
  1/1 mismatches
  [1] 956 - 68.5 == 888
  ── Failure ('tests.R:268:3'): lmmpower (hu) ────────────────────────────────────
  ...[] not equal to 67.1745.
  1/1 mismatches
  [1] 954 - 67.2 == 887
  
  [ FAIL 4 | WARN 4 | SKIP 0 | PASS 43 ]
  Error: Test failures
  Execution halted
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.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/lotri.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 20.1.0-rc2’
* used C++ compiler: ‘clang version 20.1.0-rc2’
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.
Namespaces in Imports field not imported from:
  ‘Icens’ ‘interval’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘rpostgis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
Running ‘azimuth.R’
  Comparing ‘azimuth.Rout’ to ‘azimuth.Rout.save’ ... OK
  Running ‘dist.R’
  Comparing ‘dist.Rout’ to ‘dist.Rout.save’ ... OK
  Running ‘geod.R’
  Comparing ‘geod.Rout’ to ‘geod.Rout.save’ ... OK
  Running ‘perimeter.R’
  Comparing ‘perimeter.Rout’ to ‘perimeter.Rout.save’ ...9c9
< [1] 176215.7 149266.8 199587.9 375136.8 263512.7
---
> [1] 176214.9 149265.4 199586.8 375137.8 263512.6
12c12
< [1] 176215.7 149266.8 199587.9 375136.8 263512.7
---
> [1] 176214.9 149265.4 199586.8 375137.8 263512.6
  Running ‘testthat.R’
  Comparing ‘testthat.Rout’ to ‘testthat.Rout.save’ ... OK
  Running ‘twkb.R’
  Comparing ‘twkb.Rout’ to ‘twkb.Rout.save’ ... OK
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/lzstring.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ngram’ ‘shinythemes’ ‘topicmodels’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shinythemes’ ‘topicmodels’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rlang’ ‘torch’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/magick.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘cli’ ‘nomnoml’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Running examples in ‘mapping-Ex.R’ failed
The error most likely occurred in:

> ### Name: mapping
> ### Title: Static maps
> ### Aliases: mapping
> 
> ### ** Examples
> 
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(sf)
Linking to GEOS 3.12.2, GDAL 3.5.3, PROJ 9.3.1; sf_use_s2() is TRUE
> 
> data("popIT")
> popIT <- popIT
> coords <- loadCoordIT(unit = "provincia", year = '2019')
> cr <- left_join(coords, popIT, by = c( "provincia" = "ID"))
> 
> ###############
> #   Statics   #
> ###############
> 
> mapping(cr)

── tmap v3 code detected ───────────────────────────────────────────────────────
[v3->v4] `tm_borders()`: use 'fill' for the fill color of polygons/symbols
(instead of 'col'), and 'col' for the outlines (instead of 'border.col').
This message is displayed once every 8 hours.
[v3->v4] `tm_borders()`: use `fill_alpha` instead of `alpha`.
Error in `<current-expression>` : node stack overflow
Calls: <Anonymous> ... as.data.table -> as.data.table.data.frame -> as.data.table
Execution halted
Namespace in Imports field not imported from: ‘pbmcapply’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/marquee.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 20.1.0-rc2’
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespace in Imports field not imported from: ‘formatR’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Running ‘testthat.R’ [8s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(MazamaRollUtils)
  > 
  > test_check("MazamaRollUtils")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 560 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-na_rm.R:33:3'): na removal is supported ──────────────────────
  roll_median(x, 3, na.rm = TRUE) not equal to c(NA, 2, 3, 4, NA, 6, 7, 8, 9, NA).
  3/10 mismatches (average diff: 1)
  [4]  3 -  4 == -1
  [5]  6 - NA == NA
  [6] NA -  6 == NA
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 560 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘effsize’ ‘psych’
  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.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’ ‘copula’ ‘missMethods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lars’ ‘methods’ ‘parallel’ ‘smoothmest’
  All declared Imports should be used.
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.
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.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
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.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/meltr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Running examples in ‘memisc-Ex.R’ failed
The error most likely occurred in:

> ### Name: html
> ### Title: Building Blocks for HTML Code
> ### Aliases: html print.html_elem as.character.html_elem c.html_elem
> ###   html_group as.html_group as.character.html_group print.html_group
> ###   [.html_group [<-.html_group c.html_group content content<- setContent
> ###   attribs attribs<- setAttribs setAttribs.character
> ###   setAttribs.html_elem setAttribs.html_group [<-.html_attributes css
> ###   as.css style style<- setStyle setStyle.character setStyle.html_elem
> ###   setStyle.html_group as.character.css print.css [<-.css
> 
> ### ** Examples
> 
> 
> html("img")
<img> 
> html("img",src="test.png")
<img src="test.png"> 
> html("div",class="element",id="first","Sisyphus")
Warning in is.na(recursive) :
  is.na() applied to non-(list or vector) of type 'builtin'
Error in islistfactor(x, recursive) : NA in coercion to Rboolean
Calls: <Anonymous> ... cat -> as.character -> as.character.html_elem -> unlist
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘anes48.Rmd’ using rmarkdown

Quitting from lines 122-123 [unnamed-chunk-6] (anes48.Rmd)
Error: processing vignette 'anes48.Rmd' failed with diagnostics:
NA in coercion to Rboolean
--- failed re-building ‘anes48.Rmd’

--- re-building ‘ftable-matrix.Rmd’ using rmarkdown

Quitting from lines 53-54 [unnamed-chunk-7] (ftable-matrix.Rmd)
Error: processing vignette 'ftable-matrix.Rmd' failed with diagnostics:
NA in coercion to Rboolean
--- failed re-building ‘ftable-matrix.Rmd’

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

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

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

Quitting from lines 380-381 [unnamed-chunk-25] (items.Rmd)
Error: processing vignette 'items.Rmd' failed with diagnostics:
NA in coercion to Rboolean
--- failed re-building ‘items.Rmd’

--- re-building ‘mtable-html.Rmd’ using rmarkdown

Quitting from lines 42-43 [unnamed-chunk-5] (mtable-html.Rmd)
Error: processing vignette 'mtable-html.Rmd' failed with diagnostics:
NA in coercion to Rboolean
--- failed re-building ‘mtable-html.Rmd’

SUMMARY: processing the following files failed:
  ‘anes48.Rmd’ ‘ftable-matrix.Rmd’ ‘items.Rmd’ ‘mtable-html.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat-a_m.R’ [63s/51s]
  Running ‘testthat-m_z.R’ [74s/58s]
Running the tests in ‘tests/testthat-m_z.R’ failed.
Complete output:
  > library(testthat)
  > library(merTools)
  Loading required package: arm
  Loading required package: MASS
  Loading required package: Matrix
  Loading required package: lme4
  
  arm (Version 1.14-4, built: 2024-4-1)
  
  Working directory is /data/gannet/ripley/R/packages/tests-clang/merTools.Rcheck/tests
  
  > 
  > 
  > test_check("merTools", filter = "^[m-z]")
  Starting 2 test processes
  [ FAIL 1 | WARN 50 | SKIP 36 | PASS 249 ]
  
  ══ Skipped tests (36) ══════════════════════════════════════════════════════════
  • On CRAN (36): 'test-merModList.R:10:3', 'test-merModList.R:46:3',
    'test-merModList.R:72:3', 'test-merModList.R:128:3', 'test-plots.R:6:3',
    'test-predict.R:6:3', 'test-predict.R:28:3', 'test-predict.R:99:3',
    'test-predict1.R:7:3', 'test-predict1.R:35:3', 'test-predict1.R:76:3',
    'test-predict1.R:118:3', 'test-predict2.R:4:3', 'test-predict2.R:27:3',
    'test-predict2.R:55:3', 'test-predict2.R:86:3', 'test-predict2.R:132:3',
    'test-predict2.R:150:3', 'test-predict2.R:165:3', 'test-predict2.R:200:3',
    'test-predict2.R:228:3', 'test-predict3.R:5:3', 'test-predict3.R:42:3',
    'test-predict3.R:108:3', 'test-predict3.R:135:3', 'test-predict3.R:156:3',
    'test-predict4.R:6:3', 'test-predict4.R:40:3', 'test-predict4.R:105:3',
    'test-predict4.R:198:3', 'test-subboot.R:31:3', 'test-subboot.R:51:3',
    'test-substEff.R:9:3', 'test-substEff.R:27:3', 'test-substEff.R:56:3',
    'test-substEff.R:103:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-seeds.R:45:3'): Equivalent seeds return equivalent results ───
  identical(s1a, s2) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  
  [ FAIL 1 | WARN 50 | SKIP 36 | PASS 249 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘gbm’ ‘ggplot2’ ‘graphics’ ‘randomForest’
  All declared Imports should be used.
Running examples in ‘metalite.ae-Ex.R’ failed
The error most likely occurred in:

> ### Name: tlf_ae_specific
> ### Title: Specific adverse events table
> ### Aliases: tlf_ae_specific
> 
> ### ** Examples
> 
> meta <- meta_ae_example()
> 
> meta |>
+   prepare_ae_specific(
+     population = "apat",
+     observation = "wk12",
+     parameter = "rel"
+   ) |>
+   format_ae_specific() |>
+   tlf_ae_specific(
+     source = "Source:  [CDISCpilot: adam-adsl; adae]",
+     meddra_version = "24.0",
+     path_outdata = tempfile(fileext = ".Rdata"),
+     path_outtable = tempfile(fileext = ".rtf")
+   )
The outdata is saved in/tmp/Rtmplm2rf6/working_dir/RtmpQDQR5p/file3479a175d2dc2f.Rdata
Error in unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"),  : 
  'recursive' must be of length 1
Calls: tlf_ae_specific ... rtf_encode_table -> paste -> as_rtf_footnote -> unlist
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ae-listing.Rmd’ using rmarkdown

Quitting from lines 100-107 [unnamed-chunk-10] (ae-listing.Rmd)
Error: processing vignette 'ae-listing.Rmd' failed with diagnostics:
'recursive' must be of length 1
--- failed re-building ‘ae-listing.Rmd’

--- re-building ‘ae-specific-subgroup.Rmd’ using rmarkdown

Quitting from lines 159-166 [unnamed-chunk-17] (ae-specific-subgroup.Rmd)
Error: processing vignette 'ae-specific-subgroup.Rmd' failed with diagnostics:
'recursive' must be of length 1
--- failed re-building ‘ae-specific-subgroup.Rmd’

--- re-building ‘ae-specific.Rmd’ using rmarkdown

Quitting from lines 253-260 [unnamed-chunk-22] (ae-specific.Rmd)
Error: processing vignette 'ae-specific.Rmd' failed with diagnostics:
'recursive' must be of length 1
--- failed re-building ‘ae-specific.Rmd’

--- re-building ‘ae-summary.Rmd’ using rmarkdown
--- finished re-building ‘ae-summary.Rmd’

--- re-building ‘exposure-adjusted-event-rate.Rmd’ using rmarkdown
--- finished re-building ‘exposure-adjusted-event-rate.Rmd’

--- re-building ‘metalite-ae.Rmd’ using rmarkdown
--- finished re-building ‘metalite-ae.Rmd’

--- re-building ‘rate-compare.Rmd’ using rmarkdown
--- finished re-building ‘rate-compare.Rmd’

SUMMARY: processing the following files failed:
  ‘ae-listing.Rmd’ ‘ae-specific-subgroup.Rmd’ ‘ae-specific.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘metalite.sl-Ex.R’ failed
The error most likely occurred in:

> ### Name: rtf_exp_duration
> ### Title: Exposure duration table
> ### Aliases: rtf_exp_duration
> 
> ### ** Examples
> 
> meta <- meta_sl_exposure_example()
> 
> meta |>
+   prepare_exp_duration(population = "apat", parameter = "expdur") |>
+   format_exp_duration(display_col = c("n", "prop", "total")) |>
+   rtf_exp_duration(
+     source = "Source: [CDISCpilot: adam-adsl; adex]",
+     path_outdata = tempfile(fileext = ".Rdata"),
+     path_outtable = tempfile(fileext = ".rtf")
+   )
The outdata is saved in/tmp/Rtmp83TD5h/working_dir/RtmpcuI9h1/file34a70f1fe49c29.Rdata
Error in unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"),  : 
  'recursive' must be of length 1
Calls: rtf_exp_duration ... rtf_encode_table -> paste -> as_rtf_footnote -> unlist
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘baseline-character.Rmd’ using rmarkdown
--- finished re-building ‘baseline-character.Rmd’

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

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

Quitting from lines 149-155 [unnamed-chunk-11] (exp_duration.Rmd)
Error: processing vignette 'exp_duration.Rmd' failed with diagnostics:
'recursive' must be of length 1
--- failed re-building ‘exp_duration.Rmd’

--- re-building ‘interactive-baseline.Rmd’ using rmarkdown
--- finished re-building ‘interactive-baseline.Rmd’

--- re-building ‘metalite.sl.Rmd’ using rmarkdown
--- finished re-building ‘metalite.sl.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘lmerTest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ade4’ ‘dendextend’ ‘ggforce’ ‘ggrepel’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyBS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘boot’ ‘energy’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘R6’ ‘reticulate’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘curl’ ‘jsonlite’ ‘parallel’ ‘tools’ ‘vctrs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/minired.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/tzdb/include/date/date.h:966:34: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/tzdb/include/date/date.h:967:34: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/tzdb/include/date/date.h:1975:13: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/tzdb/include/date/date.h:1983:13: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/minty.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘pracma’ ‘rstantools’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘mcmcr’
  All declared Imports should be used.
Found the following files/directories:
  ‘par-7269706c6579’
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/MixAll.Rcheck/00install.out’ for details.
Running examples in ‘MixRF-Ex.R’ failed
The error most likely occurred in:

> ### Name: MixRF
> ### Title: Mixed Random Forest
> ### Aliases: MixRF
> 
> ### ** Examples
> 
> 
> data(sleepstudy)
> 
> tmp = MixRF(Y = sleepstudy$Reaction, X = as.data.frame(sleepstudy$Days), 
+     random = "(Days|Subject)", data = sleepstudy, initialRandomEffects = 0, 
+     ErrorTolerance = 0.01, MaxIterations = 100)
Warning in optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower,  :
  convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  unable to evaluate scaled gradient
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
Error in while (ContinueCondition) { : 
  missing value where TRUE/FALSE needed
Calls: MixRF
Execution halted
Namespaces in Imports field not imported from:
  ‘ashr’ ‘fdrtool’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ConfusionTableR’ ‘OddsPlotty’ ‘caret’ ‘dplyr’ ‘ggplot2’ ‘parsnip’
  ‘ranger’ ‘recipes’ ‘rsample’ ‘varhandle’ ‘workflows’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ClusterR’ ‘MASS’ ‘Rdpack’ ‘multiwave’ ‘randomForest’ ‘ranger’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/mlpack.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘caret’ ‘randomForest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘GGally’ ‘Metrics’ ‘data.table’ ‘dplyr’ ‘ggparty’ ‘mlr3’
  ‘mlr3learners’ ‘mlr3measures’ ‘mlr3pipelines’ ‘mlr3viz’ ‘patchwork’
  ‘plyr’ ‘purrr’ ‘shinyWidgets’ ‘shinyalert’ ‘shinydashboard’ ‘shinyjs’
  ‘stats’ ‘stringr’
  All declared Imports should be used.
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.
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.
Namespace in Imports field not imported from: ‘GFM’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘magrittr’ ‘reticulate’ ‘tensorflow’ ‘usethis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.
Running ‘testthat.R’ [63s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > #
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > library(testthat)
  > library(modelbased)
  > 
  > test_check("modelbased")
  Starting 2 test processes
  [ FAIL 1 | WARN 22 | SKIP 17 | PASS 168 ]
  
  ══ Skipped tests (17) ══════════════════════════════════════════════════════════
  • .Platform$OS.type == "windows" is not TRUE (1):
    'test-estimate_predicted.R:56:3'
  • On CRAN (13): 'test-brms-marginaleffects.R:1:1', 'test-brms.R:1:1',
    'test-estimate_contrasts.R:1:1', 'test-estimate_contrasts_methods.R:1:1',
    'test-estimate_means.R:1:1', 'test-estimate_means_counterfactuals.R:1:1',
    'test-estimate_means_mixed.R:1:1', 'test-g_computation.R:1:1',
    'test-get_marginaltrends.R:1:1', 'test-glmmTMB.R:1:1', 'test-ordinal.R:1:1',
    'test-predict-dpar.R:1:1', 'test-vcov.R:1:1'
  • On Linux (3): 'test-plot-facet.R:1:1', 'test-plot.R:1:1', 'test-print.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-estimate_predicted.R:204:3'): estimate_expectation - predicting RE works ──
  out$Predicted (`actual`) not equal to c(...) (`expected`).
  
    `actual`: 12.2617 12.0693 11.1560 11.6318 11.1657 10.3811 11.1074 11.0749
  `expected`: 12.2064 12.0631 11.2071 11.6286 11.2327 10.5839 11.2085 11.1229
  
  [ FAIL 1 | WARN 22 | SKIP 17 | PASS 168 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘DALEX’ ‘DT’ ‘auditor’ ‘breakDown’ ‘drifter’ ‘svglite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘crayon’ ‘dials’ ‘glue’ ‘parsnip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘NlcOptim’
  All declared Imports should be used.
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.
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.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘grDevices’ ‘graphics’ ‘iterators’ ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘markdown’ ‘methods’ ‘vctrs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
1585,1588d1584
< Warning in optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower,  :
<   convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
< Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
<   Model failed to converge with max|grad| = 1.60567 (tol = 0.002, component 1)
Running ‘bugfix.R’ [5s/10s]
  Comparing ‘bugfix.Rout’ to ‘bugfix.Rout.save’ ... OK
  Running ‘regtest-Tukey.R’
  Comparing ‘regtest-Tukey.Rout’ to ‘regtest-Tukey.Rout.save’ ... OK
  Running ‘regtest-anova.R’
  Comparing ‘regtest-anova.Rout’ to ‘regtest-anova.Rout.save’ ... OK
  Running ‘regtest-fixest.R’
  Running ‘regtest-interface-extended.R’
  Comparing ‘regtest-interface-extended.Rout’ to ‘regtest-interface-extended.Rout.save’ ... OK
  Running ‘regtest-interface.R’
  Comparing ‘regtest-interface.Rout’ to ‘regtest-interface.Rout.save’ ... OK
  Running ‘regtest-lme.R’
  Comparing ‘regtest-lme.Rout’ to ‘regtest-lme.Rout.save’ ...59c59
< 1 53.53  3  1.416e-11
---
> 1 67.07  3  1.812e-14
67,71d66
< Warning messages:
< 1: In optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower,  :
<   convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
< 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
<   Model failed to converge with max|grad| = 1.60567 (tol = 0.002, component 1)
  Running ‘regtest-mmm.R’
  Comparing ‘regtest-mmm.Rout’ to ‘regtest-mmm.Rout.save’ ... OK
  Running ‘regtest-survival.R’
  Comparing ‘regtest-survival.Rout’ to ‘regtest-survival.Rout.save’ ... OK
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.
Found the following significant warnings:
  src/core/attributes/date.hpp:1189:13: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  src/core/attributes/date.hpp:1191:13: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  src/core/attributes/date.hpp:2195:13: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  src/core/attributes/date.hpp:2203:13: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/multinet.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘fields’ ‘optmatch’ ‘rcbalance’ ‘utils’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/multipleDL.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘poweRlaw’ ‘rmutil’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘grDevices’ ‘knitr’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘glue’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Kendall’ ‘perm’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/RcppDate/include/date.h:966:34: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/RcppDate/include/date.h:967:34: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/RcppDate/include/date.h:1975:13: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/RcppDate/include/date.h:1983:13: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/nanotime.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘rrpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magick’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
Found the following significant warnings:
  ../inst/include/json.h:22665:35: warning: identifier '_json' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/json.h:22684:49: warning: identifier '_json_pointer' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/ndjson.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘quickcode’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘curl’ ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nflfastR’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NHSRdatasets’ ‘grid’ ‘utils’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘digest’ ‘hash’
  All declared Imports should be used.
Running examples in ‘noegletalR-Ex.R’ failed
The error most likely occurred in:

> ### Name: noegletal_get
> ### Title: Get data from noegletal.dk
> ### Aliases: noegletal_get
> 
> ### ** Examples
> 
> noegletal_get(muni_codes = c(101, 155), years = 2018:2024, variable_ids = c(001))
Getting requested data from noegletal.dk ...
Error in `dplyr::select()`:
! Can't select columns past the end.
ℹ Location 1 doesn't exist.
ℹ There are only 0 columns.
Backtrace:
     ▆
  1. ├─noegletalR::noegletal_get(...)
  2. │ └─noegletalR:::noegletal_parse_html(...)
  3. │   ├─dplyr::select(tibble::as_tibble(data_matrix), -1)
  4. │   └─dplyr:::select.data.frame(tibble::as_tibble(data_matrix), -1)
  5. │     └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call)
  6. │       └─tidyselect:::eval_select_impl(...)
  7. │         ├─tidyselect:::with_subscript_errors(...)
  8. │         │ └─base::withCallingHandlers(...)
  9. │         └─tidyselect:::vars_select_eval(...)
 10. │           └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 11. │             └─tidyselect:::eval_c(expr, data_mask, context_mask)
 12. │               └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 13. │                 └─tidyselect:::sel_diff(out, new, vars, error_call = error_call)
 14. │                   └─tidyselect:::loc_validate(y, vars, call = error_call)
 15. │                     └─vctrs::vec_as_location(pos, n = length(vars), call = call)
 16. └─vctrs (local) `<fn>`()
 17.   └─vctrs:::stop_subscript_oob(...)
 18.     └─vctrs:::stop_subscript(...)
 19.       └─rlang::abort(...)
Execution halted
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.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘e1071’ ‘glmnet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’ ‘base’ ‘graphics’ ‘parallel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘optparse’ ‘vcfR’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pedtools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ape’
  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.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘usage.Rmd’ using rmarkdown

Quitting from lines 129-140 [glmnet-offset-fix] (usage.Rmd)
Error: processing vignette 'usage.Rmd' failed with diagnostics:
unused argument (call = call)
--- failed re-building ‘usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ohtadstats-Ex.R’ failed
The error most likely occurred in:

> ### Name: dheatmap
> ### Title: Heatmap Plot
> ### Aliases: dheatmap
> 
> ### ** Examples
> 
> data(miyashita_langley_data)
> miyashita_langley_subset <- miyashita_langley_data[,1:15]
> ml_results <- dwrapper(miyashita_langley_subset)
Error in sum(geno[, 1], na.rm = T) : NA in coercion to Rboolean
Calls: dwrapper ... structure -> eval -> eval -> tapply -> lapply -> FUN -> FUN
Execution halted
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.
Namespaces in Imports field not imported from:
  ‘crayon’ ‘testthat’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/OncoBayes2.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘rlang’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘glue’ ‘httpcode’ ‘httr’ ‘jsonlite’ ‘tidyr’
  All declared Imports should be used.
Running ‘buffer.R’
  Comparing ‘buffer.Rout’ to ‘buffer.Rout.save’ ...5,10d4
< > 
< > if (!length(oclPlatforms())) {
< +     cat("== Cannot run tests as there is no platform")
< +     q("no")
< + }
< > 
  Running ‘kernel.R’
  Comparing ‘kernel.Rout’ to ‘kernel.Rout.save’ ...5,10d4
< > 
< > if (!length(oclPlatforms())) {
< +     cat("== Cannot run tests as there is no platform")
< +     q("no")
< + }
< >
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.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘scales’ ‘tools’
  All declared Imports should be used.
Running examples in ‘ormBigData-Ex.R’ failed
The error most likely occurred in:

> ### Name: ormBD
> ### Title: Cumulative Probability Model for Big Data
> ### Aliases: ormBD
> 
> ### ** Examples
> 
> ## generate a small example data and run one of the three methods 
> set.seed(1)
> n <- 200
> x1 = rnorm(n); x2 = rnorm(n)
> tmpdata = data.frame(x1 = x1, x2 = x2, y = rnorm(n) + x1 + 2*x2)
> modbinning <- ormBD(y ~ x1 + x2, data = tmpdata, family = loglog,
+                      approach = "binning", target_num = 100)
Error: object 'loglog' not found
Execution halted
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘openssl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘astsa’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘smoothmest’
  All declared Imports should be used.
Running ‘regtest-plot.R’
  Running ‘regtest-summarize.R’
  Running ‘testthat.R’ [24s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(papeR)
  Loading required package: car
  Loading required package: carData
  Loading required package: xtable
  Registered S3 method overwritten by 'papeR':
    method    from
    Anova.lme car 
  
  Attaching package: 'papeR'
  
  The following object is masked from 'package:utils':
  
      toLatex
  
  > 
  > test_check("papeR")
  [ FAIL 1 | WARN 15 | SKIP 0 | PASS 237 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-prettify.R:190:13'): lme4 interface works ──────────────────────
  Error in `expect_match(all.equal(res[[1]], res[[5]], check.attributes = FALSE)[1], 
      "lower")`: is.character(act$val) is not TRUE
  Backtrace:
      ▆
   1. └─testthat::expect_match(...) at test-prettify.R:190:13
   2.   └─base::stopifnot(is.character(act$val))
  
  [ FAIL 1 | WARN 15 | SKIP 0 | PASS 237 ]
  Error: Test failures
  Execution halted
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/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/particles.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘ComplexHeatmap’ ‘mathjaxr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘testthat’ ‘usethis’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘clusterProfiler’ ‘purrr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘cohort-intersect.Rmd’ using rmarkdown

Quitting from lines 23-38 [unnamed-chunk-1] (cohort-intersect.Rmd)
Error: processing vignette 'cohort-intersect.Rmd' failed with diagnostics:
'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
--- failed re-building ‘cohort-intersect.Rmd’

--- re-building ‘concept-intersect.Rmd’ using rmarkdown

Quitting from lines 36-40 [unnamed-chunk-2] (concept-intersect.Rmd)
Error: processing vignette 'concept-intersect.Rmd' failed with diagnostics:
could not find function "eunomia_is_available"
--- failed re-building ‘concept-intersect.Rmd’

--- re-building ‘demographics.rmd’ using rmarkdown

Quitting from lines 20-28 [unnamed-chunk-1] (demographics.rmd)
Error: processing vignette 'demographics.rmd' failed with diagnostics:
'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
--- failed re-building ‘demographics.rmd’

--- re-building ‘summarise.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB


Quitting from lines 85-138 [unnamed-chunk-4] (summarise.Rmd)
Error: processing vignette 'summarise.Rmd' failed with diagnostics:
error in evaluating the argument 'dbObj' in selecting a method for function 'dbIsValid': could not find function "eunomia_dir"
--- failed re-building ‘summarise.Rmd’

--- re-building ‘table-intersect.Rmd’ using rmarkdown

Quitting from lines 35-39 [unnamed-chunk-3] (table-intersect.Rmd)
Error: processing vignette 'table-intersect.Rmd' failed with diagnostics:
could not find function "eunomia_is_available"
--- failed re-building ‘table-intersect.Rmd’

SUMMARY: processing the following files failed:
  ‘cohort-intersect.Rmd’ ‘concept-intersect.Rmd’ ‘demographics.rmd’
  ‘summarise.Rmd’ ‘table-intersect.Rmd’

Error: Vignette re-building failed.
Execution halted
---- unloading
[gannet:2171092:0:2171092] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x7fefe51b6960)
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
File ‘pbivnorm/libs/pbivnorm.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.
Error(s) in re-building vignettes:
--- re-building ‘a01-pbkrtest.rmd’ using knitr
** Processing: figure/unnamed-chunk-3-1.png
504x504 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 9715 bytes
Input file size = 9805 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 7884
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 7884

Output IDAT size = 7884 bytes (1831 bytes decrease)
Output file size = 7962 bytes (1843 bytes = 18.80% decrease)


Quitting from lines 153-156 [unnamed-chunk-15] (a01-pbkrtest.rmd)
Error: processing vignette 'a01-pbkrtest.rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘a01-pbkrtest.rmd’

--- re-building ‘a02-coercion.rmd’ using knitr
--- finished re-building ‘a02-coercion.rmd’

SUMMARY: processing the following file failed:
  ‘a01-pbkrtest.rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
File ‘pdc/libs/pdc.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.
Running examples in ‘PDE-Ex.R’ failed
The error most likely occurred in:

> ### Name: PDE_analyzer
> ### Title: Extracting data from PDF (Portable Document Format) files
> ### Aliases: PDE_analyzer
> 
> ### ** Examples
> 
>  if(PDE_check_Xpdf_install() == TRUE){
+    PDE_analyzer(paste0(system.file(package = "PDE"),
+    "/examples/tsvs/PDE_parameters_v1.4_all_files+-0.tsv"))
+  }
Error in `<current-expression>` : error in running command
Calls: PDE_check_Xpdf_install
Execution halted
File ‘pdist/libs/pdist.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: ‘ncvreg’
  All declared Imports should be used.
File ‘PDSCE/libs/PDSCE.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 ‘penMSM/libs/penMSM.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: ‘fixest’
  All declared Imports should be used.
File ‘PerfMeas/libs/PerfMeas.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: ‘rms’
  All declared Imports should be used.
File ‘pgee.mixed/libs/pgee.mixed.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 ‘ph2bye/libs/ph2bye.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:
  ‘C50’ ‘HDclassif’ ‘MASS’ ‘MLmetrics’ ‘Matrix’ ‘adabag’ ‘base’
  ‘caTools’ ‘e1071’ ‘earth’ ‘evtree’ ‘frbs’ ‘glmnet’ ‘hda’ ‘ipred’
  ‘kernlab’ ‘kknn’ ‘klaR’ ‘mda’ ‘nnet’ ‘party’ ‘pls’ ‘randomForest’
  ‘rpartScore’ ‘sparseLDA’ ‘themis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tidyverse’ ‘usethis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘BH’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘PlackettLuce’ ‘StatRank’ ‘pmr’ ‘prefmod’ ‘rankdist’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ssh’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘base’ ‘grDevices’
  All declared Imports should be used.
Running ‘testthat.R’ [99s/99s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(poems)
  > 
  > test_check("poems")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1093 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_results_manager.R:385:5'): calculate summary weighted averages ──
  Error in `FUN(newX[, i], ...)`: NA in coercion to Rboolean
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(results_manager$calculate_summary_weighted_averages(na_replacements = list(abundance = na_function))) at test_results_manager.R:388:3
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. └─results_manager$calculate_summary_weighted_averages(na_replacements = list(abundance = na_function))
   10.   └─na_replacements[[param]](summary_matrix_list[[param]])
   11.     └─base::apply(a, 2, min, na.rm = NA) at test_results_manager.R:385:5
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1093 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘car’ ‘formula.tools’ ‘ggplot2’ ‘gplots’ ‘graphics’ ‘purrr’
  ‘rstatix’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
File ‘population/libs/population.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:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/poputils.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/rvinecopulib/include/vinecopulib/misc/nlohmann_json.hpp:25226:47: warning: identifier '_json' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/rvinecopulib/include/vinecopulib/misc/nlohmann_json.hpp:25245:61: warning: identifier '_json_pointer' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/portvine.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘rpart’ ‘withr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bslib’ ‘shinyjs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’ ‘numDeriv’ ‘tidyr’
  All declared Imports should be used.
File ‘prclust/libs/prclust.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:
  ‘class’ ‘forcats’ ‘irr’ ‘lpSolve’ ‘purrr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
Running ‘test01-utility.R’
  Comparing ‘test01-utility.Rout’ to ‘test01-utility.Rout.save’ ... OK
  Running ‘test03-channel-type.R’
  Comparing ‘test03-channel-type.Rout’ to ‘test03-channel-type.Rout.save’ ... OK
  Running ‘test04-channel.R’
  Comparing ‘test04-channel.Rout’ to ‘test04-channel.Rout.save’ ...42c42
<    0.2436  280.0141  675.7335  987.6435 1355.5114 9630.5918 
---
>    0.244  280.014  675.734  987.643 1355.511 9630.592 
  Running ‘test05-processor.R’
  Comparing ‘test05-processor.Rout’ to ‘test05-processor.Rout.save’ ... OK
  Running ‘test06-pipeline.R’
  Comparing ‘test06-pipeline.Rout’ to ‘test06-pipeline.Rout.save’ ... OK
  Running ‘test07-complete-channel.R’
  Comparing ‘test07-complete-channel.Rout’ to ‘test07-complete-channel.Rout.save’ ...22,27c22,27
<  Min.   :6.560e-02   Min.   :33.61   Min.   :    0.0  
<  1st Qu.:2.855e+02   1st Qu.:55.95   1st Qu.:  225.7  
<  Median :6.874e+02   Median :60.01   Median :  626.7  
<  Mean   :1.003e+03   Mean   :59.99   Mean   :  944.6  
<  3rd Qu.:1.396e+03   3rd Qu.:64.07   3rd Qu.: 1336.5  
<  Max.   :1.178e+04   Max.   :85.24   Max.   :11718.9  
---
>  Min.   :    0.066   Min.   :33.61   Min.   :    0.0  
>  1st Qu.:  285.474   1st Qu.:55.95   1st Qu.:  225.7  
>  Median :  687.351   Median :60.01   Median :  626.7  
>  Mean   : 1002.718   Mean   :59.99   Mean   :  944.6  
>  3rd Qu.: 1395.736   3rd Qu.:64.07   3rd Qu.: 1336.5  
>  Max.   :11776.787   Max.   :85.24   Max.   :11718.9
Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
Running examples in ‘PResiduals-Ex.R’ failed
The error most likely occurred in:

> ### Name: conditional_Spearman
> ### Title: Conditional Partial Spearman's Rank Correlation
> ### Aliases: conditional_Spearman
> 
> ### ** Examples
> 
> data(PResidData)
> library(rms)
Loading required package: Hmisc

Attaching package: ‘Hmisc’

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

    format.pval, units

> #### fitting cumulative link models for both Y and W
> result <- conditional_Spearman(c|y~ x + w, conditional.by="w",
+                                        conditional.method="lm", conditional.formula="~rcs(w)",
+                                        fit.x="poisson",fit.y="orm",
+                                        data=PResidData, fisher=TRUE)
Error in -as.matrix(mod$info.matrix) : invalid argument to unary operator
Calls: conditional_Spearman -> orm.scores
Execution halted
File ‘PRIMAL/libs/PRIMAL.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:
  ‘tidyr’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘LaplacesDemon’ ‘epitools’ ‘rpivotTable’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘StanHeaders’ ‘methods’ ‘rstantools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
File ‘prototest/libs/prototest.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:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/ProTrackR2.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Running ‘basic.R’ [56s/149s]
  Comparing ‘basic.Rout’ to ‘basic.Rout.save’ ...294,307c294,307
<       YYYY         MM          DD      timestamp           Qobs   deseaonalized
<  Min.   :0   Min.   :0   Min.   :0   Min.   :0 secs   Min.   :0   Min.   :0    
<  1st Qu.:0   1st Qu.:0   1st Qu.:0   1st Qu.:0 secs   1st Qu.:0   1st Qu.:0    
<  Median :0   Median :0   Median :0   Median :0 secs   Median :0   Median :0    
<  Mean   :0   Mean   :0   Mean   :0   Mean   :0 secs   Mean   :0   Mean   :0    
<  3rd Qu.:0   3rd Qu.:0   3rd Qu.:0   3rd Qu.:0 secs   3rd Qu.:0   3rd Qu.:0    
<  Max.   :0   Max.   :0   Max.   :0   Max.   :0 secs   Max.   :0   Max.   :0    
<        r1   
<  Min.   :0  
<  1st Qu.:0  
<  Median :0  
<  Mean   :0  
<  3rd Qu.:0  
<  Max.   :0  
---
>       YYYY         MM          DD     timestamp             Qobs  
>  Min.   :0   Min.   :0   Min.   :0   Length:1825       Min.   :0  
>  1st Qu.:0   1st Qu.:0   1st Qu.:0   Class :difftime   1st Qu.:0  
>  Median :0   Median :0   Median :0   Mode  :numeric    Median :0  
>  Mean   :0   Mean   :0   Mean   :0                     Mean   :0  
>  3rd Qu.:0   3rd Qu.:0   3rd Qu.:0                     3rd Qu.:0  
>  Max.   :0   Max.   :0   Max.   :0                     Max.   :0  
>  deseaonalized       r1   
>  Min.   :0     Min.   :0  
>  1st Qu.:0     1st Qu.:0  
>  Median :0     Median :0  
>  Mean   :0     Mean   :0  
>  3rd Qu.:0     3rd Qu.:0  
>  Max.   :0     Max.   :0
File ‘pRSR/libs/pRSR.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:
  ‘devtools’ ‘qpdf’
  All declared Imports should be used.
File ‘pspearman/libs/pspearman.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: ‘longpower’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lifecycle’ ‘patchwork’
  All declared Imports should be used.
Running examples in ‘ptable-Ex.R’ failed
The error most likely occurred in:

> ### Name: modify_cnt_ptable
> ### Title: Modify a ptable suitable for frequency count variables
> ### Aliases: modify_cnt_ptable modify_cnts_ptable
> 
> ### ** Examples
> 
> # Original ptable
> ptab <- create_cnt_ptable(3, 1)
Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
Error: The ptable can't be calculated without a violation of the constraints. The combination of the input parameters you set (e.g. D=3, V=1, js=0 or pstay) doesn't work. Please try another specification: either change the arguments 'mono=' or 'optim=' or try to use a different combination of input parameters (hint: changing the variance is sufficient in most cases).
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 78-81 [unnamed-chunk-4] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
The ptable can't be calculated without a violation of the constraints. The combination of the input parameters you set (e.g. D=2, V=1, js=0 or pstay) doesn't work. Please try another specification: either change the arguments 'mono=' or 'optim=' or try to use a different combination of input parameters (hint: changing the variance is sufficient in most cases).
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘ptinpoly/libs/ptinpoly.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:
  ‘itsadug’ ‘mgcv’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘readr’ ‘tidyverse’
  All declared Imports should be used.
File ‘PWEALL/libs/PWEALL.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: ‘progressr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppEigen’
  All declared Imports should be used.
Running examples in ‘qdapRegex-Ex.R’ failed
The error most likely occurred in:

> ### Name: cheat
> ### Title: A Cheat Sheet of Common Regex Task Chunks
> ### Aliases: cheat
> 
> ### ** Examples
> 
> cheat()
Error in islistfactor(x, recursive) : NA in coercion to Rboolean
Calls: cheat -> sapply -> lapply -> FUN -> unlist
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("qdapRegex")
  > 
  > 
  > test_check("qdapRegex")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 177 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cheat.R:28:5'): cheat returns as expected ──────────────────────
  Error in `islistfactor(x, recursive)`: NA in coercion to Rboolean
  Backtrace:
      ▆
   1. └─qdapRegex::cheat(print = FALSE) at test-cheat.R:28:5
   2.   └─base::sapply(...)
   3.     └─base::lapply(X = X, FUN = FUN, ...)
   4.       └─qdapRegex (local) FUN(X[[i]], ...)
   5.         └─base::unlist(dictionary[[i]], colnames(dictionary)[i])
  ── Error ('test-cheat.R:63:5'): cheat prints as expected ───────────────────────
  Error in `islistfactor(x, recursive)`: NA in coercion to Rboolean
  Backtrace:
       ▆
    1. ├─testthat::expect_equivalent(capture.output(cheat()), out2) at test-cheat.R:63:5
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─utils::capture.output(cheat())
    5. │ └─base::withVisible(...elt(i))
    6. └─qdapRegex::cheat()
    7.   └─base::sapply(...)
    8.     └─base::lapply(X = X, FUN = FUN, ...)
    9.       └─qdapRegex (local) FUN(X[[i]], ...)
   10.         └─base::unlist(dictionary[[i]], colnames(dictionary)[i])
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 177 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘rmarkdown’ ‘stats’
  All declared Imports should be used.
Running examples in ‘qMRI-Ex.R’ failed
The error most likely occurred in:

> ### Name: estimateIRfluid
> ### Title: Estimate parameters in Inversion Recovery MRI experiments model
> ###   for CSF voxel
> ### Aliases: estimateIRfluid
> ### Keywords: models regression
> 
> ### ** Examples
> 
> dataDir0 <- system.file("extdataIR", package = "qMRI")
> dataDir <- tempdir("IRdata")
Error in tempdir(check) : NA in coercion to Rboolean
Execution halted
Namespace in Imports field not imported from: ‘missMethods’
  All declared Imports should be used.
File ‘qrencoder/libs/qrencoder.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:
  ./io/io_common.h:87:44: warning: identifier '_u8' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/qs2.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  ./qs_common.h:98:44: warning: identifier '_u8' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./qs_common.h:101:44: warning: identifier '_u16' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/qs.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespace in Imports field not imported from: ‘MatrixModels’
  All declared Imports should be used.
Found the following significant warnings:
  ../inst/include/cpp11/R.hpp:54:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/cpp11/named_arg.hpp:44:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/QuickJSR.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 20.1.0-rc2’
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘pracma’ ‘zoo’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘quickcode’ ‘stats’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘asd’ ‘cubature’ ‘data.table’ ‘ggplot2’ ‘multxpert’ ‘survival’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘comat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘car’ ‘dplyr’ ‘grid’ ‘gridExtra’ ‘knitr’ ‘lmerTest’ ‘tidyr’
  All declared Imports should be used.
File ‘RANKS/libs/RANKS.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:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/rar.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  vcglib/wrap/callback.h:79:12: warning: address of stack memory associated with local variable 'formatted' returned [-Wreturn-stack-address]
See ‘/data/gannet/ripley/R/packages/tests-clang/ravetools.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/rayrender.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘rex’
  All declared Imports should be used.
File ‘rBeta2009/libs/rBeta2009.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.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/rbioacc.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’ ‘shinythemes’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlemon’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/RcppAlgos.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/RcppBigIntAlgos.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Running ‘simpleTest.R’
Running the tests in ‘tests/simpleTest.R’ failed.
Complete output:
  > 
  > library(RcppNLoptExample)
  > 
  > expected <- c(0.3333333, 0.2962963)
  > 
  > val <- testConstrainedProblem("MMA")
  > stopifnot(all.equal(val, expected, tolerance=1e-5))
  Error: val and expected are not equal:
    Mean relative difference: 0.0001599895
  Execution halted
Registration problem:
  symbol ‘symbol’ in the local frame:
   .Call(symbol)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  ../inst/include/RcppSimdJson/deserialize/../../simdjson.h:3644:44: warning: identifier '_padded' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/RcppSimdJson/deserialize/../../simdjson.h:4026:44: warning: identifier '_padded' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/simdjson.h:3644:44: warning: identifier '_padded' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/simdjson.h:4026:44: warning: identifier '_padded' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/RcppSimdJson.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  ../inst/include/toml++/impl/path.h:793:19: warning: identifier '_tpath' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/toml++/impl/parser.h:348:27: warning: identifier '_toml' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/RcppTOML.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Running ‘zigguratTest.R’
  Comparing ‘zigguratTest.Rout’ to ‘zigguratTest.Rout.save’ ...19c19
< -5.1850164 -0.6758794 -0.0004694 -0.0007290  0.6747338  5.4121839 
---
> -5.185016 -0.675879 -0.000469 -0.000729  0.674734  5.412184 
  Running ‘zigguratTestAll.R’
  Comparing ‘zigguratTestAll.Rout’ to ‘zigguratTestAll.Rout.save’ ... OK
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/readNSx.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/readODS.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/tzdb/include/date/date.h:966:34: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/tzdb/include/date/date.h:967:34: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/tzdb/include/date/date.h:1975:13: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/tzdb/include/date/date.h:1983:13: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/readr.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 20.1.0-rc2’
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/readxl.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 20.1.0-rc2’
* used C++ compiler: ‘clang version 20.1.0-rc2’
Running ‘testthat.R’ [131s/132s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rearrr)
  > 
  > if (require("xpectr")) {
  +   test_check("rearrr")
  + }
  Loading required package: xpectr
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 7341 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_n_fn.R:842:3'): testing quantile_index() ─────────────────────
  xpectr::strip(side_effects_19148[["error"]]) does not match "probs outside 01".
  Actual value: "ℹ In index 1Caused by error in quantiledefault type must be an integer in 19"
  Backtrace:
      ▆
   1. └─testthat::expect_match(...) at test_n_fn.R:842:3
   2.   └─testthat:::expect_match_(...)
  ── Failure ('test_n_fn.R:859:3'): testing quantile_index() ─────────────────────
  xpectr::strip(side_effects_19148[["error"]]) does not match "object a not found".
  Actual value: "ℹ In index 1Caused by error in quantiledefault type must be an integer in 19"
  Backtrace:
      ▆
   1. └─testthat::expect_match(...) at test_n_fn.R:859:3
   2.   └─testthat:::expect_match_(...)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 7341 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/redatam.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/redatamx.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘SemiPar’ ‘caret’ ‘dplyr’ ‘scales’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Deriv’
  All declared Imports should be used.
File ‘remote/libs/remote.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.
Running examples in ‘rempsyc-Ex.R’ failed
The error most likely occurred in:

> ### Name: cormatrix_excel
> ### Title: Easy export of correlation matrix to Excel
> ### Aliases: cormatrix_excel
> ### Keywords: Excel correlation matrix
> 
> ### ** Examples
> 
> ## Don't show: 
> if (requireNamespace("correlation", quietly = TRUE) && requireNamespace("openxlsx2", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ ## Don't show: 
+ .old_wd <- setwd(tempdir())
+ ## End(Don't show)
+ # Basic example
+ cormatrix_excel(mtcars, select = c("mpg", "cyl", "disp", "hp", "carb"), filename = "cormatrix1")
+ cormatrix_excel(iris, p_adjust = "none", filename = "cormatrix2")
+ cormatrix_excel(airquality, method = "spearman", filename = "cormatrix3")
+ ## Don't show: 
+ setwd(.old_wd)
+ ## End(Don't show)
+ ## Don't show: 
+ }) # examplesIf
> .old_wd <- setwd(tempdir())
> cormatrix_excel(mtcars, select = c("mpg", "cyl", "disp", "hp", "carb"), 
+     filename = "cormatrix1")
# Correlation Matrix (pearson-method)

Parameter |      mpg |      cyl |     disp |       hp |    carb
---------------------------------------------------------------
mpg       |          | -0.85*** | -0.85*** | -0.78*** | -0.55**
cyl       | -0.85*** |          |  0.90*** |  0.83*** |  0.53**
disp      | -0.85*** |  0.90*** |          |  0.79*** |   0.39*
hp        | -0.78*** |  0.83*** |  0.79*** |          | 0.75***
carb      |  -0.55** |   0.53** |    0.39* |  0.75*** |        

p-value adjustment method: none
Error: x must be class wbColour
Execution halted
Running ‘testthat.R’ [28s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rempsyc)
  Suggested APA citation: Thériault, R. (2023). rempsyc: Convenience functions for psychology. 
  Journal of Open Source Software, 8(87), 5466. https://doi.org/10.21105/joss.05466
  > 
  > test_check("rempsyc")
  [ FAIL 1 | WARN 0 | SKIP 19 | PASS 46 ]
  
  ══ Skipped tests (19) ══════════════════════════════════════════════════════════
  • On CRAN (19): 'test-best_duplicate.R:8:3', 'test-extract_duplicates.R:8:3',
    'test-find_mad.R:2:3', 'test-format_value.R:2:3',
    'test-nice_assumptions.R:9:3', 'test-nice_contrasts.R:7:3',
    'test-nice_lm.R:5:3', 'test-nice_lm_contrasts.R:12:3',
    'test-nice_lm_slopes.R:5:3', 'test-nice_mod.R:4:3', 'test-nice_na.R:2:3',
    'test-nice_randomize.R:5:3', 'test-nice_reverse.R:3:3',
    'test-nice_slopes.R:4:3', 'test-nice_t_test.R:5:3', 'test-nice_table.R:13:3',
    'test-nice_var.R:2:3', 'test-scale_mad.R:2:3', 'test-winsorize_mad.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cormatrix_excel.R:5:3'): cormatrix_excel ───────────────────────
  Error: x must be class wbColour
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-cormatrix_excel.R:5:3
   2.   └─rlang::cnd_signal(state$error)
  
  [ FAIL 1 | WARN 0 | SKIP 19 | PASS 46 ]
  Error: Test failures
  Execution halted
File ‘repolr/libs/repolr.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.
Running examples in ‘reservr-Ex.R’ failed
The error most likely occurred in:

> ### Name: quantile.Distribution
> ### Title: Quantiles of Distributions
> ### Aliases: quantile.Distribution
> 
> ### ** Examples
> 
> # With quantiles available
> dist <- dist_normal(sd = 1)
> qqs <- quantile(dist, probs = rep(0.5, 3), with_params = list(mean = 1:3))
> stopifnot(all.equal(qqs, 1:3))
> 
> # Without quantiles available
> dist <- dist_erlangmix(shapes = list(1, 2, 3), scale = 1.0)
> my_probs <- c(0, 0.01, 0.25, 0.5, 0.75, 1)
> qqs <- quantile(
+   dist, probs = my_probs,
+   with_params = list(probs = list(0.5, 0.3, 0.2)), .start = 2
+ )
Error in uniroot(diff_prob, lower = q0_min, upper = .start, prob_target = prob) : 
  lower < upper  is not fulfilled
Calls: quantile -> quantile.Distribution -> uniroot
Execution halted
Found the following significant warnings:
  ./nonstd/string_view.hpp:145:40: warning: identifier '_sv' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./nonstd/string_view.hpp:150:43: warning: identifier '_sv' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./nonstd/string_view.hpp:155:43: warning: identifier '_sv' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./nonstd/string_view.hpp:160:41: warning: identifier '_sv' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/RestRserve.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  ../inst/include/nlohmann/json.hpp:26439:35: warning: identifier '_json' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/nlohmann/json.hpp:26458:49: warning: identifier '_json_pointer' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/rethnicity.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  ../inst/include/nlohmann/json.hpp:24392:35: warning: identifier '_json' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/nlohmann/json.hpp:24400:49: warning: identifier '_json_pointer' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/nlohmann/json.hpp:24464:58: warning: identifier '_json' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/nlohmann/json.hpp:24465:58: warning: identifier '_json_pointer' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/rflashtext.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘attempt’ ‘curl’ ‘knitr’
  All declared Imports should be used.
File ‘RI2by2/libs/RI2by2.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.
Running examples in ‘rim-Ex.R’ failed
The error most likely occurred in:

> ### Name: rim-package
> ### Title: rim
> ### Aliases: rim rim-package maxima.start maxima.stop maxima.get
> ###   maxima.load maxima.apropos maxima.version maxima.isInstalled iprint
> ###   print.maxima maxima.eval
> 
> ### ** Examples
> 
> if(maxima.isInstalled()) maxima.start(restart = TRUE)
> if(maxima.isInstalled()) {
+   maxima.start(restart = TRUE)
+   maxima.stop()
+ }
> if(maxima.isInstalled()) maxima.get("2+2;")
> if(maxima.isInstalled()) maxima.load("abs_integrate")
Error in self$get(paste0("load(\"", module, "\")$")) : 
  TEXT;>>file_search1: <<TEXT;
 -- an error. To debug this try: debugmode(true);
Calls: maxima.load -> <Anonymous> -> <Anonymous>
Execution halted
File ‘rIsing/libs/rIsing.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: ‘maxLik’
  All declared Imports should be used.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/rJava.Rcheck/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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/jsoncons/basic_json.hpp:6446:32: warning: identifier '_json' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/jsoncons/basic_json.hpp:6452:33: warning: identifier '_json' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/jsoncons/basic_json.hpp:6458:33: warning: identifier '_ojson' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/jsoncons/basic_json.hpp:6464:34: warning: identifier '_ojson' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/rjsoncons.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
File ‘rkvo/libs/rkvo.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.
Running examples in ‘rllama-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_defillama_stablecoin_data
> ### Title: Stablecoins Data
> ### Aliases: get_defillama_stablecoin_data
> 
> ### ** Examples
> 
> stablecoin_data = get_defillama_stablecoin_data()
Error in circulating * price : non-numeric argument to binary operator
Calls: get_defillama_stablecoin_data -> [ -> [.data.table -> eval -> eval
Execution halted
File ‘Rlof/libs/Rlof.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:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/RMariaDB.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
File ‘RMKdiscrete/libs/RMKdiscrete.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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(rMOST)
  Welcome to rMOST.
  rMOST estimates Pareto-optimal solutions for personnel selection with 3 objectives using Normal Boundary Intersection algorithm.
  > 
  > test_check("rMOST")
  
   Estimating Multi-Objective Optimal Solution ... 
  
  Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
  Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
  Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-MOST.R:27:1'): (code run outside of `test_that()`) ─────────────
  Error in `is.nloptr(ret)`: equality constraints in x0 returns NA
  Backtrace:
       ▆
    1. └─rMOST::MOST(...) at test-MOST.R:27:1
    2.   └─rMOST::ParetoR_3C(...)
    3.     ├─base::suppressWarnings(...)
    4.     │ └─base::withCallingHandlers(...)
    5.     └─rMOST:::NBI_3C(X0, Spac, Fnum, VLB, VUB, TolX, TolF, TolCon)
    6.       ├─base::suppressMessages(...)
    7.       │ └─base::withCallingHandlers(...)
    8.       └─nloptr::slsqp(...)
    9.         └─nloptr::nloptr(...)
   10.           └─nloptr::is.nloptr(ret)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘rMOST-vignette.Rmd’ using rmarkdown

Quitting from lines 61-73 [unnamed-chunk-3] (rMOST-vignette.Rmd)
Error: processing vignette 'rMOST-vignette.Rmd' failed with diagnostics:
equality constraints in x0 returns NA
--- failed re-building ‘rMOST-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qtl’
  All declared Imports should be used.
File ‘rnetcarto/libs/rnetcarto.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: ‘impute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘attention’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
File ‘robustETM/libs/robustETM.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.
Running examples in ‘rock-Ex.R’ failed
The error most likely occurred in:

> ### Name: qna_to_tlm
> ### Title: Convert a QNA network to Linear Topic Map format
> ### Aliases: qna_to_tlm
> 
> ### ** Examples
> 
> ### Get path to example source
> examplePath <-
+   system.file("extdata", package="rock");
> 
> ### Read a souce coded with the Qualitative Network Approach
> qnaExample <-
+   rock::parse_source(
+     file.path(
+       examplePath,
+       "network-example-1.rock"
+     )
+   );
> 
> ### Convert and show the topic map
> cat(
+   rock::qna_to_tlm(
+     qnaExample
+   ),
+   sep="\n"
+ );
Error in unlist(df$from, df$to) : 'recursive' must be of length 1
Calls: cat -> <Anonymous> -> lapply -> FUN -> unique -> unlist
Execution halted
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/roxygen2.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/RPostgres.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 20.1.0-rc2’
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘SparseM’ ‘nlme’ ‘timeDate’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ROCit’ ‘corrplot’ ‘kableExtra’ ‘purrr’ ‘reshape2’
  All declared Imports should be used.
File ‘rsdepth/libs/rsdepth.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:
  ‘keys’ ‘shinyWidgets’ ‘testthat’
  All declared Imports should be used.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/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_Outputfile’,
    ‘R_TempDir’, ‘R_Visible’, ‘R_curErrorBuf’, ‘ptr_R_Busy’,
    ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’, ‘ptr_R_ReadConsole’,
    ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’, ‘ptr_R_WriteConsole’,
    ‘ptr_R_WriteConsoleEx’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
File ‘RSKC/libs/RSKC.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: ‘h2o’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MatrixExtra’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/RSQLite.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 20.1.0-rc2’
* used C++ compiler: ‘clang version 20.1.0-rc2’
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/rstanarm.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
File ‘RTextTools/libs/RTextTools.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:
  ‘httr’ ‘logger’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘MASS’ ‘gridExtra’
  All declared Imports should be used.
Running examples in ‘ruimtehol-Ex.R’ failed
The error most likely occurred in:

> ### Name: embed_articlespace
> ### Title: Build a Starspace model for learning the mapping between
> ###   sentences and articles (articlespace)
> ### Aliases: embed_articlespace
> 
> ### ** Examples
> 
> ## Don't show: 
> if(require(udpipe)){
+ ## End(Don't show)
+ library(udpipe)
+ data(brussels_reviews_anno, package = "udpipe")
+ x <- subset(brussels_reviews_anno, language == "nl")
+ x$token <- x$lemma
+ x <- x[, c("doc_id", "sentence_id", "token")]
+ set.seed(123456789)
+ model <- embed_articlespace(x, early_stopping = 1,
+                             dim = 25, epoch = 25, minCount = 2,
+                             negSearchLimit = 1, maxNegSamples = 2)
+ plot(model)
+ sentences <- c("ook de keuken zijn zeer goed uitgerust .",
+                "het appartement zijn met veel smaak inrichten en zeer proper .")
+ predict(model, sentences, type = "embedding")
+ starspace_embedding(model, sentences)
+ ## Don't show: 
+ } # End of main if statement running only if the required packages are installed
Loading required package: udpipe
Start to initialize starspace model.
Build dict from input file : /tmp/Rtmp8AeXQB/working_dir/RtmpUGqoNy/textspace_31438f76b3ceed.txt

Read 0M words
Number of words in dictionary:  1273
Number of labels in dictionary: 0
Loading data from file : /tmp/Rtmp8AeXQB/working_dir/RtmpUGqoNy/textspace_31438f76b3ceed.txt
Total number of examples loaded : 470
2025-02-19 09:27:53 Initialising with learning rate 0.01
Error(s) in re-building vignettes:
--- re-building ‘ground-control-to-ruimtehol.Rnw’ using Sweave
Namespace in Imports field not imported from: ‘XML’
  All declared Imports should be used.
Found the following significant warnings:
  vcglib/wrap/callback.h:78:12: warning: address of stack memory associated with local variable 'formatted' returned [-Wreturn-stack-address]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rvcg.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 20.1.0-rc2’
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  ../inst/include/vinecopulib/misc/nlohmann_json.hpp:25226:47: warning: identifier '_json' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/vinecopulib/misc/nlohmann_json.hpp:25245:61: warning: identifier '_json_pointer' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/rvinecopulib.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
File ‘rwfec/libs/rwfec.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:
  ‘lifecycle’ ‘mathjaxr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘CARBayesdata’ ‘MASS’ ‘nimble’
  All declared Imports should be used.
File ‘saturnin/libs/saturnin.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: ‘crayon’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘network’
  All declared Imports should be used.
File ‘sBIC/libs/sBIC.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 ‘sbmSDP/libs/sbmSDP.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: ‘pvclust’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mathjaxr’
  All declared Imports should be used.
File ‘SCEPtERbinary/libs/SCEPtERbinary.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 ‘SCEPtER/libs/SCEPtER.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:
  ‘Matrix’ ‘pracma’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RhpcBLASctl’
  All declared Imports should be used.
Running examples in ‘ScottKnott-Ex.R’ failed
The error most likely occurred in:

> ### Name: SK
> ### Title: The SK Test for Single Experiments
> ### Aliases: SK SK.default SK.aov SK.lm SK.formula SK.aovlist SK.lmerMod
> ### Keywords: package
> 
> ### ** Examples
> 
> ##
> ## Examples:Randomized Complete Block Design (RCBD)
> ## More details: demo(package='SK')
> ##
> 
> ## The parameters can be: formula, aov, lm, aovlist and lmerMod
> 
> data(RCBD)
> 
> ## From: formula
> sk1 <- with(RCBD,
+             SK(y ~ blk + tra,
+                data=dfm,
+                which='tra'))
Error in data.frame(means = aux_mt1, reps = reps) : 
  arguments imply differing number of rows: 0, 5
Calls: with ... eval -> SK -> SK.formula -> SK -> SK.lm -> data.frame
Execution halted
File ‘scout/libs/scout.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 ‘scquantum/libs/scquantum.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:
  ‘BiocManager’ ‘crayon’ ‘knitr’ ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘pbapply’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fansi’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘testit’
  All declared Imports should be used.
File ‘segmag/libs/segmag.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:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘webp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘editData’ ‘miniUI’
  All declared Imports should be used.
File ‘semver/libs/semver.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 ‘sgeostat/libs/sgeostat.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:
  ‘MASS’ ‘kableExtra’ ‘tidyverse’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/tzdb/include/date/date.h:966:34: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/tzdb/include/date/date.h:967:34: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/tzdb/include/date/date.h:1975:13: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/tzdb/include/date/date.h:1983:13: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/shide.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shinyCLT)
  > 
  > test_check("shinyCLT")
  Loading required package: shiny
  Loading required package: gamlss
  Loading required package: splines
  Loading required package: gamlss.data
  
  Attaching package: 'gamlss.data'
  
  The following object is masked from 'package:datasets':
  
      sleep
  
  Loading required package: gamlss.dist
  Loading required package: nlme
  Loading required package: parallel
   **********   GAMLSS Version 5.4-22  ********** 
  For more on GAMLSS look at https://www.gamlss.com/
  Type gamlssNews() to see new features/changes/bug fixes.
  
  Loading required package: plotly
  Loading required package: ggplot2
  
  Attaching package: 'plotly'
  
  The following object is masked from 'package:ggplot2':
  
      last_plot
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following object is masked from 'package:graphics':
  
      layout
  
  Loading required package: future
  Loading required package: shinycssloaders
  Loading required package: waiter
  Loading required package: shinythemes
  Loading required package: shinyWidgets
  Loading required package: cachem
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-plot.R:99:3'): plot_compare_density_qq works correctly ─────────
  Error in `unlist(d.x1, d.x2)`: 'recursive' must be of length 1
  Backtrace:
      ▆
   1. └─global plot_compare_density_qq(group1, group2, input) at test-plot.R:99:3
   2.   └─base::unlist(d.x1, d.x2)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘DT’ ‘billboarder’ ‘glue’ ‘scrypt’ ‘yaml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reactable’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shiny.info)
  > 
  > test_check("shiny.info")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 24 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-lintr.R:1:1'): (code run outside of `test_that()`) ─────────────
  Error: Function with_defaults was deprecated in lintr version 3.0.0. Use linters_with_defaults or modify_defaults instead.
  Backtrace:
      ▆
   1. └─lintr::with_defaults(...) at test-lintr.R:1:1
   2.   └─lintr:::lintr_deprecated(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 24 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/shinytest2.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/sift.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
File ‘signal/libs/signal.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:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘pedtools’ ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
File ‘simplexreg/libs/simplexreg.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.
Running ‘test-all.R’ [56s/68s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > if(require(testthat)) {
  + 
  +     test_check("simr")
  + }
  Loading required package: testthat
  Loading required package: simr
  Loading required package: lme4
  Loading required package: Matrix
  
  Attaching package: 'simr'
  
  The following object is masked from 'package:lme4':
  
      getData
  
  The following object is masked from 'package:testthat':
  
      compare
  
  boundary (singular) fit: see help('isSingular')
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 113 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_new.R:23:5'): makeLmer works ─────────────────────────────────
  nrow(ps$warnings) not equal to 0.
  1/1 mismatches
  [1] 4 - 0 == 4
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 113 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘examples.Rmd’ using rmarkdown

Quitting from lines 75-76 [unnamed-chunk-8] (examples.Rmd)
Error: processing vignette 'examples.Rmd' failed with diagnostics:
Test did not return a p-value
--- failed re-building ‘examples.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gsDesign2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘rmarkdown’ ‘yaml’
  All declared Imports should be used.
Running examples in ‘skellam-Ex.R’ failed
The error most likely occurred in:

> ### Name: skellam.reg
> ### Title: Regression assuming a Skellam distribution
> ### Aliases: skellam.reg
> ### Keywords: Skellam regression
> 
> ### ** Examples
> 
> require('skellam')
> 
> set.seed(0)
> 
> x <- rnorm(1000)
> y1 <- rpois(1000, exp(1 + 1 * x) )
> y2 <- rpois(1000 , exp(-1 + 1 * x) )
> y <- y2 - y1
> skellam.reg(y, x)
Error in stats::optim(mod$estimate, skelreg, hessian = TRUE, control = list(maxit = 5000)) : 
  function cannot be evaluated at initial parameters
Calls: skellam.reg -> <Anonymous>
Execution halted
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’
  All declared Imports should be used.
File ‘skm/libs/skm.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:
  ‘numDeriv’ ‘png’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
File ‘SLHD/libs/SLHD.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 ‘slp/libs/slp.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: ‘covr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  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:
  ‘lseq’
Running ‘testthat.R’ [106s/107s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("smurf")
  > 
  > test_check("smurf")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 591 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_output.R:323:3'): Test n.par.cov in output ─────────────────────
  Error in `islistfactor(x, recursive)`: NA in coercion to Rboolean
  Backtrace:
      ▆
   1. ├─testthat::expect_true(...) at test_output.R:323:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::unlist(munich.fit$n.par.cov, length)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 591 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘backports’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘flextable’ ‘htmlTable’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘lgr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlist’
  All declared Imports should be used.
File ‘som/libs/som.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:
  ‘RSQLite’ ‘dbplyr’
  All declared Imports should be used.
File ‘SoundexBR/libs/SoundexBR.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: ‘RcppEigen’
  All declared Imports should be used.
Running ‘testthat.R’ [49s/90s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spant)
  spant 3.2.0
  
  Attaching package: 'spant'
  
  The following object is masked from 'package:stats':
  
      sd
  
  > 
  > test_check("spant")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 16 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_fitting.R:57:3'): Test ABfit coarse-fitting steps only ───────
  `fit_res` has changed from known value recorded in 'abfit_res_coarse.rds'.
  Component "res_tab": Component "res.niter": Mean relative difference: 0.6688525
  Backtrace:
      ▆
   1. └─testthat::expect_equal_to_reference(...) at test_fitting.R:57:3
   2.   └─testthat::expect_known_value(..., update = update)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 16 ]
  Error: Test failures
  Execution halted
File ‘sparcl/libs/sparcl.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:
  ‘gtable’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
File ‘sparseLTSEigen/libs/sparseLTSEigen.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:
  ‘future’ ‘geosphere’ ‘lubridate’ ‘tidyverse’ ‘viridis’
  All declared Imports should be used.
File ‘sparsereg/libs/sparsereg.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 ‘sparseSVM/libs/sparseSVM.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.
File ‘SparseTSCGM/libs/SparseTSCGM.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:
  ‘Rcpp’ ‘base’ ‘utils’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/SpatialKDE.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/spatialsample.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
File ‘spcr/libs/spcr.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 ‘SPECIES/libs/SPECIES.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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spectralGraphTopology)
  
  Attaching package: 'spectralGraphTopology'
  
  The following object is masked from 'package:stats':
  
      D
  
  > 
  > test_check("spectralGraphTopology")
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-learnGraphTopology.R:21:1'): (code run outside of `test_that()`) ──
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  ── Error ('test-learnSmoothSignalGraph.R:9:1'): (code run outside of `test_that()`) ──
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  ── Error ('test-operators.R:122:1'): (code run outside of `test_that()`) ───────
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘glue’ ‘httptest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘RSpectra’ ‘ggplot2’ ‘latex2exp’ ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘RSQLite’ ‘dbplyr’ ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘arm’ ‘brms’ ‘lme4’ ‘plotly’ ‘shinyMatrix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘mice’ ‘sandwich’ ‘zoo’
  All declared Imports should be used.
Running ‘testthat.R’ [14s/42s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.unsetenv("R_TESTS")
  > if (require(testthat, quietly = TRUE)) {
  +   require(stan4bart)
  +   test_check("stan4bart")
  + } else {
  +   cat("package 'testthat' not available; cannot run unit tests\n")
  + }
  Loading required package: stan4bart
  Loading required package: dbarts
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 205 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test-01-continuous.R:124:3', 'test-01-continuous.R:163:3',
    'test-02-binary.R:33:3', 'test-02-binary.R:128:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-01-continuous.R:277:3'): ppd has approximately right amount of noise ──
  ... <= 0.1 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 205 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘httr’ ‘latex2exp’ ‘rstantools’ ‘tibble’ ‘tidyverse’
  ‘utils’
  All declared Imports should be used.
File ‘starma/libs/starma.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:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘statgenGWAS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gbm’ ‘ggfortify’ ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
File ‘steadyICA/libs/steadyICA.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 ‘StepwiseTest/libs/StepwiseTest.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 ‘stlplus/libs/stlplus.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:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/stochtree.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
File ‘strat/libs/strat.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: ‘ks’
  All declared Imports should be used.
Running examples in ‘STRMPS-Ex.R’ failed
The error most likely occurred in:

> ### Name: findStutter,stringCoverageGenotypeList-method
> ### Title: Find stutters
> ### Aliases: findStutter,stringCoverageGenotypeList-method
> 
> ### ** Examples
> 
> # The object returned by merging a stringCoverageList-Object
> # and a genotypeList-Object.
> data("stringCoverageGenotypeList")
> 
> stutterList <- findStutter(stringCoverageGenotypeList)
Error in unlist(substitutionMatrix, substitutionMatrix) : 
  'recursive' must be of length 1
Calls: findStutter ... mpi.XStringSet.pairwiseAlignment -> XStringSet.pairwiseAlignment -> array -> unlist
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘STRMPSworkflow.Rmd’ using rmarkdown

Quitting from lines 169-174 [unnamed-chunk-14] (STRMPSworkflow.Rmd)
Error: processing vignette 'STRMPSworkflow.Rmd' failed with diagnostics:
'recursive' must be of length 1
--- failed re-building ‘STRMPSworkflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘grDevices’ ‘graphics’ ‘jsonlite’
  ‘purrr’ ‘shinyjs’
  All declared Imports should be used.
File ‘SummaryLasso/libs/SummaryLasso.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:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/supercells.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘pROC’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
File ‘survivalROC/libs/survivalROC.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:
  ‘jsonlite’ ‘readr’ ‘stringr’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/svglite.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/rvinecopulib/include/vinecopulib/misc/nlohmann_json.hpp:25226:47: warning: identifier '_json' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/rvinecopulib/include/vinecopulib/misc/nlohmann_json.hpp:25245:61: warning: identifier '_json_pointer' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/svines.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tidyquant’ ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘prettymapr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘htmltools’ ‘markdown’ ‘nextGenShinyApps’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/packages/tests-clang/symengine/src/upstream/symengine/mp_class.h:77:33: warning: identifier '_z' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/packages/tests-clang/symengine/src/upstream/symengine/mp_class.h:82:34: warning: identifier '_q' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/packages/tests-clang/symengine/src/upstream/symengine/mp_class.h:77:33: warning: identifier '_z' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]   
See ‘/data/gannet/ripley/R/packages/tests-clang/symengine.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
File ‘SynchWave/libs/SynchWave.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:
  ‘MASS’ ‘StackImpute’ ‘arm’ ‘boot’ ‘broom’ ‘knitr’ ‘mvtnorm’
  ‘randomForest’
  All declared Imports should be used.
Running examples in ‘syrup-Ex.R’ failed
The error most likely occurred in:

> ### Name: syrup
> ### Title: Memory and CPU Usage Information for Parallel R Code
> ### Aliases: syrup
> 
> ### ** Examples
> 
> ## Don't show: 
> if (ps::ps_os_type()[["POSIX"]]) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ # pass any expression to syrup. first, sequentially:
+ res_syrup <- syrup({res_output <- Sys.sleep(1)})
+ 
+ res_syrup
+ 
+ # to snapshot memory and CPU information more (or less) often, set `interval`
+ syrup(Sys.sleep(1), interval = .01)
+ 
+ # use `peak = TRUE` to return only the snapshot with
+ # the highest memory usage (as `sum(rss)`)
+ syrup(Sys.sleep(1), interval = .01, peak = TRUE)
+ 
+ # results from syrup are more---or maybe only---useful when
+ # computations are evaluated in parallel. see package README
+ # for an example.
+ ## Don't show: 
+ }) # examplesIf
> res_syrup <- syrup({
+     res_output <- Sys.sleep(1)
+ })
Error in `syrup()`:
! Unable to retrieve resource usage results from the temporary session.
ℹ This is an internal error that was detected in the syrup package.
  Please report it at <https://github.com/simonpcouch/syrup/issues> with a reprex (<https://tidyverse.org/help/>) and the full backtrace.
Backtrace:
    ▆
 1. ├─(if (getRversion() >= "3.4") withAutoprint else force)(...)
 2. │ └─base::source(...)
 3. │   ├─base::withVisible(eval(ei, envir))
 4. │   └─base::eval(ei, envir)
 5. │     └─base::eval(ei, envir)
 6. └─syrup::syrup(...)
 7.   └─syrup:::retrieve_results(sesh)
 8.     └─rlang::abort(...)
Execution halted
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/systemfonts.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following files/directories:
  ‘lilypond-tmp-midi-cda648’ ‘lilypond-tmp-midi-f3ea8f’
Found the following significant warnings:
  ./tabulate.h:5454:57: warning: identifier '_sv' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./tabulate.h:5459:60: warning: identifier '_sv' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./tabulate.h:5464:60: warning: identifier '_sv' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ./tabulate.h:5469:58: warning: identifier '_sv' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/tabulate.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘stringr’ ‘tibble’
  All declared Imports should be used.
File ‘tagcloud/libs/tagcloud.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:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/tardis.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘drat’ ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘quadprog’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘reshape2’ ‘truncnorm’ ‘xtable’
  All declared Imports should be used.
Running ‘ttclust.R’ [30s/21s]
  Comparing ‘ttclust.Rout’ to ‘ttclust.Rout.save’ ...21,22d20
< OMP: Warning #96: Cannot form a team with 8 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).
Running examples in ‘teal.modules.clinical-Ex.R’ failed
The error most likely occurred in:

> ### Name: tm_a_gee
> ### Title: teal Module: Generalized Estimating Equations (GEE) analysis
> ### Aliases: tm_a_gee
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> data <- teal_data()
> data <- within(data, {
+   ADSL <- tmc_ex_adsl
+   ADQS <- tmc_ex_adqs %>%
+     filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
+     mutate(
+       AVISIT = as.factor(AVISIT),
+       AVISITN = rank(AVISITN) %>%
+         as.factor() %>%
+         as.numeric() %>%
+         as.factor(),
+       AVALBIN = AVAL < 50 # Just as an example to get a binary endpoint.
+     ) %>%
+     droplevels()
+ })
> datanames <- c("ADSL", "ADQS")
> datanames(data) <- datanames
Warning: `datanames<-()` was deprecated in teal.data 0.7.0.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
  `teal_data`. See ?names.teal_data
> join_keys(data) <- default_cdisc_join_keys[datanames]
> 
> app <- init(
+   data = data,
+   modules = modules(
+     tm_a_gee(
+       label = "GEE",
+       dataname = "ADQS",
+       aval_var = choices_selected("AVALBIN", fixed = TRUE),
+       id_var = choices_selected(c("USUBJID", "SUBJID"), "USUBJID"),
+       arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
+       visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
+       paramcd = choices_selected(
+         choices = value_choices(data[["ADQS"]], "PARAMCD", "PARAM"),
+         selected = "FKSI-FWB"
+       ),
+       cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL)
+     )
+   )
+ )
Initializing tm_a_gee (prototype)
Error in as.list(data@env) : 
  no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
Running examples in ‘teal.modules.general-Ex.R’ failed
The error most likely occurred in:

> ### Name: tm_a_pca
> ### Title: 'teal' module: Principal component analysis
> ### Aliases: tm_a_pca
> 
> ### ** Examples
> 
> library(teal.widgets)
> 
> # general data example
> data <- teal_data()
> data <- within(data, {
+   require(nestcolor)
+   USArrests <- USArrests
+ })
> 
> datanames(data) <- "USArrests"
Warning: `datanames<-()` was deprecated in teal.data 0.7.0.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
  `teal_data`. See ?names.teal_data
> 
> app <- init(
+   data = data,
+   modules = modules(
+     tm_a_pca(
+       "PCA",
+       dat = data_extract_spec(
+         dataname = "USArrests",
+         select = select_spec(
+           choices = variable_choices(
+             data = data[["USArrests"]], c("Murder", "Assault", "UrbanPop", "Rape")
+           ),
+           selected = c("Murder", "Assault"),
+           multiple = TRUE
+         ),
+         filter = NULL
+       ),
+       ggplot2_args = ggplot2_args(
+         labs = list(subtitle = "Plot generated by PCA Module")
+       )
+     )
+   )
+ )
[INFO] 2025-02-21 17:02:44.4427 pid:3225022 token:[] teal.modules.general Initializing tm_a_pca
Error in as.list(data@env) : 
  no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
Running examples in ‘teal-Ex.R’ failed
The error most likely occurred in:

> ### Name: example_module
> ### Title: An example 'teal' module
> ### Aliases: example_module
> 
> ### ** Examples
> 
> app <- init(
+   data = teal_data(IRIS = iris, MTCARS = mtcars),
+   modules = example_module()
+ )
Error in as.list(data@env) : 
  no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘adding-support-for-reporting.Rmd’ using rmarkdown

Quitting from lines 106-112 [unnamed-chunk-4] (adding-support-for-reporting.Rmd)
Error: processing vignette 'adding-support-for-reporting.Rmd' failed with diagnostics:
no slot of name "env" for this object of class "teal_data"
--- failed re-building ‘adding-support-for-reporting.Rmd’

--- re-building ‘bootstrap-themes-in-teal.Rmd’ using rmarkdown
--- finished re-building ‘bootstrap-themes-in-teal.Rmd’

--- re-building ‘creating-custom-modules.Rmd’ using rmarkdown

Quitting from lines 174-183 [unnamed-chunk-4] (creating-custom-modules.Rmd)
Error: processing vignette 'creating-custom-modules.Rmd' failed with diagnostics:
no slot of name "env" for this object of class "teal_data"
--- failed re-building ‘creating-custom-modules.Rmd’

--- re-building ‘data-as-shiny-module.Rmd’ using rmarkdown
--- finished re-building ‘data-as-shiny-module.Rmd’

--- re-building ‘filter-panel.Rmd’ using rmarkdown
--- finished re-building ‘filter-panel.Rmd’

--- re-building ‘getting-started-with-teal.Rmd’ using rmarkdown

Quitting from lines 33-52 [unnamed-chunk-1] (getting-started-with-teal.Rmd)
Error: processing vignette 'getting-started-with-teal.Rmd' failed with diagnostics:
no slot of name "env" for this object of class "teal_data"
--- failed re-building ‘getting-started-with-teal.Rmd’

--- re-building ‘including-data-in-teal-applications.Rmd’ using rmarkdown
--- finished re-building ‘including-data-in-teal-applications.Rmd’

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

SUMMARY: processing the following files failed:
  ‘adding-support-for-reporting.Rmd’ ‘creating-custom-modules.Rmd’
  ‘getting-started-with-teal.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘TEAM-Ex.R’ failed
The error most likely occurred in:

> ### Name: TEAM
> ### Title: Testing on an Aggregation Tree Method
> ### Aliases: TEAM
> 
> ### ** Examples
> 
> set.seed(1)
> # Simulate local shift difference for each population from mixture of normals
> N1 <- N2 <- 1e6
> require(ks) #loads rnorm.mixt function
Loading required package: ks
> #Controls
> x1 <- rnorm.mixt(N1,mus=c(0.2,0.89),sigmas=c(0.04,0.01),props=c(0.97,0.03))
> #Cases
> x2 <- rnorm.mixt(N2,mus=c(0.2,0.88),sigmas=c(0.04,0.01),props=c(0.97,0.03))
> res <- TEAM(x1,x2,K=14,alpha=0.05,L=3)
Error in unlist(indx.list[rej.x], rej.xtra) : 'recursive' is NA
Calls: TEAM -> unique -> unlist
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘tern-rbmi.Rmd’ using rmarkdown
0,248,Js_of_ocaml__Js.Error,18,TypeError: not a function

Quitting from lines 164-172 [unnamed-chunk-7] (tern-rbmi.Rmd)
Error: processing vignette 'tern-rbmi.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘tern-rbmi.Rmd’

SUMMARY: processing the following file failed:
  ‘tern-rbmi.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘testforDEP/libs/testforDEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/TestGenerator.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘forecast’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/textshaping.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespace in Imports field not imported from: ‘doRNG’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘base’ ‘graphics’ ‘janitor’ ‘rlang’ ‘testthat’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘badger’ ‘ggplot2’ ‘lubridate’ ‘scales’ ‘xgboost’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Ckmeans.1d.dp’ ‘autostats’ ‘badger’ ‘framecleaner’ ‘presenter’
  ‘tidybins’ ‘validata’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/tidyfast.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Running ‘testthat.R’ [47s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(tidyfit)
  > 
  > test_check("tidyfit")
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:tidyfit':
  
      explain
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 184 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-glmm.R:6:3'): glmm regression works ──────────────────────────
  nrow(coef(m_reg)) (`actual`) not equal to 11 (`expected`).
  
    `actual`: 20.0
  `expected`: 11.0
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 184 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(tidyformula)
  > 
  > test_check("tidyformula")
  [ FAIL 1 | WARN 39 | SKIP 0 | PASS 19 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-tidyformula.R:65:3'): tidyformula handles weird data frames ──
  `tidyformula(~everything(), df_empty)` did not throw the expected error.
  
  [ FAIL 1 | WARN 39 | SKIP 0 | PASS 19 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/tidygraph.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/tidyr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/timechange.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 20.1.0-rc2’
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/timeplyr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/tipitaka.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘cpp11’ ‘dplyr’ ‘magrittr’ ‘stringi’
  All declared Imports should be used.
File ‘tmvnsim/libs/tmvnsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘hdi’
  All declared Imports should be used.
Running ‘testthat.R’ [35s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(trace)
  > 
  > test_check("trace")
  [ FAIL 3 | WARN 0 | SKIP 1 | PASS 66 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-shinytest2.R:7:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-call_repeats.R:275:3'): batch correction ─────────────────────
  all.equal(...) is not TRUE
  
  `actual` is a character vector ('Mean relative difference: 0.8841185')
  `expected` is a logical vector (TRUE)
  ── Failure ('test-call_repeats.R:328:3'): batch correction with no data in one batch ──
  grepl(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-call_repeats.R:454:3'): repeat correction with one sample off warning ──
  grepl("had no batch correction carried out", assignment_warning) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 3 | WARN 0 | SKIP 1 | PASS 66 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
Running ‘Coxph-Ex.R’ [20s/51s]
  Comparing ‘Coxph-Ex.Rout’ to ‘Coxph-Ex.Rout.save’ ... OK
  Running ‘KaplanMeier-Ex.R’ [4s/11s]
  Running ‘PI_OVL-Ex.R’ [5s/13s]
  Running ‘Polr-Ex.R’ [4s/10s]
  Comparing ‘Polr-Ex.Rout’ to ‘Polr-Ex.Rout.save’ ... OK
  Running ‘Survreg-Ex.R’ [7s/16s]
  Comparing ‘Survreg-Ex.Rout’ to ‘Survreg-Ex.Rout.save’ ... OK
  Running ‘bugfixes.R’ [114s/255s]
  Running ‘intercepts-Ex.R’ [7s/14s]
  Comparing ‘intercepts-Ex.Rout’ to ‘intercepts-Ex.Rout.save’ ... OK
  Running ‘mmlt-Ex.R’ [254s/418s]
  Comparing ‘mmlt-Ex.Rout’ to ‘mmlt-Ex.Rout.save’ ... OK
  Running ‘mmlt-interface.R’ [82s/122s]
  Running ‘mtram-Ex.R’ [21s/27s]
  Comparing ‘mtram-Ex.Rout’ to ‘mtram-Ex.Rout.save’ ...11,17d10
< Warning messages:
< 1: In optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower,  :
<   convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
< 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
<   unable to evaluate scaled gradient
< 3: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
<   Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
27c20
< 'log Lik.' -Inf (df=6)
---
> 'log Lik.' -876 (df=6)
34c27
< [1] 0.041
---
> [1] 0.039
43c36
<      -10.38        0.43 
---
>       -9.82        0.41 
51c44
< [1] 1 0 1
---
> [1] 0.929 0.018 0.223
60,61c53,54
< [1,]  506   10
< [2,]   10   29
---
> [1,]  565   11
> [2,]   11   33
68,69c61,62
< (Intercept)         587    0
< Days                  0  587
---
> (Intercept)         565   11
> Days                 11   33
72c65
<          24          24 
---
>        23.8         5.7 
75,76c68,69
< (Intercept)           1    0
< Days                  0    1
---
> (Intercept)       1.000 0.081
> Days              0.081 1.000
  Running ‘stram-Ex.R’ [23s/34s]
  Comparing ‘stram-Ex.Rout’ to ‘stram-Ex.Rout.save’ ... OK
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/transformr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tree’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
File ‘TrialSize/libs/TrialSize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/triangulr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/triptych.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Running examples in ‘trouBBlme4SolveR-Ex.R’ failed
The error most likely occurred in:

> ### Name: dwmw
> ### Title: Solver for (generalized) linear MM warnings
> ### Aliases: dwmw trouBBlme4SolveR
> ### Keywords: models
> 
> ### ** Examples
> 
> 
> if(requireNamespace("nlme")){
+ 	library(lme4)
+ 	data(Orthodont, package = "nlme")
+ 	Orthodont$nsex <- as.numeric(Orthodont$Sex == "Male")
+ 	Orthodont$nsexage <- with(Orthodont, nsex*age)
+ 	## Without using dwmw, the next model is singular
+ 	fmo <- lmer(distance ~ age + (age|Subject) + (0+nsex|Subject) +
+ 		    (0 + nsexage|Subject), data = Orthodont)
+ 	summary(fmo)
+ 
+ 	## Using dwmw, we remove the singularity of the model
+ 	fmo1 <- dwmw(lmer(distance ~ age + (age|Subject) + (0+nsex|Subject) +
+ 			  (0 + nsexage|Subject), data = Orthodont))
+ 	summary(fmo1)
+ 
+ 	## It also can be used on the output object
+ 
+ 	fmo2 <- dwmw(fmo)
+ 	summary(fmo2)
+ }
Loading required package: Matrix
Warning in optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower,  :
  convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  unable to evaluate scaled gradient
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge: degenerate  Hessian with 2 negative eigenvalues
Error in dwmw(lmer(distance ~ age + (age | Subject) + (0 + nsex | Subject) +  : 
  Too many iterations!! to get the model distance ~ age + (age | Subject) + (0 + nsex | Subject) + (0 + nsexage | Subject) to converge. Check it!!
Execution halted
Namespace in Imports field not imported from: ‘tseries’
  All declared Imports should be used.
File ‘tseriesChaos/libs/tseriesChaos.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [378s/381s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(tsgarch)
  Loading required package: tsmethods
  > 
  > test_check("tsgarch")
  Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
  Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
  Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
  Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
  [ FAIL 4 | WARN 4 | SKIP 0 | PASS 133 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-benchmarks.R:8:5'): fcp laurent ──────────────────────────────
  all(b$lre$coefficient > 4) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-estimation.R:145:5'): estimate: igarch(1,1) ──────────────────
  as.numeric(logLik(mod)) (`actual`) not equal to -1082.6435 (`expected`).
  
    `actual`:    -Inf
  `expected`: -1082.6
  ── Failure ('test-estimation.R:165:5'): estimate: igarch(2,1)-partially fixed parameters ──
  persistence(mod) (`actual`) not equal to 1 (`expected`).
  
    `actual`: 0.985
  `expected`: 1.000
  ── Failure ('test-estimation.R:166:5'): estimate: igarch(2,1)-partially fixed parameters ──
  as.numeric(logLik(mod)) (`actual`) not equal to -1088.12 (`expected`).
  
    `actual`:    -Inf
  `expected`: -1088.1
  
  [ FAIL 4 | WARN 4 | SKIP 0 | PASS 133 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘R6’ ‘crosstalk’
  All declared Imports should be used.
File ‘tspmeta/libs/tspmeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘EMD’ ‘vars’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Running examples in ‘TT-Ex.R’ failed
The error most likely occurred in:

> ### Name: treetable
> ### Title: Display tree structured data using 'datatable' widget
> ### Aliases: treetable
> 
> ### ** Examples
> 
> data("org")
> data("col_order")
> colnames <- factor(c("org",org$attributesAll),
+                    levels =  col_order)
> treetable(org, color="#FFFFFF", colnames=colnames)
Warning: Automatic coercion from double to character was deprecated in purrr 1.0.0.
ℹ Please use an explicit call to `as.character()` within `map_chr()` instead.
ℹ The deprecated feature was likely used in the TT package.
  Please report the issue to the authors.
Error in unlist(x, recursive, use.names) : 
  'length = 517' in coercion to 'logical(1)'
Calls: treetable -> %>% -> <Anonymous> -> list2 -> unlist
Execution halted
Running examples in ‘TukeyC-Ex.R’ failed
The error most likely occurred in:

> ### Name: TukeyC
> ### Title: The TukeyC Test for Single Experiments
> ### Aliases: TukeyC TukeyC.default TukeyC.lm TukeyC.formula TukeyC.aovlist
> ###   TukeyC.lmerMod
> ### Keywords: package
> 
> ### ** Examples
> 
> ##
> ## Examples:Randomized Complete Block Design (RCBD)
> ## More details: demo(package='TukeyC')
> ##
> 
> ## The parameters can be: formula, aov, lm, aovlist and lmerMod
> 
> data(RCBD)
> 
> ## From: formula
> tk1 <- with(RCBD,
+             TukeyC(y ~ blk + tra,
+                    data=dfm,
+                    which='tra'))
Error in data.frame(means = aux_mt1, reps = reps) : 
  arguments imply differing number of rows: 0, 5
Calls: with ... TukeyC.formula -> TukeyC -> TukeyC.lm -> data.frame
Execution halted
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/tweenr.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 20.1.0-rc2’
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/twosamples.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Found the following significant warnings:
  ../inst/include/date/date.h:966:34: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/date/date.h:967:34: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/date/date.h:1975:13: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  ../inst/include/date/date.h:1983:13: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/tzdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘foreign’ ‘psychTools’ ‘pwr’ ‘rmarkdown’
  All declared Imports should be used.
Running examples in ‘Unico-Ex.R’ failed
The error most likely occurred in:

> ### Name: Unico
> ### Title: Fitting the Unico model
> ### Aliases: Unico
> 
> ### ** Examples
> 
> data = simulate_data(n=100, m=2, k=3, p1=1, p2=1, taus_std=0, log_file=NULL)
> res = list()
> res$params.hat = Unico(data$X, data$W, data$C1, data$C2, parallel=FALSE, log_file=NULL)
Error in is.nloptr(ret) : at least one element in x0 < lb
Calls: Unico ... lapply -> FUN -> fit_mean_var -> nloptr -> is.nloptr
Execution halted
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/unigd.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
Running ‘testthat.R’ [76s/77s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(uwot)
  Loading required package: Matrix
  > 
  > test_check("uwot")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 705 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_errors.R:28:1'): (code run outside of `test_that()`) ─────────
  `umap(iris10, pca = 500)` threw an error with unexpected message.
  Expected match: "'pca' must be <="
  Actual message: "'length = 40' in coercion to 'logical(1)'"
  Backtrace:
      ▆
   1. ├─testthat::expect_error(umap(iris10, pca = 500), "'pca' must be <=") at test_errors.R:28:1
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─uwot::umap(iris10, pca = 500)
   7.   └─uwot:::uwot(...)
  ── Error ('test_output.R:395:1'): (code run outside of `test_that()`) ──────────
  Error in `min(nrow(X), na.rm = col(X))`: 'length = 40' in coercion to 'logical(1)'
  Backtrace:
      ▆
   1. └─uwot::umap(...) at test_output.R:395:1
   2.   └─uwot:::uwot(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 705 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘Cairo’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘BBmisc’ ‘badger’
  All declared Imports should be used.
File ‘valorate/libs/valorate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘varTestnlme.Rmd’ using rmarkdown

Quitting from lines 60-62 [unnamed-chunk-4] (varTestnlme.Rmd)
Error: processing vignette 'varTestnlme.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘varTestnlme.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘methods’ ‘survival’
  All declared Imports should be used.
File ‘vdg/libs/vdg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/vdiffr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘foreach’ ‘iterators’ ‘maps’ ‘spam’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘leaflet’ ‘mapview’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mclust’ ‘rlang’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/rvinecopulib/include/vinecopulib/misc/nlohmann_json.hpp:25226:47: warning: identifier '_json' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/rvinecopulib/include/vinecopulib/misc/nlohmann_json.hpp:25245:61: warning: identifier '_json_pointer' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/vinereg.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Running examples in ‘vioplot-Ex.R’ failed
The error most likely occurred in:

> ### Name: add_labels
> ### Title: Annotated Violin Plot
> ### Aliases: add_labels
> ### Keywords: annotation. graphics plot violin
> 
> ### ** Examples
> 
> 
> # box- vs violin-plot
> par(mfrow=c(2,1))
> mu<-2
> si<-0.6
> bimodal<-c(rnorm(1000,-mu,si),rnorm(1000,mu,si))
> uniform<-runif(2000,-4,4)
> normal<-rnorm(2000,0,3)
> 
> # annotate a violin plot
> group <- rep(c("bimodal", "uniform", "normal"),
+              sapply(list(bimodal, uniform, normal), length))
> table(group)
group
bimodal  normal uniform 
   2000    2000    2000 
> vioplot(bimodal,uniform,normal)
> add_labels(unlist(bimodal,uniform,normal), group, height = 3, cex = 0.8)
Error in unlist(bimodal, uniform, normal) : 
  'recursive' must be of length 1
Calls: add_labels -> text -> text.default -> unlist
Execution halted
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
File ‘vita/libs/vita.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/tzdb/include/date/date.h:966:34: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/tzdb/include/date/date.h:967:34: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/tzdb/include/date/date.h:1975:13: warning: identifier '_d' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/tzdb/include/date/date.h:1983:13: warning: identifier '_y' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/vroom.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 20.1.0-rc2’
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
File ‘wavelets/libs/wavelets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
  /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
See ‘/data/gannet/ripley/R/packages/tests-clang/websocket.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘here’ ‘tibble’
  All declared Imports should be used.
File ‘weightedCL/libs/weightedCL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘WeightIt.Rmd’ using rmarkdown_notangle
--- finished re-building ‘WeightIt.Rmd’

--- re-building ‘estimating-effects.Rmd’ using rmarkdown_notangle

Quitting from lines 398-410 [unnamed-chunk-16] (estimating-effects.Rmd)
Error: processing vignette 'estimating-effects.Rmd' failed with diagnostics:
Assertion failed. One of the following must apply:
 * checkmate::check_character(hypothesis): Must comply to pattern '='
 * checkmate::check_numeric(hypothesis): Must be of type 'numeric', not 'character'
 * checkmate::check_formula(hypothesis): Must be a formula, not character
 * checkmate::check_matrix(hypothesis): Must be of type 'matrix', not 'character'
 * checkmate::check_function(hypothesis): Must be a function, not 'character'
 * checkmate::check_null(hypothesis): Must be NULL
--- failed re-building ‘estimating-effects.Rmd’

--- re-building ‘installing-packages.Rmd’ using rmarkdown_notangle
--- finished re-building ‘installing-packages.Rmd’

SUMMARY: processing the following file failed:
  ‘estimating-effects.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘roxygen2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fdadensity’ ‘locfit’ ‘locpol’ ‘modeest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘future’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
Found the following significant warnings:
  DocParse.c:67:25: warning: '__xmlDoValidityCheckingDefaultValue' is deprecated [-Wdeprecated-declarations]
  DocParse.c:70:6: warning: '__xmlDoValidityCheckingDefaultValue' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:134:7: warning: 'xmlSkipBlankChars' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:135:7: warning: 'xmlParseMarkupDecl' is deprecated [-Wdeprecated-declarations]
  RUtils.c:142:13: warning: 'xmlSubstituteEntitiesDefault' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/XML.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 20.1.0-rc2’
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
File ‘XNomial/libs/XNomial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘spelling’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
Running ‘Ch-Basics.R’
  Comparing ‘Ch-Basics.Rout’ to ‘Ch-Basics.Rout.save’ ... OK
  Running ‘Ch-Intro.R’ [5s/12s]
  Comparing ‘Ch-Intro.Rout’ to ‘Ch-Intro.Rout.save’ ... OK
  Running ‘Ch-LinearRegression.R’ [9s/23s]
  Comparing ‘Ch-LinearRegression.Rout’ to ‘Ch-LinearRegression.Rout.save’ ...46,51c46,51
<  Min.   :   2   Min.   :  20   Min.   : 0.00522  
<  1st Qu.:  52   1st Qu.: 134   1st Qu.: 0.46449  
<  Median : 122   Median : 282   Median : 1.32051  
<  Mean   : 197   Mean   : 418   Mean   : 2.54846  
<  3rd Qu.: 268   3rd Qu.: 541   3rd Qu.: 3.44017  
<  Max.   :1098   Max.   :2120   Max.   :24.45946  
---
>  Min.   :   2   Min.   :  20   Min.   : 0.005  
>  1st Qu.:  52   1st Qu.: 134   1st Qu.: 0.464  
>  Median : 122   Median : 282   Median : 1.321  
>  Mean   : 197   Mean   : 418   Mean   : 2.548  
>  3rd Qu.: 268   3rd Qu.: 541   3rd Qu.: 3.440  
>  Max.   :1098   Max.   :2120   Max.   :24.459  
886c886
< -0.619068 -0.025568  0.000000 -0.000134  0.033201  0.641027 
---
> -0.6191 -0.0256  0.0000 -0.0001  0.0332  0.6410 
  Running ‘Ch-Microeconometrics.R’ [5s/14s]
  Comparing ‘Ch-Microeconometrics.Rout’ to ‘Ch-Microeconometrics.Rout.save’ ... OK
  Running ‘Ch-Programming.R’ [55s/136s]
  Comparing ‘Ch-Programming.Rout’ to ‘Ch-Programming.Rout.save’ ... OK
  Running ‘Ch-TimeSeries.R’ [9s/21s]
  Comparing ‘Ch-TimeSeries.Rout’ to ‘Ch-TimeSeries.Rout.save’ ... OK
  Running ‘Ch-Validation.R’ [72s/193s]
  Comparing ‘Ch-Validation.Rout’ to ‘Ch-Validation.Rout.save’ ... OK
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/akc.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [38s/45s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > if (require(testthat, quietly = TRUE)) {
  +   test_check("blme")
  + } else {
  +   cat("package 'testthat' not available; cannot run unit tests\n")
  + }
  Loading required package: blme
  Loading required package: lme4
  Loading required package: Matrix
  [ FAIL 2 | WARN 15 | SKIP 0 | PASS 109 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-06-lmm_resid.R:20:3'): blmer fits the eight schools example correctly ──
  eightSchools@theta not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  ── Error ('test-07-lmm_fixef.R:120:3'): blmer fits sleep study example in documentation ──
  Error in `optwrap(optimizer, devfun, startingValues, lower = lowerBounds, 
      control = control, adj = FALSE, verbose = verbose, ...)`: (converted from warning) convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
  Backtrace:
      ▆
   1. └─blme::blmer(...) at test-07-lmm_fixef.R:120:3
   2.   └─blme:::optimizeLmer(...)
   3.     └─lme4:::optwrap(...)
  
  [ FAIL 2 | WARN 15 | SKIP 0 | PASS 109 ]
  Error: Test failures
  Execution halted
Running ‘BRugs.R’
  Comparing ‘BRugs.Rout’ to ‘BRugs.Rout.save’ ... OK
  Running ‘examples.R’ [31s/40s]
  Comparing ‘examples.Rout’ to ‘examples.Rout.save’ ...165c165
< 20000 updates took 1 s
---
> 20000 updates took 0 s
218c218
< 20000 updates took 1 s
---
> 20000 updates took 2 s
  Running ‘examples.stats.R’
  Running ‘functions.R’ [15s/23s]
  Comparing ‘functions.Rout’ to ‘functions.Rout.save’ ... OK
  Running ‘local.R’
Running ‘testthat.R’ [57s/66s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > 
  > test_check("btergm")
  Loading required package: btergm
  Registered S3 methods overwritten by 'btergm':
    method    from
    plot.gof  ergm
    print.gof ergm
  Package:  btergm
  Version:  1.10.12
  Date:     2024-03-31
  Authors:  Philip Leifeld (University of Manchester)
            Skyler J. Cranmer (The Ohio State University)
            Bruce A. Desmarais (Pennsylvania State University)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test-btergm.R:82:3', 'test-btergm.R:180:3',
    'test-btergm.R:197:3', 'test-data.R:4:3', 'test-interpret.R:4:3',
    'test-interpret.R:32:3', 'test-interpret.R:59:3', 'test-interpret.R:87:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-btergm.R:73:3'): offset argument in btergm works without composition change ──
  Error in `ergm::ergm.pl(nw, Clist.miss, model, theta.offset = c(rep(FALSE, 
      length(l$rhs.terms) - 1), TRUE), verbose = FALSE, control = control.ergm)`: VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-btergm.R:73:3
   2. │ └─base::withCallingHandlers(...)
   3. └─btergm::btergm(...)
   4.   └─ergm::ergm.pl(...)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  Error: Test failures
  Execution halted
Running examples in ‘CensSpatial-Ex.R’ failed
The error most likely occurred in:

> ### Name: algnaive12
> ### Title: Naive 1 and Naive 2 method for spatial prediction.
> ### Aliases: algnaive12
> ### Keywords: Spatial Censored SAEM
> 
> ### ** Examples
> 
> ###simulated coordinates
> n<-200 ### sample size for estimation.
> n1=100 ### number of observation used in the prediction.
> 
> ###simulated coordinates
> r1=sample(seq(1,30,length=400),n+n1)
> r2=sample(seq(1,30,length=400),n+n1)
> coords=cbind(r1,r2)### total coordinates (used in estimation and prediction).
> 
> coords1=coords[1:n,]####coordinates used for estimation.
> 
> type="matern"### covariance structure.
> 
> xtot<-cbind(1,runif((n+n1)),runif((n+n1),2,3))## X matrix for estimation and prediction.
> xobs=xtot[1:n,]## X matrix for estimation.
> 
> ###simulated data
> obj=rspacens(cov.pars=c(3,.3,0),beta=c(5,3,1),x=xtot,coords=coords,kappa=1.2,
+ cens=0.25,n=(n+n1),n1=n1,cov.model=type,cens.type="left")
> 
> data2=obj$datare
> data2[,4:5]=xobs[,-1]
> 
> cc=obj$cc
> y=obj$datare[,3]
> cutoff=rep(obj$cutoff,length(y[cc==1]))
> 
> 
> aux2=algnaive12(data=data2,cc=obj$cc,covar=TRUE,covar.col=4:5,
+ copred=obj$coords1,thetaini=c(.1,.2),y.col=3,coords.col=1:2,
+ fix.nugget=TRUE,nugget=0,kappa=1.2,cutoff=cutoff,trend=~V4+V5,
+ cov.model=type)
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(centr)
  > 
  > test_check("centr")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-median_center.R:15:3'): median_center ────────────────────────
  sf::st_coordinates(...) (`actual`) not equal to as.matrix(data.frame(X = -96.0135231, Y = 28.6822725)) (`expected`).
  
  actual vs expected
                       [,1]     [,2]
  - actual[1, ]   -96.01353 28.68227
  + expected[1, ] -96.01352 28.68227
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
  Error: Test failures
  Execution halted
Running ‘exprSet-example.R’ [10s/14s]
  Comparing ‘exprSet-example.Rout’ to ‘exprSet-example.Rout.save’ ... OK
  Running ‘test00-color.R’
  Comparing ‘test00-color.Rout’ to ‘test00-color.Rout.save’ ... OK
  Running ‘test01-distance.R’
  Comparing ‘test01-distance.Rout’ to ‘test01-distance.Rout.save’ ... OK
  Running ‘test02-cluster.R’
  Comparing ‘test02-cluster.Rout’ to ‘test02-cluster.Rout.save’ ...28c28
< 3.674e-05 6.434e-02 3.529e-01 2.976e-01 5.154e-01 6.698e-01 
---
> 0.0000367 0.0643374 0.3528907 0.2975618 0.5153581 0.6697706 
  Running ‘test02.1-just.R’
  Comparing ‘test02.1-just.Rout’ to ‘test02.1-just.Rout.save’ ... OK
  Running ‘test03-boot.R’
  Comparing ‘test03-boot.Rout’ to ‘test03-boot.Rout.save’ ... OK
  Running ‘test04-perturb.R’
  Comparing ‘test04-perturb.Rout’ to ‘test04-perturb.Rout.save’ ... OK
  Running ‘test04.1-gpca.R’
  Comparing ‘test04.1-gpca.Rout’ to ‘test04.1-gpca.Rout.save’ ... OK
  Running ‘test05-spca.R’
  Comparing ‘test05-spca.Rout’ to ‘test05-spca.Rout.save’ ... OK
  Running ‘test06-mosaic.R’
  Comparing ‘test06-mosaic.Rout’ to ‘test06-mosaic.Rout.save’ ... OK
  Running ‘test07-pcanova.R’
  Comparing ‘test07-pcanova.Rout’ to ‘test07-pcanova.Rout.save’ ... OK
Running ‘test01-Simplex.R’
  Comparing ‘test01-Simplex.Rout’ to ‘test01-Simplex.Rout.save’ ... OK
  Running ‘test02-WV.R’
  Comparing ‘test02-WV.Rout’ to ‘test02-WV.Rout.save’ ... OK
  Running ‘test03-simulate.R’ [55s/66s]
  Comparing ‘test03-simulate.Rout’ to ‘test03-simulate.Rout.save’ ...213c213
<  3rd Qu.:14.000   3rd Qu.:265.75   3rd Qu.: 0.0029188   3rd Qu.:0.5005  
---
>  3rd Qu.:14.000   3rd Qu.:265.75   3rd Qu.: 0.0029187   3rd Qu.:0.5005  
  Running ‘test04-algorithm.R’ [152s/199s]
  Comparing ‘test04-algorithm.Rout’ to ‘test04-algorithm.Rout.save’ ...177c177
<  Max.   :2.002   Max.   :0.9989221   Max.   :2747  
---
>  Max.   :2.002   Max.   :0.9989222   Max.   :2747  
238c238
<  Mean   : 7.286   Mean   :184.3   Mean   : 0.03329   Mean   :0.5902  
---
>  Mean   : 7.286   Mean   :184.3   Mean   : 0.03329   Mean   :0.5903  
244c244
<  Median :1.0415   Median :1.0144845   Median :1352  
---
>  Median :1.0415   Median :1.0144844   Median :1352
Running examples in ‘constrainedKriging-Ex.R’ failed
The error most likely occurred in:

> ### Name: CKrige
> ### Title: Constrained, Covariance-matching Constrained and Universal
> ###   Kriging
> ### Aliases: CKrige CKrige.points CKrige.polygons CKrige-methods
> ###   CKrige,formula,data.frame,formula,preCKrigePoints-method
> ###   CKrige,formula,data.frame,formula,preCKrigePolygons-method
> ###   print.CKrige.exout.polygons summary.CKrige.exout.polygons
> ###   print.CKrige.exout.points summary.CKrige.exout.points
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> 
> 
> ### example 7: universal block Kriging of mean over whole domain
> ### cf chapter 4 of vignette of package georob
> ### (https://CRAN.R-project.org/package=georob)
> if(!requireNamespace("gstat", quietly = TRUE)){
+   stop("install package gstat to run example")
+ }
> ### load coalash data
> data(coalash, package="gstat")
> 
> ### generate SpatialPointsDataFrame covering entire domain of coalash data
> coalash.domain <- rbind(c(0.5,0), c(16.5,0), c(16.5,24), c(0.5,24), c(0.5,0))
> coalash.domain <- SpatialPolygonsDataFrame(
+   SpatialPolygons(list(Polygons(list(Polygon(coalash.domain)), ID= "domain"))),
+   data=data.frame(x=8.5,y=12,row.names="domain"))
> 
> ### universal block Kriging
> preCK_coalash <- preCKrige(newdata = coalash.domain, model = covmodel(modelname =
+     "exponential", mev = 1.023, nugget = 0, variance = 0.268,
+     scale = 1.907), pwidth = 16, pheight = 24)
> UK_coalash <- CKrige(formula = coalash ~ x, data = coalash,
+   locations = ~ x+y, object = preCK_coalash, method = 1)
Running ‘testthat.R’ [51s/122s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(correlation)
  > 
  > test_check("correlation")
  
  For i = 2 j = 1  A cell entry of 0 was replaced with correct =  0.5.  Check your data!
  For i = 2 j = 1  A cell entry of 0 was replaced with correct =  0.5.  Check your data!
  [ FAIL 2 | WARN 125 | SKIP 11 | PASS 124 ]
  
  ══ Skipped tests (11) ══════════════════════════════════════════════════════════
  • On CRAN (11): 'test-as.list.R:7:3', 'test-correlation.R:172:3',
    'test-correlation.R:195:3', 'test-display_print_dataframe.R:2:3',
    'test-display_print_dataframe.R:14:3', 'test-display_print_matrix.R:4:3',
    'test-display_print_matrix.R:13:3', 'test-display_print_matrix.R:31:3',
    'test-methods.R:9:3', 'test-renaming.R:9:3',
    'test-selecting_variables.R:28:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cormatrix_to_excel.R:3:3'): cormatrix_to_excel select ──────────
  Error: x must be class wbColour
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-cormatrix_to_excel.R:3:3
   2.   └─rlang::cnd_signal(state$error)
  ── Error ('test-cormatrix_to_excel.R:16:3'): cormatrix_to_excel p_adjust ───────
  Error: x must be class wbColour
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-cormatrix_to_excel.R:16:3
   2.   └─rlang::cnd_signal(state$error)
  
  [ FAIL 2 | WARN 125 | SKIP 11 | PASS 124 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘cosa_tutorial.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/cosa.Rcheck/vign_test/cosa/vignettes/cosa_tutorial_files/figure-html/unnamed-chunk-2-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 45045 bytes
Input file size = 45183 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 35157
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 35157

Output IDAT size = 35157 bytes (9888 bytes decrease)
Output file size = 35235 bytes (9948 bytes = 22.02% decrease)


Quitting from lines 90-114 [unnamed-chunk-3] (cosa_tutorial.Rmd)
Error: processing vignette 'cosa_tutorial.Rmd' failed with diagnostics:
Solution is not feasible. Change default settings
--- failed re-building ‘cosa_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘examplepkg’
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mockery)
  > library(DataFakeR)
  > 
  > test_check("DataFakeR")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-lint_check.R:3:3'): Linting package ────────────────────────────
  Error: Function with_defaults was deprecated in lintr version 3.0.0. Use linters_with_defaults or modify_defaults instead.
  Backtrace:
      ▆
   1. └─lintr::with_defaults(...) at test-lint_check.R:3:3
   2.   └─lintr:::lintr_deprecated(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ]
  Error: Test failures
  Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’ [114s/114s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DataPackageR)
  > # Test only if pandoc is available.
  > if (rmarkdown::pandoc_available()) {
  +   test_check("DataPackageR")
  + }
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 247 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-r-processing.R:20:5'): R file processing works and creates vignettes ──
  Error in `abs_path(output_file)`: The file '/tmp/RtmpT3v5Av/working_dir/Rtmpb43zYc/file3cc6967170bb6/rfiletest/inst/extdata/Logfiles/rfileTest.pdf' does not exist.
  Backtrace:
       ▆
    1. └─base::eval(...)
    2.   └─base::eval(...)
    3.     ├─testthat::expect_equal(...) at test-r-processing.R:20:5
    4.     │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    5.     │   └─rlang::eval_bare(expr, quo_get_env(quo))
    6.     ├─base::basename(...)
    7.     └─DataPackageR::package_build(...)
    8.       └─DataPackageR:::DataPackageR(arg = package_path, deps = deps)
    9.         └─rmarkdown::render(...)
   10.           └─rmarkdown:::abs_path(output_file)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 247 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [112s/248s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dmlalg)
  > 
  > test_check("dmlalg")
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 1150 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-methods_mm.R:197:5'): print.summary.mmdml outputs right formats ──
  `res` has length 23, not length 20.
  Backtrace:
      ▆
   1. └─dmlalg (local) do_tests(fit1, 20) at test-methods_mm.R:200:3
   2.   └─testthat::expect_length(res, len) at test-methods_mm.R:197:5
  ── Failure ('test-methods_mm.R:197:5'): print.summary.mmdml outputs right formats ──
  `res` has length 30, not length 25.
  Backtrace:
      ▆
   1. └─dmlalg (local) do_tests(fit2, 25) at test-methods_mm.R:201:3
   2.   └─testthat::expect_length(res, len) at test-methods_mm.R:197:5
  
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 1150 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [45s/54s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dominanceanalysis)
  > 
  > test_check("dominanceanalysis")
  [ FAIL 2 | WARN 162 | SKIP 0 | PASS 207 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-da-with-lmm.R:17:3'): contribution.average are correct ───────
  ca$rb.r2.1 not equal to c(N = 0.34, P = -0.03, K = 0.15).
  3/3 mismatches (average diff: 0.0293)
  [1]  0.2844 -  0.34 == -0.05558
  [2] -0.0233 - -0.03 ==  0.00666
  [3]  0.1243 -  0.15 == -0.02566
  ── Failure ('test-lmmR2-lme4.R:60:2'): Report correct values for lmer comparing both models ──
  lmmR2.1$sb.r2.2 not equal to 0.25.
  1/1 mismatches
  [1] 0.435 - 0.25 == 0.185
  
  [ FAIL 2 | WARN 162 | SKIP 0 | PASS 207 ]
  Error: Test failures
  Execution halted
Running examples in ‘eudract-Ex.R’ failed
The error most likely occurred in:

> ### Name: clintrials_gov_convert
> ### Title: applies a conversion using xslt from a simple xml file to a
> ###   ClinicalTrials.gov compatible file, and checks against the schema
> ### Aliases: clintrials_gov_convert
> 
> ### ** Examples
> 
> safety_statistics <- safety_summary(safety,
+                                     exposed=c("Experimental"=60,"Control"=67))
> simple <- tempfile(fileext = ".xml")
> eudract <- tempfile(fileext = ".xml")
> ct <- tempfile(fileext = ".xml")
> simple_safety_xml(safety_statistics, simple)
'/tmp/Rtmp83wICU/working_dir/RtmpmzlNJK/filec3d7a6589a1e9.xml' is created or modified

Warning in simple_safety_xml(safety_statistics, simple) :
  local complex type: The content model is not determinist.Element 'TABLE': No matching global declaration available for the validation root.
> eudract_convert(input=simple,
+                 output=eudract)
Error in eudract_convert(input = simple, output = eudract) : 
  local complex type: The content model is not determinist.Element 'TABLE': No matching global declaration available for the validation root.
Execution halted
Running ‘testthat.R’ [130s/162s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(eyetrackingR)
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("eyetrackingR")
  Test Type:	 lmer 
  Predictor:	 (Intercept) 
  Formula:	 Prop ~ AOI + (1 | Trial) 
  Runs of Significant Time Bins: 
  Positive Run 1  ===== 
  	Time:		 15500 - 21000 Test Type:	 boot_splines 
  Predictor:	 Target 
  Formula:	 Prop ~ Target 
  Runs of Significant Time Bins: 
  Positive Run 1  ===== 
  	Time:		 15900 - 21000 [ FAIL 3 | WARN 16 | SKIP 0 | PASS 39 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_analyze_time_bins.R:105:3'): The function analyze_time_bins has correct data (interaction) ──
  Error in `compare_dfs(tb_interaction1_check, tb_interaction1)`: all(dim(df1) == dim(df2)) is not TRUE
  Backtrace:
      ▆
   1. └─eyetrackingR (local) compare_dfs(tb_interaction1_check, tb_interaction1) at test_analyze_time_bins.R:105:3
   2.   └─base::stopifnot(all(dim(df1) == dim(df2))) at test_analyze_time_bins.R:6:3
  ── Failure ('test_cluster_analysis.R:97:3'): The function make_time_cluster_data gives necessary eyetrackingR attributes with lmer ──
  nrow(attr(tclust_data_lmer, "eyetrackingR")$clusters) not equal to 2.
  1/1 mismatches
  [1] 0 - 2 == -2
  ── Failure ('test_cluster_analysis.R:98:3'): The function make_time_cluster_data gives necessary eyetrackingR attributes with lmer ──
  ncol(attr(tclust_data_lmer, "eyetrackingR")$clusters) not equal to 5.
  1/1 mismatches
  [1] 3 - 5 == -2
  
  [ FAIL 3 | WARN 16 | SKIP 0 | PASS 39 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [45s/57s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FREEtree)
  
  > 
  > test_check("FREEtree")
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_FREEtree.R:113:3'): FREEtree_time a5 estimation ────────────────
  Error in `if (continue & (abs(newloglik - oldloglik[2]) < abstol)) {
      if (newloglik > oldloglik[1]) 
          continue <- FALSE
  }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. └─FREEtree::FREEtree(...) at test_FREEtree.R:113:3
   2.   └─FREEtree:::FREEtree_time(...)
   3.     └─glmertree::lmertree(...)
  ── Error ('test_FREEtree.R:230:3'): FREEtree_PC a0 estimation ──────────────────
  Error in `if (continue & (abs(newloglik - oldloglik[2]) < abstol)) {
      if (newloglik > oldloglik[1]) 
          continue <- FALSE
  }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. └─FREEtree::FREEtree(...) at test_FREEtree.R:230:3
   2.   └─FREEtree:::FREEtree_PC(...)
   3.     └─glmertree::lmertree(...)
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘FRK_intro.Rnw’ using knitr
** Processing: figure/unnamed-chunk-27-1.png
600x600 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 99847 bytes
Input file size = 100849 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 98361
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 96990
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 96990

Output IDAT size = 96990 bytes (2857 bytes decrease)
Output file size = 97068 bytes (3781 bytes = 3.75% decrease)

** Processing: figure/unnamed-chunk-27-2.png
600x600 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 59981 bytes
Input file size = 60923 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 56451
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 56073
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 56073

Output IDAT size = 56073 bytes (3908 bytes decrease)
Output file size = 56151 bytes (4772 bytes = 7.83% decrease)

--- re-building ‘FRK_non-Gaussian.Rnw’ using knitr
--- finished re-building ‘FRK_non-Gaussian.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘georob_vignette.Rnw’ using Sweave
Loading required package: sp

Attaching package: ‘georob’

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

    step

recomputing robust Mahalanobis distances
saving the robust distances 'MD' as part of ‘r.lmrob’
Subdirectory ‘geostatsp/src’ contains apparent object files/libraries
  Matrix_stubs_here.o gmrfEdge.o gmrfLik.o matern.o maternLogL.o
  maternLogLopt.o optimize.o register.o
Object files/libraries should not be included in a source package.

Subdirectory ‘src’ contains:
  symbols.rds
These are unlikely file names for src files.
Running examples in ‘geostatsp-Ex.R’ failed
The error most likely occurred in:

> ### Name: RFsimulate
> ### Title: Simulation of Random Fields
> ### Aliases: RFsimulate modelRandomFields RFsimulate RFsimulate-methods
> ###   RFsimulate,ANY,SpatRaster-method RFsimulate,numeric,SpatRaster-method
> ###   RFsimulate,numeric,SpatVector-method
> ###   RFsimulate,RMmodel,SpatVector-method
> ###   RFsimulate,RMmodel,SpatRaster-method
> ###   RFsimulate,matrix,SpatRaster-method
> ###   RFsimulate,matrix,SpatVector-method RFsimulate,data.frame,ANY-method
> ### Keywords: spatial
> 
> ### ** Examples
> 
> library('geostatsp')
> 
> # exclude this line to use the RandomFields package
> options(useRandomFields = FALSE)
> 
> model1 <- c(var=5, range=1,shape=0.5)
> 
> 
> myraster = rast(nrows=20,ncols=30,extent = ext(0,6,0,4), 
+ 	crs="+proj=utm +zone=17 +datum=NAD27 +units=m +no_defs")
> 
> set.seed(0) 
> 
> simu <- RFsimulate(model1, x=myraster, n=3)
install the RandomFields package for faster simulations
Running ‘bsch.R’
  Comparing ‘bsch.Rout’ to ‘bsch.Rout.save’ ...3a4
> 
  Running ‘penInf.R’ [8s/11s]
  Comparing ‘penInf.Rout’ to ‘penInf.Rout.save’ ...5a6
> 
  Running ‘sh9.2012.R’
  Comparing ‘sh9.2012.Rout’ to ‘sh9.2012.Rout.save’ ...3a4
> 
  Running ‘shPUR.R’
  Comparing ‘shPUR.Rout’ to ‘shPUR.Rout.save’ ...3a4
> 
  Running ‘test1Fast.R’
  Comparing ‘test1Fast.Rout’ to ‘test1Fast.Rout.save’ ...3a4
> 
  Running ‘test1QE.R’
  Comparing ‘test1QE.Rout’ to ‘test1QE.Rout.save’ ...3a4
> 
  Running ‘test2Fast.R’
  Comparing ‘test2Fast.Rout’ to ‘test2Fast.Rout.save’ ...3a4
> 
  Running ‘test2QE.R’
  Comparing ‘test2QE.Rout’ to ‘test2QE.Rout.save’ ...3a4
> 
  Running ‘test3Fast.R’ [8s/11s]
  Comparing ‘test3Fast.Rout’ to ‘test3Fast.Rout.save’ ...3a4
> 
  Running ‘test3QE.R’
  Comparing ‘test3QE.Rout’ to ‘test3QE.Rout.save’ ...3a4
> 
  Running ‘test5Fast.R’
  Comparing ‘test5Fast.Rout’ to ‘test5Fast.Rout.save’ ...3a4
> 
  Running ‘test7Fast.R’
  Comparing ‘test7Fast.Rout’ to ‘test7Fast.Rout.save’ ...3a4
> 
  Running ‘testMyFam.R’
  Comparing ‘testMyFam.Rout’ to ‘testMyFam.Rout.save’ ...3a4
>
Subdirectory ‘gstat/src’ contains apparent object files/libraries
  block.o data.o direct.o fit.o gcdist.o getest.o gls.o glvars.o init.o
  lm.o mapio.o msim.o mtrx.o nsearch.o pqueue.o reml.o s.o select.o
  sem.o sim.o userio.o utils.o vario.o vario_fn.o vario_io.o
Object files/libraries should not be included in a source package.

Subdirectory ‘src’ contains:
  symbols.rds
These are unlikely file names for src files.
Error(s) in re-building vignettes:
--- re-building ‘GUILDS.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/GUILDS.Rcheck/vign_test/GUILDS/vignettes/GUILDS_files/figure-html/unnamed-chunk-1-1.png
576x288 pixels, 8 bits/pixel, 246 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 2947 bytes
Input file size = 3775 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 2454
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 2452
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 2452

Output IDAT size = 2452 bytes (495 bytes decrease)
Output file size = 2530 bytes (1245 bytes = 32.98% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/GUILDS.Rcheck/vign_test/GUILDS/vignettes/GUILDS_files/figure-html/unnamed-chunk-2-1.png
576x288 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4642 bytes
Input file size = 5497 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3998
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3970
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3970

Output IDAT size = 3970 bytes (672 bytes decrease)
Output file size = 4048 bytes (1449 bytes = 26.36% decrease)
Running ‘testthat.R’ [186s/232s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(HLMdiag)
  
  Attaching package: 'HLMdiag'
  
  The following object is masked from 'package:stats':
  
      covratio
  
  > library(lme4)
  Loading required package: Matrix
  > library(nlme)
  
  Attaching package: 'nlme'
  
  The following object is masked from 'package:lme4':
  
      lmList
  
  > 
  > data(sleepstudy, package = 'lme4')
  > 
  > sleepstudy2 <- sleepstudy
  > sleepstudy2[7,1] <- NA
  > sleepstudy2[2,2] <- NA
  > 
  > 
  > test_check("HLMdiag")
  [ FAIL 1 | WARN 970 | SKIP 6 | PASS 423 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (6): 'test-hlm_influence.R:32:3', 'test-hlm_influence.R:56:3',
    'test-hlm_resid.R:90:3', 'test-hlm_resid.R:111:3',
    'test-influence_functions.R:158:3', 'test-influence_functions.R:172:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-case_delete.R:545:3'): Dimenstions of variance components are correct for single case deletion for nlme models ──
  length(sleep.lme.caseD$varcomp.delete) not equal to length(varcomp.lme(sleep.lme)).
  1/1 mismatches
  [1] 3 - 4 == -1
  
  [ FAIL 1 | WARN 970 | SKIP 6 | PASS 423 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [11s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(imagefluency)
  > 
  > test_check("imagefluency")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 108 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_complexity.R:37:3'): img_complexity normalizes input image if necessary ──
  img_complexity(array(100:500, dim = c(50, 50, 3))) not equal to 0.1111398.
  1/1 mismatches
  [1] 0.0981 - 0.111 == -0.0131
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 108 ]
  Error: Test failures
  Execution halted
Found the following files/directories:
  ‘pkgbuild’
Running ‘anisotropyChoice.R’ [10s/25s]
  Running ‘biasCorr.R’ [10s/26s]
  Running ‘findLocalBias.R’ [9s/23s]
  Running ‘findRegionalBias.R’ [10s/28s]
  Running ‘optimizingTest.R’ [39m/43m]
Running the tests in ‘tests/optimizingTest.R’ failed.
Complete output:
  > options(error = recover)
  > #test = TRUE
  > test = FALSE
  > mantest = FALSE
  > set.seed(1)
  > library(intamapInteractive)
  Loading required package: intamap
  Loading required package: sp
  > library(gstat)
  > #require(maptools)
  > # for SIC2004 dataset
  > data(sic2004)
  > coordinates(sic.val) = ~x+y
  > observations = sic.val["dayx"] 
  > coordinates(sic.grid)=~x+y
  > predGrid = sic.grid
  > 
  > #Finding the polygon for the candidate locations
  > bb = bbox(predGrid)
  > boun = SpatialPoints(data.frame(x=c(bb[1,1],bb[1,2],bb[1,2],bb[1,1],bb[1,1]),
  +                                 y=c(bb[2,1],bb[2,1],bb[2,2],bb[2,2],bb[2,1])))
  > Srl = Polygons(list(Polygon(boun)),ID = as.character(1))
  > candidates = SpatialPolygonsDataFrame(SpatialPolygons(list(Srl)),
  +                                       data = data.frame(ID=1))
  > 
  > # Limits the number of prediction locations to have faster UK 
  > # computations
  > nGrid = dim(coordinates(predGrid))[1]
  > predGrid = predGrid[sample(seq(1,nGrid),1000),]
  > # Fits the variogram model (using function fit.variogram from package
  > # gstat)
  > model = fit.variogram(variogram(dayx~x+y, sic.val), vgm(50, "Sph", 250000, 250))
  > #plot(variogram(dayx~x+y, sic.val), model=model)
  > # Computes the Mukv of the current network
  > initMukv <- calculateMukv(observations, predGrid, model, formulaString = dayx~x+y)
Running ‘testthat.R’ [31m/21m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(intkrige)
  Loading required package: sp
  Loading required package: gstat
  Loading required package: raster
  > 
  > test_check("intkrige")
Running ‘local_tests.R’
  Running ‘spelling.R’
  Running ‘testthat.R’ [30m/57m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(IsoriX)
  
   IsoriX version 0.9.3 is now loaded
  
   Type:
     * `?IsoriX` for a very short description
     * `browseURL('https://bookdown.org/content/782/')` for a longer (online) documentation
     * `help(package = 'IsoriX', help_type = 'html')` for a list of the package objects and help files
     * `citation('IsoriX')` for how to cite IsoriX (i.e. the papers you should read)
     * `news(package = 'IsoriX')` for info on changed between versions of IsoriX
  
   Please join the mailing list 'https://groups.google.com/g/IsoriX'
   for help, news and discussions about IsoriX
  
  
  Attaching package: 'IsoriX'
  
  The following objects are masked from 'package:graphics':
  
      plot, points
  
  The following object is masked from 'package:base':
  
      plot
  
  > 
  > test_check("IsoriX")
Running ‘testthat.R’ [18s/44s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #This file runs all unit tests on every R CMD check.
  > #Comment this out to disable.
  > 
  > library(testthat)
  > 
  > #filter is to disable tests that rely on external servers
  > test_check("jsonlite", filter="toJSON|fromJSON|libjson|serializeJSON")
  Loading required package: jsonlite
  Failed with error:  'there is no package called 'nopackage''
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1534 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-fromJSON-datasets.R:15:5'): fromJSON datasets ────────────────
  names(object) not identical to names(newobject).
  3/17 mismatches
  x[15]: "Delta 15 N (o/oo)"
  y[15]: "Comments"
  
  x[16]: "Delta 13 C (o/oo)"
  y[16]: "Delta 15 N (o/oo)"
  
  x[17]: "Comments"
  y[17]: "Delta 13 C (o/oo)"
  Backtrace:
      ▆
   1. └─base::lapply(...) at test-fromJSON-datasets.R:12:3
   2.   └─jsonlite (local) FUN(X[[i]], ...)
   3.     └─testthat::expect_identical(names(object), names(newobject)) at test-fromJSON-datasets.R:15:5
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1534 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [28s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(konfound)
  Sensitivity analysis as described in Frank, 
  Maroulis, Duong, and Kelcey (2013) and in 
  Frank (2000).
  For more information visit http://konfound-it.com.
  > 
  > test_check("konfound")
  Dependent variable is mpg 
  Dependent variable is wt 
  Using the absolute value of the estimated effect, 
            results can be interpreted by symmetry.
  Using the absolute value of the estimated effect, 
            results can be interpreted by symmetry.
  Using the absolute value of the estimated effect, 
            results can be interpreted by symmetry.
  [ FAIL 1 | WARN 6 | SKIP 0 | PASS 181 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-konfound.R:15:5'): konfound works for lme4 model ─────────────
  output3$RIR_perc not equal to 84.826.
  1/1 mismatches
  [1] 84.3 - 84.8 == -0.517
  
  [ FAIL 1 | WARN 6 | SKIP 0 | PASS 181 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘runLifemapR.Rmd’ using rmarkdown

Quitting from lines 51-55 [buildLF] (runLifemapR.Rmd)
Error: processing vignette 'runLifemapR.Rmd' failed with diagnostics:
Can't combine `..1$taxid` <character> and `..2$taxid` <double>.
--- failed re-building ‘runLifemapR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘lme4-Ex.R’ failed
The error most likely occurred in:

> ### Name: profile-methods
> ### Title: Profile method for merMod objects
> ### Aliases: as.data.frame.thpr log.thpr logProf varianceProf
> ###   profile-methods profile.merMod
> ### Keywords: methods
> 
> ### ** Examples
> 
> fm01ML <- lmer(Yield ~ 1|Batch, Dyestuff, REML = FALSE)
Warning in optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower,  :
  convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 1.01096 (tol = 0.002, component 1)
> system.time(
+   tpr  <- profile(fm01ML, optimizer="Nelder_Mead", which="beta_")
+ )## fast; as only *one* beta parameter is profiled over -> 0.09s (2022)
Error in profile.merMod(fm01ML, optimizer = "Nelder_Mead", which = "beta_") : 
  Profiling over both the residual variance and
fixed effects is not numerically consistent with
profiling over the fixed effects only (relative difference: 1);
consider adjusting devmatchtol
Calls: system.time -> profile -> profile.merMod
Timing stopped at: 0.047 0 0.129
Execution halted
Running ‘testthat.R’ [6s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(longpower)
  Loading required package: lme4
  Loading required package: Matrix
  Loading required package: nlme
  
  Attaching package: 'nlme'
  
  The following object is masked from 'package:lme4':
  
      lmList
  
  > 
  > test_check("longpower")
  
   Converting negative delta to absolute value, you have specified:  -0.2560938 
  [ FAIL 4 | WARN 4 | SKIP 0 | PASS 43 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('tests.R:94:3'): lmmpower (diggle) ─────────────────────────────────
  lmmpower(fm1, pct.change = 0.3, t = seq(0, 9, 1), power = 0.8)$n[1] not equal to 68.4699286748582.
  1/1 mismatches
  [1] 956 - 68.5 == 888
  ── Failure ('tests.R:182:3'): lmmpower (liuliang) ──────────────────────────────
  ...[] not equal to 68.4699286748582.
  1/1 mismatches
  [1] 956 - 68.5 == 888
  ── Failure ('tests.R:211:3'): lmmpower (edland) ────────────────────────────────
  ...[] not equal to 68.4699286748582.
  1/1 mismatches
  [1] 956 - 68.5 == 888
  ── Failure ('tests.R:268:3'): lmmpower (hu) ────────────────────────────────────
  ...[] not equal to 67.1745.
  1/1 mismatches
  [1] 954 - 67.2 == 887
  
  [ FAIL 4 | WARN 4 | SKIP 0 | PASS 43 ]
  Error: Test failures
  Execution halted
Running ‘azimuth.R’
  Comparing ‘azimuth.Rout’ to ‘azimuth.Rout.save’ ... OK
  Running ‘dist.R’
  Comparing ‘dist.Rout’ to ‘dist.Rout.save’ ... OK
  Running ‘geod.R’
  Comparing ‘geod.Rout’ to ‘geod.Rout.save’ ... OK
  Running ‘perimeter.R’
  Comparing ‘perimeter.Rout’ to ‘perimeter.Rout.save’ ...9c9
< [1] 176215.7 149266.8 199587.9 375136.8 263512.7
---
> [1] 176214.9 149265.4 199586.8 375137.8 263512.6
12c12
< [1] 176215.7 149266.8 199587.9 375136.8 263512.7
---
> [1] 176214.9 149265.4 199586.8 375137.8 263512.6
  Running ‘testthat.R’ [5s/13s]
  Comparing ‘testthat.Rout’ to ‘testthat.Rout.save’ ... OK
  Running ‘twkb.R’
  Comparing ‘twkb.Rout’ to ‘twkb.Rout.save’ ... OK
Running examples in ‘mapping-Ex.R’ failed
The error most likely occurred in:

> ### Name: mapping
> ### Title: Static maps
> ### Aliases: mapping
> 
> ### ** Examples
> 
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(sf)
Linking to GEOS 3.12.2, GDAL 3.8.5, PROJ 9.3.1; sf_use_s2() is TRUE
> 
> data("popIT")
> popIT <- popIT
> coords <- loadCoordIT(unit = "provincia", year = '2019')
> cr <- left_join(coords, popIT, by = c( "provincia" = "ID"))
> 
> ###############
> #   Statics   #
> ###############
> 
> mapping(cr)

── tmap v3 code detected ───────────────────────────────────────────────────────
[v3->v4] `tm_borders()`: use 'fill' for the fill color of polygons/symbols
(instead of 'col'), and 'col' for the outlines (instead of 'border.col').
This message is displayed once every 8 hours.
[v3->v4] `tm_borders()`: use `fill_alpha` instead of `alpha`.
Error: C stack usage  19927012 is too close to the limit
Execution halted
Running examples in ‘metalite.ae-Ex.R’ failed
The error most likely occurred in:

> ### Name: tlf_ae_specific
> ### Title: Specific adverse events table
> ### Aliases: tlf_ae_specific
> 
> ### ** Examples
> 
> meta <- meta_ae_example()
> 
> meta |>
+   prepare_ae_specific(
+     population = "apat",
+     observation = "wk12",
+     parameter = "rel"
+   ) |>
+   format_ae_specific() |>
+   tlf_ae_specific(
+     source = "Source:  [CDISCpilot: adam-adsl; adae]",
+     meddra_version = "24.0",
+     path_outdata = tempfile(fileext = ".Rdata"),
+     path_outtable = tempfile(fileext = ".rtf")
+   )
The outdata is saved in/tmp/RtmpuVvhIF/working_dir/Rtmphj47as/file323baf46f4271f.Rdata
Error in unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"),  : 
  'recursive' must be of length 1
Calls: tlf_ae_specific ... rtf_encode_table -> paste -> as_rtf_footnote -> unlist
Execution halted
Running examples in ‘metalite.sl-Ex.R’ failed
The error most likely occurred in:

> ### Name: rtf_exp_duration
> ### Title: Exposure duration table
> ### Aliases: rtf_exp_duration
> 
> ### ** Examples
> 
> meta <- meta_sl_exposure_example()
> 
> meta |>
+   prepare_exp_duration(population = "apat", parameter = "expdur") |>
+   format_exp_duration(display_col = c("n", "prop", "total")) |>
+   rtf_exp_duration(
+     source = "Source: [CDISCpilot: adam-adsl; adex]",
+     path_outdata = tempfile(fileext = ".Rdata"),
+     path_outtable = tempfile(fileext = ".rtf")
+   )
The outdata is saved in/tmp/Rtmpgs8LAp/working_dir/RtmpWpViG7/file32581298f69c.Rdata
Error in unlist(attr(text, "text_indent_first"), attr(text, "text_indent_left"),  : 
  'recursive' must be of length 1
Calls: rtf_exp_duration ... rtf_encode_table -> paste -> as_rtf_footnote -> unlist
Execution halted
Running ‘testthat.R’ [64s/37s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > #
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > library(testthat)
  > library(modelbased)
  > 
  > test_check("modelbased")
  Starting 2 test processes
  [ FAIL 1 | WARN 22 | SKIP 17 | PASS 168 ]
  
  ══ Skipped tests (17) ══════════════════════════════════════════════════════════
  • .Platform$OS.type == "windows" is not TRUE (1):
    'test-estimate_predicted.R:56:3'
  • On CRAN (13): 'test-brms-marginaleffects.R:1:1', 'test-brms.R:1:1',
    'test-estimate_contrasts.R:1:1', 'test-estimate_contrasts_methods.R:1:1',
    'test-estimate_means.R:1:1', 'test-estimate_means_counterfactuals.R:1:1',
    'test-estimate_means_mixed.R:1:1', 'test-g_computation.R:1:1',
    'test-get_marginaltrends.R:1:1', 'test-glmmTMB.R:1:1', 'test-ordinal.R:1:1',
    'test-predict-dpar.R:1:1', 'test-vcov.R:1:1'
  • On Linux (3): 'test-plot-facet.R:1:1', 'test-plot.R:1:1', 'test-print.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-estimate_predicted.R:204:3'): estimate_expectation - predicting RE works ──
  out$Predicted (`actual`) not equal to c(...) (`expected`).
  
    `actual`: 12.2617 12.0693 11.1560 11.6318 11.1657 10.3811 11.1074 11.0749
  `expected`: 12.2064 12.0631 11.2071 11.6286 11.2327 10.5839 11.2085 11.1229
  
  [ FAIL 1 | WARN 22 | SKIP 17 | PASS 168 ]
  Error: Test failures
  Execution halted
Running ‘bugfix.R’ [5s/12s]
  Comparing ‘bugfix.Rout’ to ‘bugfix.Rout.save’ ... OK
  Running ‘regtest-Tukey.R’
  Comparing ‘regtest-Tukey.Rout’ to ‘regtest-Tukey.Rout.save’ ... OK
  Running ‘regtest-anova.R’
  Comparing ‘regtest-anova.Rout’ to ‘regtest-anova.Rout.save’ ... OK
  Running ‘regtest-fixest.R’
  Running ‘regtest-interface-extended.R’
  Comparing ‘regtest-interface-extended.Rout’ to ‘regtest-interface-extended.Rout.save’ ... OK
  Running ‘regtest-interface.R’
  Comparing ‘regtest-interface.Rout’ to ‘regtest-interface.Rout.save’ ... OK
  Running ‘regtest-lme.R’
  Comparing ‘regtest-lme.Rout’ to ‘regtest-lme.Rout.save’ ...59c59
< 1 53.53  3  1.416e-11
---
> 1 67.07  3  1.812e-14
67,71d66
< Warning messages:
< 1: In optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower,  :
<   convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
< 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
<   Model failed to converge with max|grad| = 1.60567 (tol = 0.002, component 1)
  Running ‘regtest-mmm.R’
  Comparing ‘regtest-mmm.Rout’ to ‘regtest-mmm.Rout.save’ ... OK
  Running ‘regtest-survival.R’
  Comparing ‘regtest-survival.Rout’ to ‘regtest-survival.Rout.save’ ... OK
Running ‘buffer.R’
  Comparing ‘buffer.Rout’ to ‘buffer.Rout.save’ ...5,10d4
< > 
< > if (!length(oclPlatforms())) {
< +     cat("== Cannot run tests as there is no platform")
< +     q("no")
< + }
< > 
  Running ‘kernel.R’ [5s/10s]
  Comparing ‘kernel.Rout’ to ‘kernel.Rout.save’ ...5,10d4
< > 
< > if (!length(oclPlatforms())) {
< +     cat("== Cannot run tests as there is no platform")
< +     q("no")
< + }
< >
Found the following files/directories:
  ‘Minimal-concordance.tex’ ‘Minimal.Rnw’ ‘Minimal.pdf’
  ‘Minimal.synctex.gz’ ‘Minimal.tex’ ‘figure’
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/paws.analytics.Rcheck/00install.out’ for details.
---- unloading
[gannet:437021:0:437021] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x7f12364bc960)
Running ‘testthat.R’ [87s/87s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(poems)
  > 
  > test_check("poems")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1093 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_results_manager.R:385:5'): calculate summary weighted averages ──
  Error in `FUN(newX[, i], ...)`: NA in coercion to Rboolean
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(results_manager$calculate_summary_weighted_averages(na_replacements = list(abundance = na_function))) at test_results_manager.R:388:3
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. └─results_manager$calculate_summary_weighted_averages(na_replacements = list(abundance = na_function))
   10.   └─na_replacements[[param]](summary_matrix_list[[param]])
   11.     └─base::apply(a, 2, min, na.rm = NA) at test_results_manager.R:385:5
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1093 ]
  Error: Test failures
  Execution halted
Running ‘basic.R’ [54s/82s]
  Comparing ‘basic.Rout’ to ‘basic.Rout.save’ ...294,307c294,307
<       YYYY         MM          DD      timestamp           Qobs   deseaonalized
<  Min.   :0   Min.   :0   Min.   :0   Min.   :0 secs   Min.   :0   Min.   :0    
<  1st Qu.:0   1st Qu.:0   1st Qu.:0   1st Qu.:0 secs   1st Qu.:0   1st Qu.:0    
<  Median :0   Median :0   Median :0   Median :0 secs   Median :0   Median :0    
<  Mean   :0   Mean   :0   Mean   :0   Mean   :0 secs   Mean   :0   Mean   :0    
<  3rd Qu.:0   3rd Qu.:0   3rd Qu.:0   3rd Qu.:0 secs   3rd Qu.:0   3rd Qu.:0    
<  Max.   :0   Max.   :0   Max.   :0   Max.   :0 secs   Max.   :0   Max.   :0    
<        r1   
<  Min.   :0  
<  1st Qu.:0  
<  Median :0  
<  Mean   :0  
<  3rd Qu.:0  
<  Max.   :0  
---
>       YYYY         MM          DD     timestamp             Qobs  
>  Min.   :0   Min.   :0   Min.   :0   Length:1825       Min.   :0  
>  1st Qu.:0   1st Qu.:0   1st Qu.:0   Class :difftime   1st Qu.:0  
>  Median :0   Median :0   Median :0   Mode  :numeric    Median :0  
>  Mean   :0   Mean   :0   Mean   :0                     Mean   :0  
>  3rd Qu.:0   3rd Qu.:0   3rd Qu.:0                     3rd Qu.:0  
>  Max.   :0   Max.   :0   Max.   :0                     Max.   :0  
>  deseaonalized       r1   
>  Min.   :0     Min.   :0  
>  1st Qu.:0     1st Qu.:0  
>  Median :0     Median :0  
>  Mean   :0     Mean   :0  
>  3rd Qu.:0     3rd Qu.:0  
>  Max.   :0     Max.   :0
Running ‘testthat.R’ [123s/124s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rearrr)
  > 
  > if (require("xpectr")) {
  +   test_check("rearrr")
  + }
  Loading required package: xpectr
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 7341 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_n_fn.R:842:3'): testing quantile_index() ─────────────────────
  xpectr::strip(side_effects_19148[["error"]]) does not match "probs outside 01".
  Actual value: "ℹ In index 1Caused by error in quantiledefault type must be an integer in 19"
  Backtrace:
      ▆
   1. └─testthat::expect_match(...) at test_n_fn.R:842:3
   2.   └─testthat:::expect_match_(...)
  ── Failure ('test_n_fn.R:859:3'): testing quantile_index() ─────────────────────
  xpectr::strip(side_effects_19148[["error"]]) does not match "object a not found".
  Actual value: "ℹ In index 1Caused by error in quantiledefault type must be an integer in 19"
  Backtrace:
      ▆
   1. └─testthat::expect_match(...) at test_n_fn.R:859:3
   2.   └─testthat:::expect_match_(...)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 7341 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [29s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rempsyc)
  Suggested APA citation: Thériault, R. (2023). rempsyc: Convenience functions for psychology. 
  Journal of Open Source Software, 8(87), 5466. https://doi.org/10.21105/joss.05466
  > 
  > test_check("rempsyc")
  [ FAIL 1 | WARN 0 | SKIP 19 | PASS 46 ]
  
  ══ Skipped tests (19) ══════════════════════════════════════════════════════════
  • On CRAN (19): 'test-best_duplicate.R:8:3', 'test-extract_duplicates.R:8:3',
    'test-find_mad.R:2:3', 'test-format_value.R:2:3',
    'test-nice_assumptions.R:9:3', 'test-nice_contrasts.R:7:3',
    'test-nice_lm.R:5:3', 'test-nice_lm_contrasts.R:12:3',
    'test-nice_lm_slopes.R:5:3', 'test-nice_mod.R:4:3', 'test-nice_na.R:2:3',
    'test-nice_randomize.R:5:3', 'test-nice_reverse.R:3:3',
    'test-nice_slopes.R:4:3', 'test-nice_t_test.R:5:3', 'test-nice_table.R:13:3',
    'test-nice_var.R:2:3', 'test-scale_mad.R:2:3', 'test-winsorize_mad.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cormatrix_excel.R:5:3'): cormatrix_excel ───────────────────────
  Error: x must be class wbColour
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-cormatrix_excel.R:5:3
   2.   └─rlang::cnd_signal(state$error)
  
  [ FAIL 1 | WARN 0 | SKIP 19 | PASS 46 ]
  Error: Test failures
  Execution halted
Found the following files/directories:
  ‘rnaturalearthhires’
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/rJava.Rcheck/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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/Rserve.Rcheck/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_Outputfile’,
    ‘R_TempDir’, ‘R_Visible’, ‘R_curErrorBuf’, ‘ptr_R_Busy’,
    ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’, ‘ptr_R_ReadConsole’,
    ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’, ‘ptr_R_WriteConsole’,
    ‘ptr_R_WriteConsoleEx’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following files/directories:
  ‘shinyscholard’
Running ‘test-all.R’ [53s/74s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > if(require(testthat)) {
  + 
  +     test_check("simr")
  + }
  Loading required package: testthat
  Loading required package: simr
  Loading required package: lme4
  Loading required package: Matrix
  
  Attaching package: 'simr'
  
  The following object is masked from 'package:lme4':
  
      getData
  
  The following object is masked from 'package:testthat':
  
      compare
  
  boundary (singular) fit: see help('isSingular')
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 113 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_new.R:23:5'): makeLmer works ─────────────────────────────────
  nrow(ps$warnings) not equal to 0.
  1/1 mismatches
  [1] 4 - 0 == 4
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 113 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [169s/173s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("smurf")
  > 
  > test_check("smurf")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 591 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_output.R:323:3'): Test n.par.cov in output ─────────────────────
  Error in `islistfactor(x, recursive)`: NA in coercion to Rboolean
  Backtrace:
      ▆
   1. ├─testthat::expect_true(...) at test_output.R:323:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::unlist(munich.fit$n.par.cov, length)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 591 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [55s/96s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spant)
  spant 3.2.0
  
  Attaching package: 'spant'
  
  The following object is masked from 'package:stats':
  
      sd
  
  > 
  > test_check("spant")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 16 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_fitting.R:57:3'): Test ABfit coarse-fitting steps only ───────
  `fit_res` has changed from known value recorded in 'abfit_res_coarse.rds'.
  Component "res_tab": Component "res.niter": Mean relative difference: 0.6688525
  Backtrace:
      ▆
   1. └─testthat::expect_equal_to_reference(...) at test_fitting.R:57:3
   2.   └─testthat::expect_known_value(..., update = update)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 16 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/spmodel.Rcheck/vign_test/spmodel/vignettes/introduction_files/figure-html/unnamed-chunk-6-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 88879 bytes
Input file size = 89077 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 75790
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 75790

Output IDAT size = 75790 bytes (13089 bytes decrease)
Output file size = 75868 bytes (13209 bytes = 14.83% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/spmodel.Rcheck/vign_test/spmodel/vignettes/introduction_files/figure-html/unnamed-chunk-14-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 130624 bytes
Input file size = 130882 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 100995
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 100995

Output IDAT size = 100995 bytes (29629 bytes decrease)
Output file size = 101073 bytes (29809 bytes = 22.78% decrease)
Running ‘testthat.R’ [14s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.unsetenv("R_TESTS")
  > if (require(testthat, quietly = TRUE)) {
  +   require(stan4bart)
  +   test_check("stan4bart")
  + } else {
  +   cat("package 'testthat' not available; cannot run unit tests\n")
  + }
  Loading required package: stan4bart
  Loading required package: dbarts
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 205 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test-01-continuous.R:124:3', 'test-01-continuous.R:163:3',
    'test-02-binary.R:33:3', 'test-02-binary.R:128:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-01-continuous.R:277:3'): ppd has approximately right amount of noise ──
  ... <= 0.1 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 205 ]
  Error: Test failures
  Execution halted
Found the following files/directories:
  ‘JMRData’
Running examples in ‘syrup-Ex.R’ failed
The error most likely occurred in:

> ### Name: syrup
> ### Title: Memory and CPU Usage Information for Parallel R Code
> ### Aliases: syrup
> 
> ### ** Examples
> 
> ## Don't show: 
> if (ps::ps_os_type()[["POSIX"]]) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ # pass any expression to syrup. first, sequentially:
+ res_syrup <- syrup({res_output <- Sys.sleep(1)})
+ 
+ res_syrup
+ 
+ # to snapshot memory and CPU information more (or less) often, set `interval`
+ syrup(Sys.sleep(1), interval = .01)
+ 
+ # use `peak = TRUE` to return only the snapshot with
+ # the highest memory usage (as `sum(rss)`)
+ syrup(Sys.sleep(1), interval = .01, peak = TRUE)
+ 
+ # results from syrup are more---or maybe only---useful when
+ # computations are evaluated in parallel. see package README
+ # for an example.
+ ## Don't show: 
+ }) # examplesIf
> res_syrup <- syrup({
+     res_output <- Sys.sleep(1)
+ })
Superclass process has cloneable=FALSE, but subclass r_session has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for r_session.
Error in `syrup()`:
! Unable to retrieve resource usage results from the temporary session.
ℹ This is an internal error that was detected in the syrup package.
  Please report it at <https://github.com/simonpcouch/syrup/issues> with a reprex (<https://tidyverse.org/help/>) and the full backtrace.
Backtrace:
    ▆
 1. ├─(if (getRversion() >= "3.4") withAutoprint else force)(...)
 2. │ └─base::source(...)
 3. │   ├─base::withVisible(eval(ei, envir))
 4. │   └─base::eval(ei, envir)
 5. │     └─base::eval(ei, envir)
 6. └─syrup::syrup(...)
 7.   └─syrup:::retrieve_results(sesh)
 8.     └─rlang::abort(...)
Execution halted
Found the following files/directories:
  ‘lilypond-tmp-midi-2841aa’ ‘lilypond-tmp-midi-2be579’
Running examples in ‘teal.modules.general-Ex.R’ failed
The error most likely occurred in:

> ### Name: tm_a_pca
> ### Title: 'teal' module: Principal component analysis
> ### Aliases: tm_a_pca
> 
> ### ** Examples
> 
> library(teal.widgets)
> 
> # general data example
> data <- teal_data()
> data <- within(data, {
+   require(nestcolor)
+   USArrests <- USArrests
+ })
> 
> datanames(data) <- "USArrests"
Warning: `datanames<-()` was deprecated in teal.data 0.7.0.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
  `teal_data`. See ?names.teal_data
> 
> app <- init(
+   data = data,
+   modules = modules(
+     tm_a_pca(
+       "PCA",
+       dat = data_extract_spec(
+         dataname = "USArrests",
+         select = select_spec(
+           choices = variable_choices(
+             data = data[["USArrests"]], c("Murder", "Assault", "UrbanPop", "Rape")
+           ),
+           selected = c("Murder", "Assault"),
+           multiple = TRUE
+         ),
+         filter = NULL
+       ),
+       ggplot2_args = ggplot2_args(
+         labs = list(subtitle = "Plot generated by PCA Module")
+       )
+     )
+   )
+ )
[INFO] 2025-02-21 13:53:01.9872 pid:2802150 token:[] teal.modules.general Initializing tm_a_pca
Error in as.list(data@env) : 
  no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
Running examples in ‘telefit-Ex.R’ failed
The error most likely occurred in:

> ### Name: stFit
> ### Title: Fit the remote effects spatial process (RESP) model
> ### Aliases: stFit
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(foreach)
> library(itertools)
Loading required package: iterators
> 
> set.seed(2018)
> 
> data("coprecip")
> data("coprecip.fit")
> attach(coprecip)
> 
> coprecip.fit = stFit(stData = coprecip, priors = coprecip.fit$priors, 
+                      maxIt = 10, coords.knots = coprecip.fit$coords.knots)
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/TestGenerator.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [80s/96s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(tidyfit)
  > 
  > test_check("tidyfit")
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:tidyfit':
  
      explain
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 184 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-glmm.R:6:3'): glmm regression works ──────────────────────────
  nrow(coef(m_reg)) (`actual`) not equal to 11 (`expected`).
  
    `actual`: 20.0
  `expected`: 11.0
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 184 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [36s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(trace)
  > 
  > test_check("trace")
  [ FAIL 3 | WARN 0 | SKIP 1 | PASS 66 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-shinytest2.R:7:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-call_repeats.R:275:3'): batch correction ─────────────────────
  all.equal(...) is not TRUE
  
  `actual` is a character vector ('Mean relative difference: 0.8841185')
  `expected` is a logical vector (TRUE)
  ── Failure ('test-call_repeats.R:328:3'): batch correction with no data in one batch ──
  grepl(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-call_repeats.R:454:3'): repeat correction with one sample off warning ──
  grepl("had no batch correction carried out", assignment_warning) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 3 | WARN 0 | SKIP 1 | PASS 66 ]
  Error: Test failures
  Execution halted
Running ‘Coxph-Ex.R’ [23s/66s]
  Comparing ‘Coxph-Ex.Rout’ to ‘Coxph-Ex.Rout.save’ ... OK
  Running ‘KaplanMeier-Ex.R’ [4s/11s]
  Running ‘PI_OVL-Ex.R’ [5s/15s]
  Running ‘Polr-Ex.R’
  Comparing ‘Polr-Ex.Rout’ to ‘Polr-Ex.Rout.save’ ... OK
  Running ‘Survreg-Ex.R’ [7s/20s]
  Comparing ‘Survreg-Ex.Rout’ to ‘Survreg-Ex.Rout.save’ ... OK
  Running ‘bugfixes.R’ [112s/233s]
  Running ‘intercepts-Ex.R’ [7s/12s]
  Comparing ‘intercepts-Ex.Rout’ to ‘intercepts-Ex.Rout.save’ ... OK
  Running ‘mmlt-Ex.R’ [248s/442s]
  Comparing ‘mmlt-Ex.Rout’ to ‘mmlt-Ex.Rout.save’ ... OK
  Running ‘mmlt-interface.R’ [79s/131s]
  Running ‘mtram-Ex.R’ [26s/39s]
  Comparing ‘mtram-Ex.Rout’ to ‘mtram-Ex.Rout.save’ ...11,17d10
< Warning messages:
< 1: In optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower,  :
<   convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
< 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
<   unable to evaluate scaled gradient
< 3: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
<   Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
27c20
< 'log Lik.' -Inf (df=6)
---
> 'log Lik.' -876 (df=6)
34c27
< [1] 0.041
---
> [1] 0.039
43c36
<      -10.38        0.43 
---
>       -9.82        0.41 
51c44
< [1] 1 0 1
---
> [1] 0.929 0.018 0.223
60,61c53,54
< [1,]  506   10
< [2,]   10   29
---
> [1,]  565   11
> [2,]   11   33
68,69c61,62
< (Intercept)         587    0
< Days                  0  587
---
> (Intercept)         565   11
> Days                 11   33
72c65
<          24          24 
---
>        23.8         5.7 
75,76c68,69
< (Intercept)           1    0
< Days                  0    1
---
> (Intercept)       1.000 0.081
> Days              0.081 1.000
  Running ‘stram-Ex.R’ [23s/35s]
  Comparing ‘stram-Ex.Rout’ to ‘stram-Ex.Rout.save’ ... OK
Running ‘testthat.R’ [13m/13m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(tsgarch)
  Loading required package: tsmethods
  > 
  > test_check("tsgarch")
  Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
  Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
  Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
  Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
  [ FAIL 4 | WARN 2 | SKIP 0 | PASS 133 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-benchmarks.R:8:5'): fcp laurent ──────────────────────────────
  all(b$lre$coefficient > 4) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-estimation.R:145:5'): estimate: igarch(1,1) ──────────────────
  as.numeric(logLik(mod)) (`actual`) not equal to -1082.6435 (`expected`).
  
    `actual`:    -Inf
  `expected`: -1082.6
  ── Failure ('test-estimation.R:165:5'): estimate: igarch(2,1)-partially fixed parameters ──
  persistence(mod) (`actual`) not equal to 1 (`expected`).
  
    `actual`: 0.985
  `expected`: 1.000
  ── Failure ('test-estimation.R:166:5'): estimate: igarch(2,1)-partially fixed parameters ──
  as.numeric(logLik(mod)) (`actual`) not equal to -1088.12 (`expected`).
  
    `actual`:    -Inf
  `expected`: -1088.1
  
  [ FAIL 4 | WARN 2 | SKIP 0 | PASS 133 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [71s/72s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(uwot)
  Loading required package: Matrix
  > 
  > test_check("uwot")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 705 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_errors.R:28:1'): (code run outside of `test_that()`) ─────────
  `umap(iris10, pca = 500)` threw an error with unexpected message.
  Expected match: "'pca' must be <="
  Actual message: "'length = 40' in coercion to 'logical(1)'"
  Backtrace:
      ▆
   1. ├─testthat::expect_error(umap(iris10, pca = 500), "'pca' must be <=") at test_errors.R:28:1
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─uwot::umap(iris10, pca = 500)
   7.   └─uwot:::uwot(...)
  ── Error ('test_output.R:395:1'): (code run outside of `test_that()`) ──────────
  Error in `min(nrow(X), na.rm = col(X))`: 'length = 40' in coercion to 'logical(1)'
  Backtrace:
      ▆
   1. └─uwot::umap(...) at test_output.R:395:1
   2.   └─uwot:::uwot(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 705 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  RUtils.c:142:5: warning: ‘xmlSubstituteEntitiesDefault’ is deprecated [-Wdeprecated-declarations]
  DocParse.c:67:2: warning: ‘__xmlDoValidityCheckingDefaultValue’ is deprecated [-Wdeprecated-declarations]
  DocParse.c:70:6: warning: ‘__xmlDoValidityCheckingDefaultValue’ is deprecated [-Wdeprecated-declarations]
  RSDTD.c:134:7: warning: ‘xmlSkipBlankChars’ is deprecated [-Wdeprecated-declarations]
  RSDTD.c:135:7: warning: ‘xmlParseMarkupDecl’ is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/XML.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
checkRd: (-1) varipart.Rd:19: Lost braces
    19 | \item{type}{a character specifying the algorithm which should be used to adjust R-squared (either \code{"simulated"} or \ code{"parametric"}).}
       |                                                                                                                               ^
Package required but not available: ‘org.Hs.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘ascariasis.Rmd’ using rmarkdown
File figure/asc_plot_mixt-1.png not found in resource path
Error: processing vignette 'ascariasis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘ascariasis.Rmd’

--- re-building ‘simulation_study.Rmd’ using rmarkdown
File figure/sim_plot_true_data-1.png not found in resource path
Error: processing vignette 'simulation_study.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘simulation_study.Rmd’

SUMMARY: processing the following files failed:
  ‘ascariasis.Rmd’ ‘simulation_study.Rmd’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘bulkAnalyseR-Ex.R’ failed
The error most likely occurred in:

> ### Name: DEanalysis
> ### Title: Perform differential expression (DE) analysis on an expression
> ###   matrix
> ### Aliases: DEanalysis DEanalysis_edger DEanalysis_deseq2
> 
> ### ** Examples
> 
> expression.matrix.preproc <- as.matrix(read.csv(
+   system.file("extdata", "expression_matrix_preprocessed.csv", package = "bulkAnalyseR"), 
+   row.names = 1
+ ))[1:100, 1:4]
> 
> anno <- AnnotationDbi::select(
+   getExportedValue('org.Mm.eg.db', 'org.Mm.eg.db'),
+   keys = rownames(expression.matrix.preproc),
+   keytype = 'ENSEMBL',
+   columns = 'SYMBOL'
+ ) %>%
+   dplyr::distinct(ENSEMBL, .keep_all = TRUE) %>%
+   dplyr::mutate(NAME = ifelse(is.na(SYMBOL), ENSEMBL, SYMBOL))
Error in (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 'select': there is no package called ‘org.Mm.eg.db’
Calls: %>% ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘bunching_examples.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'bunching_examples.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.5/bunching.Rcheck/vign_test/bunching/vignettes/bunching_examples.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See bunching_examples.log for more info.
--- failed re-building ‘bunching_examples.Rmd’

--- re-building ‘bunching_theory.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'bunching_theory.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.5/bunching.Rcheck/vign_test/bunching/vignettes/bunching_theory.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See bunching_theory.log for more info.
--- failed re-building ‘bunching_theory.Rmd’

SUMMARY: processing the following files failed:
  ‘bunching_examples.Rmd’ ‘bunching_theory.Rmd’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'org.Hs.eg.db', 'org.Dr.eg.db', 'org.Mm.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘cartographr.R’ ‘utils.R’
Error(s) in re-building vignettes:
--- re-building ‘atp_calculation.Rmd’ using rmarkdown
File mito_glyco_tests.png not found in resource path
Error: processing vignette 'atp_calculation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘atp_calculation.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘README.Rmd’ using rmarkdown
File man/figures/logo.png not found in resource path
Error: processing vignette 'README.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘README.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘0_pt-ex.R’ [1s/2s]
  Running ‘ex1.R’ [3s/4s]
  Running ‘ex2-long.R’ [3s/4s]
  Running ‘ex3.R’ [1s/1s]
  Comparing ‘ex3.Rout’ to ‘ex3.Rout.save’ ... OK
  Running ‘multi-constr.R’ [2s/2s]
  Comparing ‘multi-constr.Rout’ to ‘multi-constr.Rout.save’ ...175a176,178
> 5: In rq.fit.sfn(Xeq, Yeq, tau = tau, rhs = rhs, control = rqCtrl) :
>   tiny diagonals replaced with Inf when calling blkfct
> 
219a223,229
> Warning messages:
> 1: In rq.fit.sfn(Xeq, Yeq, tau = tau, rhs = rhs, control = rqCtrl) :
>   tiny diagonals replaced with Inf when calling blkfct
> 
> 2: In rq.fit.sfn(Xeq, Yeq, tau = tau, rhs = rhs, control = rqCtrl) :
>   tiny diagonals replaced with Inf when calling blkfct
> 
  Running ‘roof.R’ [1s/2s]
  Comparing ‘roof.Rout’ to ‘roof.Rout.save’ ... OK
  Running ‘small-ex.R’ [1s/1s]
  Comparing ‘small-ex.Rout’ to ‘small-ex.Rout.save’ ... OK
  Running ‘spline-ex.R’ [1s/1s]
  Comparing ‘spline-ex.Rout’ to ‘spline-ex.Rout.save’ ... OK
  Running ‘temp.R’ [1s/2s]
  Comparing ‘temp.Rout’ to ‘temp.Rout.save’ ... OK
  Running ‘wind.R’ [4s/6s]
Packages required but not available: 'org.Hs.eg.db', 'org.Mm.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘cplm.Rnw’ using Sweave
Loading required package: coda
Loading required package: Matrix
Loading required package: splines
Error: processing vignette 'cplm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cplm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘cplm.Rnw’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘ex1.R’ [0s/0s]
  Comparing ‘ex1.Rout’ to ‘ex1.Rout.save’ ...53c53
<  $ lo.hi      : int [1:2] 1 2
---
>  $ lo.hi      : int [1:2] 3 4
55,56c55,56
<  $ gcm        : int [1:2] 2 1
<  $ lcm        : int [1:2] 1 2
---
>  $ gcm        : int [1:2] 4 3
>  $ lcm        : int [1:2] 3 4
61,62c61,62
<  $ xl         : num 0
<  $ xu         : num 1
---
>  $ xl         : num 3
>  $ xu         : num 4
  Running ‘mechler-ex.R’ [0s/0s]
  Comparing ‘mechler-ex.Rout’ to ‘mechler-ex.Rout.save’ ... OK
  Running ‘sim1.R’ [1s/1s]
  Comparing ‘sim1.Rout’ to ‘sim1.Rout.save’ ... OK
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/Directional.Rcheck/00install.out’ for details.
Packages required but not available:
  'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Hsapiens.UCSC.hg38.knownGene', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘advanced_vignette.Rmd’ using rmarkdown

Quitting from lines 13-25 [setup] (advanced_vignette.Rmd)
Error: processing vignette 'advanced_vignette.Rmd' failed with diagnostics:
there is no package called 'terra'
--- failed re-building ‘advanced_vignette.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(EGRETci)
  > test_check("EGRETci")
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 16 ]
  
  ══ Skipped tests (10) ══════════════════════════════════════════════════════════
  • On CRAN (10): 'tests_boot_tests.R:68:3', 'tests_boot_tests.R:86:3',
    'tests_boot_tests.R:130:3', 'tests_boot_tests.R:148:3',
    'tests_boot_tests.R:184:3', 'tests_boot_tests.R:213:3', 'tests_kalman.R:4:3',
    'tests_kalman.R:21:3', 'tests_kalman.R:46:3', 'tests_kalman.R:71:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('tests_boot_tests.R:112:3'): paVector ──────────────────────────────
  `paIndexWinter` not equal to 11:13.
  Lengths differ: 4 is not 3
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 16 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ellipticpaper.Rnw’ using Sweave

Attaching package: ‘elliptic’

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

    sd, sigma

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

    is.primitive

Loading required package: emulator
Loading required package: mvtnorm
Loading required package: calibrator
Error: processing vignette 'ellipticpaper.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'ellipticpaper.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm6): Font bbm6 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘ellipticpaper.Rnw’

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

Attaching package: ‘elliptic’

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

    sd, sigma

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

    is.primitive

--- finished re-building ‘residuetheorem.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Running ‘EpiILM.network.R’ [2s/3s]
  Comparing ‘EpiILM.network.Rout’ to ‘EpiILM.network.Rout.save’ ...9817c9817
<  [ reached 'max' / getOption("max.print") -- omitted 301 rows ]
---
>  [ reached getOption("max.print") -- omitted 301 rows ]
19695c19695
<  [ reached 'max' / getOption("max.print") -- omitted 301 rows ]
---
>  [ reached getOption("max.print") -- omitted 301 rows ]
  Running ‘EpiILM.spatial.R’ [1s/1s]
  Comparing ‘EpiILM.spatial.Rout’ to ‘EpiILM.spatial.Rout.save’ ... OK
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/evesim.Rcheck/00install.out’ for details.
Unknown package ‘quanteda.textmodels’ in Rd xrefs
Error(s) in re-building vignettes:
--- re-building ‘jss.Rmd’ using rmarkdown
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
Error: processing vignette 'jss.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.5/fairadapt.Rcheck/vign_test/fairadapt/vignettes/jss.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips.
--- failed re-building ‘jss.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown

Quitting from lines 22-24 [unnamed-chunk-1] (fitbitScraper-examples.Rmd)
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

SUMMARY: processing the following file failed:
  ‘fitbitScraper-examples.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) NEWS.Rd:234: Escaped LaTeX specials: \_
checkRd: (-1) NEWS.Rd:257: Escaped LaTeX specials: \_ \_
checkRd: (-1) NEWS.Rd:258: Escaped LaTeX specials: \_ \_
checkRd: (-1) NEWS.Rd:259: Escaped LaTeX specials: \_
checkRd: (-1) NEWS.Rd:262: Escaped LaTeX specials: \_
checkRd: (-1) NEWS.Rd:265: Escaped LaTeX specials: \_
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/fRLR.Rcheck/00install.out’ for details.
Running examples in ‘froggeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: quarto_project
> ### Title: Create a Custom 'Quarto' Project
> ### Aliases: quarto_project
> 
> ### ** Examples
> 
> if (quarto::quarto_version() >= "1.4") {
+   # Create a temporary directory for testing
+   tmp_dir <- tempdir()
+ 
+   # Create the Quarto project with custom YAML & associated files
+   quarto_project("frogs", path = tempdir(), custom_yaml = TRUE)
+ 
+   # Confirms files were created (optional, for user confirmation)
+   file.exists(file.path(tmp_dir, "frogs.rproj"))  # Rproj file
+   file.exists(file.path(tmp_dir, "frog.qmd"))     # Quarto doc
+   file.exists(file.path(tmp_dir, "_quarto.yml"))  # project YAML file
+ 
+   # Create a new Quarto project with standard Quarto YAML
+   # quarto_project('frogs_standard', path = tempdir(), custom_yaml = FALSE)
+ 
+   # Clean up: Remove the created temp directory and all files
+   unlink(list.files(tempdir(), full.names = TRUE), recursive = TRUE)
+ }
Error in `find_quarto()`:
! Quarto command-line tools path not found!
Please make sure you have installed and added Quarto to your PATH or set the
QUARTO_PATH environment variable.
Backtrace:
    ▆
 1. └─quarto::quarto_version()
 2.   └─quarto:::find_quarto()
 3.     └─cli::cli_abort(quarto_not_found_msg)
 4.       └─rlang::abort(...)
Execution halted
Running examples in ‘GEC-Ex.R’ failed
The error most likely occurred in:

> ### Name: eep_optim
> ### Title: The Wrapper Function that Returns the Final Estimates from
> ###   Maximum Likelihood Estimation for EEP.
> ### Aliases: eep_optim
> 
> ### ** Examples
> 
> eep_optim(seq(1:100))
Error in stats::optim(init, lower = lower_bound, eep_nll, method = "L-BFGS-B",  : 
  L-BFGS-B needs finite values of 'fn'
Calls: eep_optim -> raw_est_eep -> <Anonymous>
Execution halted
Package required but not available: ‘reactome.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘geoAr_geofacet.Rmd’ using rmarkdown
File figure/tucmap-1.png not found in resource path
Error: processing vignette 'geoAr_geofacet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘geoAr_geofacet.Rmd’

--- re-building ‘geoAr_leaflet.Rmd’ using rmarkdown
File figure/map-1.png not found in resource path
Error: processing vignette 'geoAr_leaflet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘geoAr_leaflet.Rmd’

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

SUMMARY: processing the following files failed:
  ‘geoAr_geofacet.Rmd’ ‘geoAr_leaflet.Rmd’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘bsch.R’ [1s/1s]
  Comparing ‘bsch.Rout’ to ‘bsch.Rout.save’ ...3a4
> 
  Running ‘penInf.R’ [2s/3s]
  Comparing ‘penInf.Rout’ to ‘penInf.Rout.save’ ...5a6
> 
  Running ‘sh9.2012.R’ [2s/2s]
  Comparing ‘sh9.2012.Rout’ to ‘sh9.2012.Rout.save’ ...3a4
> 
  Running ‘shPUR.R’ [2s/2s]
  Comparing ‘shPUR.Rout’ to ‘shPUR.Rout.save’ ...3a4
> 
  Running ‘test1Fast.R’ [2s/2s]
  Comparing ‘test1Fast.Rout’ to ‘test1Fast.Rout.save’ ...3a4
> 
  Running ‘test1QE.R’ [1s/1s]
  Comparing ‘test1QE.Rout’ to ‘test1QE.Rout.save’ ...3a4
> 
  Running ‘test2Fast.R’ [2s/2s]
  Comparing ‘test2Fast.Rout’ to ‘test2Fast.Rout.save’ ...3a4
> 
  Running ‘test2QE.R’ [1s/1s]
  Comparing ‘test2QE.Rout’ to ‘test2QE.Rout.save’ ...3a4
> 
  Running ‘test3Fast.R’ [2s/3s]
  Comparing ‘test3Fast.Rout’ to ‘test3Fast.Rout.save’ ...3a4
> 
  Running ‘test3QE.R’ [1s/1s]
  Comparing ‘test3QE.Rout’ to ‘test3QE.Rout.save’ ...3a4
> 
  Running ‘test5Fast.R’ [2s/3s]
  Comparing ‘test5Fast.Rout’ to ‘test5Fast.Rout.save’ ...3a4
> 
  Running ‘test7Fast.R’ [3s/3s]
  Comparing ‘test7Fast.Rout’ to ‘test7Fast.Rout.save’ ...3a4
> 
  Running ‘testMyFam.R’ [0s/0s]
  Comparing ‘testMyFam.Rout’ to ‘testMyFam.Rout.save’ ...3a4
>
Package required but not available: ‘EnsDb.Hsapiens.v75’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘hetGP_vignette.Rnw’ using knitr


Quitting from lines 2154-2174 [Contour_ahead] (hetGP_vignette.Rnw)
Execution halted

* checking PDF version of manual ...* using check arguments '--no-clean-on-error '
Note: skipping ‘hexagon_binning.Rnw’ due to unavailable dependencies:
  'marray'
Found the following significant warnings:
  clang: warning: argument unused during compilation: '-mpopcnt' [-Wunused-command-line-argument]
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/highs.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’
File ‘JavaGD/libs/JavaGD.so’:
  Found non-API call to R: ‘Rf_gsetVar’

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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘Instruction_of_functions_of_R_package_KINSIMU.Rnw’ using Sweave
Error: processing vignette 'Instruction_of_functions_of_R_package_KINSIMU.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'Instruction_of_functions_of_R_package_KINSIMU.tex' failed.
LaTeX errors:
! LaTeX Error: Command \gather already defined.
               Or name \end... illegal, see p.192 of the manual.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! Emergency stop.
 ...                                              
                                                  
l.1560 }
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘Instruction_of_functions_of_R_package_KINSIMU.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘using_latent2likert.Rmd’ using rmarkdown
File man/figures/courses-grouped-min.png not found in resource path
Error: processing vignette 'using_latent2likert.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘using_latent2likert.Rmd’

SUMMARY: processing the following file failed:
  ‘using_latent2likert.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 22-30 [unnamed-chunk-2] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'org.Mm.eg.db'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error in ls.problem(model.text.lsp) : 
  has.localsolver(ls.path) is not TRUE
Calls: ls.problem -> stopifnot
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘localsolver.Rmd’ using knitr
sh: localsolver: command not found

Quitting from lines 66-68 [unnamed-chunk-3] (localsolver.Rmd)
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
--- failed re-building ‘localsolver.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error: package or namespace load failed for ‘LSTbook’:
 .onLoad failed in loadNamespace() for 'LSTbook', details:
  call: loadNamespace(name)
  error: there is no package called ‘mosaicData’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
ADPopSel: no visible global function definition for ‘%dorng%’
ADRand: no visible global function definition for ‘%dorng%’
ADSSMod: no visible global function definition for ‘%dorng%’
ADTreatSel: no visible global function definition for ‘%dorng%’
ClustRand: no visible global function definition for ‘%dorng%’
EventPred: no visible global function definition for ‘%dorng%’
FutRuleNCores: no visible global function definition for ‘%dorng%’
MultAdj1NCores: no visible global function definition for ‘%dorng%’
MultAdj2NCores: no visible global function definition for ‘%dorng%’
MultAdj3NCores: no visible global function definition for ‘%dorng%’
Undefined global functions or variables:
  %dorng%
Package required but not available: ‘microbiome’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘MicroSEC-Ex.R’ failed
The error most likely occurred in:

> ### Name: fun_load_genome
> ### Title: Genome loading function.
> ### Aliases: fun_load_genome
> 
> ### ** Examples
> 
> fun_load_genome("Human")
Error: Install BSgenome.Hsapiens.UCSC.hg38 package.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘my-vignette.Rmd’ using rmarkdown

Quitting from lines 125-195 [analysis] (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
there is no package called 'BSgenome.Hsapiens.UCSC.hg38'
--- failed re-building ‘my-vignette.Rmd’

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

Execution halted
Package required but not available: ‘doMPI’

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

Packages suggested but not available for checking:
  'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene',
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'org.Hs.eg.db',
  'BSgenome.Hsapiens.UCSC.hg19', 'chromVAR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘multipol.Rnw’ using Sweave
Loading required package: multipol
Loading required package: abind

Attaching package: ‘multipol’

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

    deriv

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

    single

Loading required package: polynom
Error: processing vignette 'multipol.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'multipol.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘multipol.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘cias.Rnw’ using Sweave

Attaching package: ‘multivator’

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

    levels, rbind

--- finished re-building ‘cias.Rnw’

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

Attaching package: 'multivator'

The following objects are masked from 'package:base':

    levels, rbind

Error: processing vignette 'multivator.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'multivator.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'multivator.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/nmixgof.Rcheck/00install.out’ for details.
checkRd: (-1) nplr.Rd:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:52-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:56-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:82: Lost braces in \itemize; meant \describe ?
Packages required but not available:
  'org.Hs.eg.db', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'TCGAbiolinks'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/pbdMPI.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘tutorial.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.5/pcSteiner.Rcheck/vign_test/pcSteiner/vignettes/tutorial.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See tutorial.log for more info.
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/prqlr.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘ragtop_convertibles_in_r.Rmd’ using rmarkdown

Quitting from lines 425-461 [twitter_cb_via_BondValuation] (ragtop_convertibles_in_r.Rmd)
Error: processing vignette 'ragtop_convertibles_in_r.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘ragtop_convertibles_in_r.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘realTimeloads-Ex.R’ failed
The error most likely occurred in:

> ### Name: impute_data
> ### Title: Returns x with gaps imputed using ARIMA and Decision Trees,
> ###   optional uncertainty estimation using Monte Carlo resampling
> ### Aliases: impute_data
> 
> ### ** Examples
> 
> # Impute non-tidal data
> time <- realTimeloads::ExampleData$Sediment_Samples$time
> xo <- realTimeloads::ExampleData$Sediment_Samples$SSCxs_mg_per_liter
> Q <- realTimeloads::ExampleData$Discharge$Discharge_m_cubed_per_s
> idata <- sample(1:length(xo),round(length(xo)*0.5),replace=FALSE)
> x <- rep(NA,length(xo))
> x[idata] <- xo[idata] # simulated samples
> flow_concentrtion_ratio <- imputeTS::na_interpolation(Q/x)
> Xreg <- cbind(Q,flow_concentrtion_ratio)
> Output <- impute_data(time,x,Xreg,MC = 10,ptrain = 0.8)
Error in optim(init[mask], getLike, method = "L-BFGS-B", lower = rep(0,  : 
  L-BFGS-B needs finite values of 'fn'
Calls: impute_data -> <Anonymous> -> <Anonymous> -> optim
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Using_Rgff.Rmd’ using rmarkdown

Quitting from lines 344-349 [unnamed-chunk-23] (Using_Rgff.Rmd)
Error: processing vignette 'Using_Rgff.Rmd' failed with diagnostics:
Package "rtracklayer" is required to convert from GTF to GFF3. Please install it.
--- failed re-building ‘Using_Rgff.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Running examples in ‘RISCA-Ex.R’ failed
The error most likely occurred in:

> ### Name: markov.3states.rsadd
> ### Title: 3-state Relative Survival Markov Model with Additive Risks
> ### Aliases: markov.3states.rsadd
> ### Keywords: Markov
> 
> ### ** Examples
> 
> # import the observed data
> # (X=1 corresponds to initial state with a functioning graft, X=2 to acute rejection episode, 
> # X=3 to return to dialysis, X=4 to death with a functioning graft)
> 
> data(dataDIVAT1)
> 
> # A subgroup analysis to reduce the time needed for this example
> 
> dataDIVAT1$id<-c(1:nrow(dataDIVAT1))
> set.seed(2)
> d3<-dataDIVAT1[dataDIVAT1$id %in% sample(dataDIVAT1$id, 200, replace = FALSE),]
> 
> # Individuals with trajectory 13 and 123 are 
> # censored at the time of transition into state X=3
> 
> d3$trajectory[d3$trajectory==13]<-1
> d3$trajectory[d3$trajectory==123]<-12
> d3$trajectory[d3$trajectory==14]<-13
> d3$trajectory[d3$trajectory==124]<-123
> 
> # import the expected mortality rates
> 
> data(fr.ratetable)
> 
> # 3-state Markov model with additive risks including one explicative variable 
> # (z is the delayed graft function) on all transitions. We only reduced
> # the precision and the number of iteration to save time in this example,
> # prefer the default values.
> 
> markov.3states.rsadd(times1=d3$time1, times2=d3$time2, sequences=d3$trajectory,
+   dist=c("E","E","E"), ini.dist.12=c(8.34),
+   ini.dist.13=c(10.70), ini.dist.23=c(11.10),
+   cov.12=d3$z, init.cov.12=c(0.04), names.12=c("beta12_z"),
+   cov.13=d3$z, init.cov.13=c(1.04), names.13=c("beta1E_z"),
+   cov.23=d3$z, init.cov.23=c(0.29), names.23=c("beta2E_z"),
+   p.age=d3$ageR*365.24, p.sex=d3$sexR,
+   p.year=as.date(paste("01","01",d3$year.tx), order = "mdy"),
+   p.rate.table=fr.ratetable,  conf.int=TRUE,
+   silent=FALSE, precision=0.001)
Error in as.date(paste("01", "01", d3$year.tx), order = "mdy") : 
  could not find function "as.date"
Calls: markov.3states.rsadd
Execution halted
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/RMark.Rcheck/00install.out’ for details.
Warning: Software mark not found in path.
         If you have mark executable, you will need to set MarkPath object to its location (e.g. MarkPath="C:/Users/Jeff Laake/Desktop"

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/RmecabKo.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘rnaCrosslinkOO.Rmd’ using rmarkdown
File rnaCrosslinkProtocol.jpg not found in resource path
Error: processing vignette 'rnaCrosslinkOO.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘rnaCrosslinkOO.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
sh: cmake: command not found
------------------ CMAKE NOT FOUND --------------------

CMake was not found on the PATH. Please install CMake:

 - installr::install.cmake()  (Windows; inside the R console)
 - yum install cmake          (Fedora/CentOS; inside a terminal)
 - apt install cmake          (Debian/Ubuntu; inside a terminal)
 - brew install cmake         (MacOS; inside a terminal with Homebrew)
 - port install cmake         (MacOS; inside a terminal with MacPorts)

Alternatively install CMake from: <https://cmake.org/>

-------------------------------------------------------


It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
sh: cmake: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_Outputfile’,
    ‘R_TempDir’, ‘R_Visible’, ‘R_curErrorBuf’, ‘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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Running examples in ‘RtsEva-Ex.R’ failed
The error most likely occurred in:

> ### Name: tsEstimateAverageSeasonality
> ### Title: Estimate Average Seasonality
> ### Aliases: tsEstimateAverageSeasonality
> 
> ### ** Examples
> 
> timeAndSeries <- ArdecheStMartin
> timeStamps <- ArdecheStMartin[,1]
> series  <- ArdecheStMartin[,2]
> timeWindow <- 30*365  # 30 years
> rs <- tsEvaDetrendTimeSeries(timeStamps, series, timeWindow)
> nRunMn <- rs@nRunMn
> cat("computing trend seasonality ...\n")
computing trend seasonality ...
> seasonalitySeries <- rs@detrendSeries
> result <- tsEstimateAverageSeasonality(timeStamps, seasonalitySeries, timeWindow=rs@nRunMn)
Warning in pracma::interp1(avgTmStamp, monthAvgVec, timeStampsN, method = "spline") :
  Points in argument in 'x' unsorted; will be sorted.
Warning in pracma::interp1(avgTmStamp, monthAvgVex, timeStampsN, method = "spline") :
  Points in argument in 'x' unsorted; will be sorted.
> plot(result$regime, type = "l", xlab = "Day", ylab = "Regime", main = "Estimated Regime")
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'ylim' values
Calls: plot -> plot.default -> localWindow -> plot.window
Execution halted
Packages required but not available: 'GSVAdata', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘Mroz87SelectionTest.R’ [2s/2s]
  Comparing ‘Mroz87SelectionTest.Rout’ to ‘Mroz87SelectionTest.Rout.save’ ... OK
  Running ‘binarySelectionOutcome.R’ [4s/5s]
  Comparing ‘binarySelectionOutcome.Rout’ to ‘binarySelectionOutcome.Rout.save’ ... OK
  Running ‘fail.R’ [1s/1s]
  Comparing ‘fail.Rout’ to ‘fail.Rout.save’ ... OK
  Running ‘heckitIvTest.R’ [1s/1s]
  Comparing ‘heckitIvTest.Rout’ to ‘heckitIvTest.Rout.save’ ... OK
  Running ‘intervalTest.R’ [5s/5s]
  Comparing ‘intervalTest.Rout’ to ‘intervalTest.Rout.save’ ... OK
  Running ‘invMillsRatioTest.R’ [6s/7s]
  Comparing ‘invMillsRatioTest.Rout’ to ‘invMillsRatioTest.Rout.save’ ...60a61
> 
  Running ‘probit.R’ [2s/2s]
  Comparing ‘probit.Rout’ to ‘probit.Rout.save’ ... OK
  Running ‘selection.R’ [6s/6s]
  Comparing ‘selection.Rout’ to ‘selection.Rout.save’ ... OK
Package required but not available: ‘ggmsa’

Package suggested but not available for checking: ‘org.Rn.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘SEI_vignette.Rnw’ using knitr
Error: processing vignette 'SEI_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'SEI_vignette.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SEI_vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘SemiCompRisks.ltx’ using tex
Error: processing vignette 'SemiCompRisks.ltx' failed with diagnostics:
Running 'texi2dvi' on 'SemiCompRisks.ltx' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm8): Font bbm8 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SemiCompRisks.ltx’

SUMMARY: processing the following file failed:
  ‘SemiCompRisks.ltx’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 100-103 [unnamed-chunk-6] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'terra'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘sim.BA.Rmd’ using rmarkdown
File images/dag.png not found in resource path
Error: processing vignette 'sim.BA.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘sim.BA.Rmd’

SUMMARY: processing the following file failed:
  ‘sim.BA.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘abind.R’ [0s/0s]
  Comparing ‘abind.Rout’ to ‘abind.Rout.save’ ... OK
  Running ‘apply.R’ [0s/0s]
  Comparing ‘apply.Rout’ to ‘apply.Rout.save’ ... OK
  Running ‘crossprod.R’ [0s/0s]
  Comparing ‘crossprod.Rout’ to ‘crossprod.Rout.save’ ... OK
  Running ‘dimgets.R’ [0s/0s]
  Running ‘extract.R’ [0s/0s]
  Comparing ‘extract.Rout’ to ‘extract.Rout.save’ ... OK
  Running ‘matrix.R’ [0s/0s]
  Comparing ‘matrix.Rout’ to ‘matrix.Rout.save’ ... OK
  Running ‘matrix_dimnames.R’ [0s/0s]
  Comparing ‘matrix_dimnames.Rout’ to ‘matrix_dimnames.Rout.save’ ... OK
  Running ‘rollup.R’ [0s/0s]
  Comparing ‘rollup.Rout’ to ‘rollup.Rout.save’ ... OK
  Running ‘split.R’ [0s/0s]
  Comparing ‘split.Rout’ to ‘split.Rout.save’ ... OK
  Running ‘ssa_valid.R’ [0s/0s]
  Comparing ‘ssa_valid.Rout’ to ‘ssa_valid.Rout.save’ ... OK
  Running ‘stm.R’ [0s/0s]
  Comparing ‘stm.Rout’ to ‘stm.Rout.save’ ... OK
  Running ‘stm_apply.R’ [0s/0s]
  Comparing ‘stm_apply.Rout’ to ‘stm_apply.Rout.save’ ... OK
  Running ‘stm_rollup.R’ [0s/0s]
  Comparing ‘stm_rollup.Rout’ to ‘stm_rollup.Rout.save’ ...113a114,115
> _row_tsums: reduced 1 (3) zeros
> _row_tsums: 0.000s [0.000s/0.000s]
  Running ‘stm_subassign.R’ [0s/0s]
  Comparing ‘stm_subassign.Rout’ to ‘stm_subassign.Rout.save’ ... OK
  Running ‘stm_ttcrossprod.R’ [0s/0s]
  Comparing ‘stm_ttcrossprod.Rout’ to ‘stm_ttcrossprod.Rout.save’ ... OK
  Running ‘stm_valid.R’ [0s/0s]
  Comparing ‘stm_valid.Rout’ to ‘stm_valid.Rout.save’ ... OK
  Running ‘stm_zeros.R’ [0s/0s]
  Comparing ‘stm_zeros.Rout’ to ‘stm_zeros.Rout.save’ ... OK
  Running ‘subassign.R’ [0s/0s]
  Comparing ‘subassign.Rout’ to ‘subassign.Rout.save’ ... OK
  Running ‘util.R’ [0s/0s]
  Comparing ‘util.Rout’ to ‘util.Rout.save’ ... OK
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/smer.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘smm.Rnw’ using Sweave
Error: processing vignette 'smm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'smm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘smm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Warning in microbenchmark::get_nanotime() :
  less accurate nanosecond times to avoid potential integer overflows

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.
Undocumented S4 methods:
  generic '[' and siglist 'SpectraInTime,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTime,missing,ANY,ANY'
  generic '[' and siglist 'SpectraInTime,missing,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,ANY,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,missing,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/SQLFormatteR.Rcheck/00install.out’ for details.
unable to reach CRAN

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Error(s) in re-building vignettes:
--- re-building ‘stratifyR-vignette.Rmd’ using rmarkdown

Quitting from lines 636-641 [unnamed-chunk-9] (stratifyR-vignette.Rmd)
Error: processing vignette 'stratifyR-vignette.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘stratifyR-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘counting.R’ [0s/0s]
  Comparing ‘counting.Rout’ to ‘counting.Rout.save’ ...26a27,28
> counting ... 9 string(s) using 19 nodes [0.00s]
> writing  ... 16 strings [0.00s]
47a50
> counting ... 9 string(s) using 19 nodes [0.00s]
49a53,54
> counting ... 9 string(s) using 19 nodes [0.00s]
> writing  ... 16 strings [0.00s]
70a76,77
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 2 strings [0.00s]
77a85,86
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 4 strings [0.00s]
86a96,97
> counting ... 2 string(s) using 6 nodes [0.00s]
> writing  ... 5 strings [0.00s]
96a108,109
> counting ... 2 string(s) using 6 nodes [0.00s]
> writing  ... 5 strings [0.00s]
106a120
> counting ... 2 string(s) using 5 nodes [0.00s]
108a123,124
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 2 strings [0.00s]
  Running ‘counting_useBytes.R’ [0s/0s]
  Comparing ‘counting_useBytes.Rout’ to ‘counting_useBytes.Rout.save’ ...32a33,34
> counting ... 10 string(s) using 19 nodes [0.00s]
> writing  ... 19 strings [0.00s]
56a59
> counting ... 10 string(s) using 19 nodes [0.00s]
58a62,63
> counting ... 10 string(s) using 19 nodes [0.00s]
> writing  ... 19 strings [0.00s]
82a88,89
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 2 strings [0.00s]
89a97,98
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 5 strings [0.00s]
99a109,110
> counting ... 2 string(s) using 6 nodes [0.00s]
> writing  ... 6 strings [0.00s]
110a122,123
> counting ... 2 string(s) using 6 nodes [0.00s]
> writing  ... 6 strings [0.00s]
121a135
> counting ... 2 string(s) using 5 nodes [0.00s]
123a138,139
> counting ... 2 string(s) using 5 nodes [0.00s]
> writing  ... 2 strings [0.00s]
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/tergo.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘creating_prompt_wraps.Rmd’ using rmarkdown
--- finished re-building ‘creating_prompt_wraps.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘getting_started.Rmd’ ‘sentiment_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/triptych.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘tsglm.Rnw’ using Sweave
Error: processing vignette 'tsglm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tsglm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'tsglm.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘use_case.Rmd’ using rmarkdown
--- finished re-building ‘use_case.Rmd’

--- re-building ‘weatherOz.Rmd’ using rmarkdown_notangle
--- finished re-building ‘weatherOz.Rmd’

--- re-building ‘weatherOz_for_BOM.Rmd’ using rmarkdown_notangle
--- finished re-building ‘weatherOz_for_BOM.Rmd’

--- re-building ‘weatherOz_for_DPIRD.Rmd’ using rmarkdown_notangle
File vignettes/view_sw_ag_region-1.png not found in resource path
Error: processing vignette 'weatherOz_for_DPIRD.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘weatherOz_for_DPIRD.Rmd’

--- re-building ‘weatherOz_for_SILO.Rmd’ using rmarkdown_notangle
--- finished re-building ‘weatherOz_for_SILO.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘features.Rmd’ using rmarkdown
--- finished re-building ‘features.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Error reading bibliography file references.bib:
(line 56, column 16):
unexpected 't'
Error: processing vignette 'overview.Rmd' failed with diagnostics:
pandoc document conversion failed with error 25
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘Ch-Basics.R’ [1s/2s]
  Comparing ‘Ch-Basics.Rout’ to ‘Ch-Basics.Rout.save’ ... OK
  Running ‘Ch-Intro.R’ [2s/2s]
  Comparing ‘Ch-Intro.Rout’ to ‘Ch-Intro.Rout.save’ ... OK
  Running ‘Ch-LinearRegression.R’ [4s/6s]
  Comparing ‘Ch-LinearRegression.Rout’ to ‘Ch-LinearRegression.Rout.save’ ...46,51c46,51
<  Min.   :   2   Min.   :  20   Min.   : 0.00522  
<  1st Qu.:  52   1st Qu.: 134   1st Qu.: 0.46449  
<  Median : 122   Median : 282   Median : 1.32051  
<  Mean   : 197   Mean   : 418   Mean   : 2.54846  
<  3rd Qu.: 268   3rd Qu.: 541   3rd Qu.: 3.44017  
<  Max.   :1098   Max.   :2120   Max.   :24.45946  
---
>  Min.   :   2   Min.   :  20   Min.   : 0.005  
>  1st Qu.:  52   1st Qu.: 134   1st Qu.: 0.464  
>  Median : 122   Median : 282   Median : 1.321  
>  Mean   : 197   Mean   : 418   Mean   : 2.548  
>  3rd Qu.: 268   3rd Qu.: 541   3rd Qu.: 3.440  
>  Max.   :1098   Max.   :2120   Max.   :24.459  
886c886
< -0.619068 -0.025568  0.000000 -0.000134  0.033201  0.641027 
---
> -0.6191 -0.0256  0.0000 -0.0001  0.0332  0.6410 
  Running ‘Ch-Microeconometrics.R’ [2s/3s]
  Comparing ‘Ch-Microeconometrics.Rout’ to ‘Ch-Microeconometrics.Rout.save’ ... OK
  Running ‘Ch-Programming.R’ [17s/23s]
  Comparing ‘Ch-Programming.Rout’ to ‘Ch-Programming.Rout.save’ ... OK
  Running ‘Ch-TimeSeries.R’ [3s/4s]
  Comparing ‘Ch-TimeSeries.Rout’ to ‘Ch-TimeSeries.Rout.save’ ... OK
  Running ‘Ch-Validation.R’ [59s/83s]
  Comparing ‘Ch-Validation.Rout’ to ‘Ch-Validation.Rout.save’ ... OK
Running examples in ‘agridat-Ex.R’ failed
The error most likely occurred in:

> ### Name: gomez.nitrogen
> ### Title: Soil nitrogen at three times for eight fertilizer treatments
> ### Aliases: gomez.nitrogen
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> library(agridat)
> 
> data(gomez.nitrogen)
> dat <- gomez.nitrogen
> 
> # Note the depletion of nitrogen over time (stage)
> libs(HH)
Installing package into ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/agridat.Rcheck’
(as ‘lib’ is unspecified)
Error in contrib.url(repos, "source") : 
  trying to use CRAN without setting a mirror
Calls: libs -> install.packages -> contrib.url
Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ale_core.R’ ‘calc_ale.R’ ‘calc_ale_ixn.R’ ‘model_bootstrap.R’
    ‘plots.R’ ‘stats.R’ ‘utils.R’ ‘validation.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘add_sites.R’ ‘calc_sun.R’ ‘clean_logs.R’ ‘clean_metadata.R’
    ‘clean_sites.R’ ‘create_patterns.R’ ‘helper.R’ ‘selections.R’
    ‘test_helper.R’ ‘utils.R’ ‘utils_wave.R’ ‘wind_detection_functions.R’
    ‘wt_assign_tasks.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘baf.R’ ‘clean.R’ ‘links.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘dexpfit.R’ ‘expfit.R’ ‘icarfit.R’ ‘logisticfit.R’ ‘plotfittedExp.R’
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 41-44 [unnamed-chunk-2] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'rstanarm'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘BeeBDC_main.Rmd’ using rmarkdown

Quitting from lines 14-63 [libraryChunk, load-packages] (BeeBDC_main.Rmd)
Error: processing vignette 'BeeBDC_main.Rmd' failed with diagnostics:
there is no package called 'bdc'
--- failed re-building ‘BeeBDC_main.Rmd’

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

Quitting from lines 14-63 [libraryChunk, load-packages] (basic_workflow.Rmd)
Error: processing vignette 'basic_workflow.Rmd' failed with diagnostics:
there is no package called 'bdc'
--- failed re-building ‘basic_workflow.Rmd’

SUMMARY: processing the following files failed:
  ‘BeeBDC_main.Rmd’ ‘basic_workflow.Rmd’

Error: Vignette re-building failed.
Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘fitting.R’ ‘fivetrial.R’ ‘mcq.R’ ‘utils.R’
Running ‘dplyr_attrib.R’ [1s/1s]
  Running ‘testthat.R’ [31s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(blocs)
  > 
  > test_check("blocs")
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  ########### TESTING WITH ANES 1996 2016 ###########
  ########### TESTING WITH ANES 2008 2012 ###########
  ########### TESTING WITH ANES 2004 2008 ###########
  ########### TESTING WITH ANES 1992 ###########
  20121952 1956 196020002016 2020########### TESTING WITH ANES 2020 ###################### TESTING WITH ANES 2012 ###################### TESTING WITH ANES 1976 1996 ###########
  [ FAIL 1 | WARN 48 | SKIP 4 | PASS 56 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • empty test (4): 'test-plot.R:1:1', 'test-plot.R:33:1', 'test-plot.R:74:1',
    'test-plot.R:117:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-wtd_table.R:8:5'): equivalent to questionr::wtd.table ──────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'questionr'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-wtd_table.R:8:5
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 48 | SKIP 4 | PASS 56 ]
  Error: Test failures
  Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bnns.R’ ‘measure.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘AddXMLInternal.R’ ‘BrowseSVG.R’ ‘Describe.R’
    ‘MakeAccessibleSVGInternal.R’ ‘RewriteSVG.R’ ‘VIInternals.R’
    ‘VIMethod3_TH.R’ ‘ViewSVG.R’
Running ‘testthat.R’ [25s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > 
  > test_check("btergm")
  Loading required package: btergm
  Registered S3 methods overwritten by 'btergm':
    method    from
    plot.gof  ergm
    print.gof ergm
  Package:  btergm
  Version:  1.10.12
  Date:     2024-03-31
  Authors:  Philip Leifeld (University of Manchester)
            Skyler J. Cranmer (The Ohio State University)
            Bruce A. Desmarais (Pennsylvania State University)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test-btergm.R:82:3', 'test-btergm.R:180:3',
    'test-btergm.R:197:3', 'test-data.R:4:3', 'test-interpret.R:4:3',
    'test-interpret.R:32:3', 'test-interpret.R:59:3', 'test-interpret.R:87:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-btergm.R:73:3'): offset argument in btergm works without composition change ──
  Error in `ergm::ergm.pl(nw, Clist.miss, model, theta.offset = c(rep(FALSE, 
      length(l$rhs.terms) - 1), TRUE), verbose = FALSE, control = control.ergm)`: VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-btergm.R:73:3
   2. │ └─base::withCallingHandlers(...)
   3. └─btergm::btergm(...)
   4.   └─ergm::ergm.pl(...)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'org.Dr.eg.db', 'org.Mm.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [68s/120s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > testthat::test_check("caretEnsemble")
  Loading required package: caretEnsemble
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 612 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-caretList.R:309:3'): caretList supports models that return an array or matrix ──
  Error: Required packages are missing: klaR
  Backtrace:
       ▆
    1. ├─testthat::expect_output(...) at test-caretList.R:309:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─testthat::capture_output_lines(code, print, width = width)
    5. │   │   └─testthat:::eval_with_output(code, print = print, width = width)
    6. │   │     ├─withr::with_output_sink(path, withVisible(code))
    7. │   │     │ └─base::force(code)
    8. │   │     └─base::withVisible(code)
    9. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   10. ├─testthat::expect_warning(...)
   11. │ └─testthat:::quasi_capture(...)
   12. │   ├─testthat (local) .capture(...)
   13. │   │ └─base::withCallingHandlers(...)
   14. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   15. └─caretEnsemble::caretList(X, y, methodList = model_names, tuneLength = 1L)
   16.   └─base::lapply(...)
   17.     └─caretEnsemble (local) FUN(X[[i]], ...)
   18.       ├─base::do.call(caret::train, model_args)
   19.       ├─caret (local) `<fn>`(...)
   20.       └─caret:::train.default(...)
   21.         └─caret::checkInstall(models$library)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 612 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘caret.Rmd’ using rmarkdown

Quitting from lines 11-41 [loadLibs] (caret.Rmd)
Error: processing vignette 'caret.Rmd' failed with diagnostics:
there is no package called 'klaR'
--- failed re-building ‘caret.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘check_hint.R’ ‘check_hints.R’ ‘check_question.R’ ‘insert_audio.R’
Packages required but not available: 'fmcsR', 'ChemmineR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: skipping ‘CIARA.Rmd’ due to unavailable dependencies: 'Seurat'
Running ‘exprSet-example.R’ [4s/5s]
  Comparing ‘exprSet-example.Rout’ to ‘exprSet-example.Rout.save’ ... OK
  Running ‘test00-color.R’ [0s/1s]
  Comparing ‘test00-color.Rout’ to ‘test00-color.Rout.save’ ... OK
  Running ‘test01-distance.R’ [0s/1s]
  Comparing ‘test01-distance.Rout’ to ‘test01-distance.Rout.save’ ... OK
  Running ‘test02-cluster.R’ [1s/1s]
  Comparing ‘test02-cluster.Rout’ to ‘test02-cluster.Rout.save’ ...28c28
< 3.674e-05 6.434e-02 3.529e-01 2.976e-01 5.154e-01 6.698e-01 
---
> 0.0000367 0.0643374 0.3528907 0.2975618 0.5153581 0.6697706 
  Running ‘test02.1-just.R’ [0s/0s]
  Comparing ‘test02.1-just.Rout’ to ‘test02.1-just.Rout.save’ ... OK
  Running ‘test03-boot.R’ [1s/2s]
  Comparing ‘test03-boot.Rout’ to ‘test03-boot.Rout.save’ ... OK
  Running ‘test04-perturb.R’ [1s/2s]
  Comparing ‘test04-perturb.Rout’ to ‘test04-perturb.Rout.save’ ... OK
  Running ‘test04.1-gpca.R’ [0s/0s]
  Comparing ‘test04.1-gpca.Rout’ to ‘test04.1-gpca.Rout.save’ ... OK
  Running ‘test05-spca.R’ [0s/0s]
  Comparing ‘test05-spca.Rout’ to ‘test05-spca.Rout.save’ ... OK
  Running ‘test06-mosaic.R’ [1s/1s]
  Comparing ‘test06-mosaic.Rout’ to ‘test06-mosaic.Rout.save’ ... OK
  Running ‘test07-pcanova.R’ [0s/1s]
  Comparing ‘test07-pcanova.Rout’ to ‘test07-pcanova.Rout.save’ ... OK
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘calc_anchor.R’ ‘calc_cutoff.R’ ‘calc_percentage.R’ ‘calc_rci.R’
    ‘calc_recovered.R’ ‘create_summary_table.R’ ‘cs_anchor.R’
    ‘cs_combined.R’ ‘cs_distribution.R’ ‘cs_get_augmented_data.R’
    ‘cs_get_cutoff.R’ ‘cs_get_cutoff_descriptives.R’ ‘cs_get_n.R’
    ‘cs_get_reliability.R’ ‘cs_percentage.R’ ‘cs_statistical.R’
    ‘package-utils.R’ ‘plot.R’ ‘prep_data.R’
Running ‘test01-Simplex.R’ [1s/1s]
  Comparing ‘test01-Simplex.Rout’ to ‘test01-Simplex.Rout.save’ ... OK
  Running ‘test02-WV.R’ [1s/1s]
  Comparing ‘test02-WV.Rout’ to ‘test02-WV.Rout.save’ ... OK
  Running ‘test03-simulate.R’ [18s/27s]
  Comparing ‘test03-simulate.Rout’ to ‘test03-simulate.Rout.save’ ...213c213
<  3rd Qu.:14.000   3rd Qu.:265.75   3rd Qu.: 0.0029188   3rd Qu.:0.5005  
---
>  3rd Qu.:14.000   3rd Qu.:265.75   3rd Qu.: 0.0029187   3rd Qu.:0.5005  
  Running ‘test04-algorithm.R’ [44s/67s]
  Comparing ‘test04-algorithm.Rout’ to ‘test04-algorithm.Rout.save’ ...177c177
<  Max.   :2.002   Max.   :0.9989221   Max.   :2747  
---
>  Max.   :2.002   Max.   :0.9989222   Max.   :2747  
238c238
<  Mean   : 7.286   Mean   :184.3   Mean   : 0.03329   Mean   :0.5902  
---
>  Mean   : 7.286   Mean   :184.3   Mean   : 0.03329   Mean   :0.5903  
244c244
<  Median :1.0415   Median :1.0144845   Median :1352  
---
>  Median :1.0415   Median :1.0144844   Median :1352
Error(s) in re-building vignettes:
--- re-building ‘createStreams.Rmd’ using knitr
--- finished re-building ‘createStreams.Rmd’

--- re-building ‘fisher.sim.Rmd’ using knitr
--- finished re-building ‘fisher.sim.Rmd’

--- re-building ‘random_numbers.Rmd’ using knitr

Quitting from lines 63-96 [rnormGpu] (random_numbers.Rmd)
Error: processing vignette 'random_numbers.Rmd' failed with diagnostics:
ViennaCL: FATAL ERROR: CL_INVALID_PROGRAM_EXECUTABLE.
If you think that this is a bug in ViennaCL, please report it at viennacl-support@lists.sourceforge.net and supply at least the following information:
 * Operating System
 * Which OpenCL implementation (AMD, NVIDIA, etc.)
 * ViennaCL version
Many thanks in advance!
--- failed re-building ‘random_numbers.Rmd’

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

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

Package suggested but not available for checking: ‘monocle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘CompareMultipleModels-Ex.R’ failed
The error most likely occurred in:

> ### Name: best_model_finder
> ### Title: Finding the Best Model Using Eight Metrics Values
> ### Aliases: best_model_finder
> 
> ### ** Examples
> 
> set.seed(123) # for reproducibility
> Y <- rnorm(100, 100, 10)
> model_1 <-CEEMDANML::carigaan(Y, ratio = 0.8, n_lag = 4)
Error in optim(init[mask], armafn, method = optim.method, hessian = TRUE,  : 
  non-finite finite-difference value [1]
Calls: <Anonymous> -> arima -> optim
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘conformalbayes.Rmd’ using rmarkdown

Quitting from lines 27-42 [data] (conformalbayes.Rmd)
Error: processing vignette 'conformalbayes.Rmd' failed with diagnostics:
there is no package called 'rstanarm'
--- failed re-building ‘conformalbayes.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘eif.R’ ‘helpers.R’ ‘make_dataset.R’ ‘permutation.R’ ‘phi.R’
    ‘sequential_module.R’ ‘theta.R’
Error(s) in re-building vignettes:
--- re-building ‘V1_dataSDA.Rmd’ using rmarkdown

Quitting from lines 21-29 [setup] (V1_dataSDA.Rmd)
Error: processing vignette 'V1_dataSDA.Rmd' failed with diagnostics:
there is no package called 'RSDA'
--- failed re-building ‘V1_dataSDA.Rmd’

SUMMARY: processing the following file failed:
  ‘V1_dataSDA.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [8s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(discrim)
  Loading required package: parsnip
  > 
  > test_check("discrim")
  [ FAIL 2 | WARN 0 | SKIP 4 | PASS 434 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test-linear-lda.R:112:3', 'test-linear-sparsediscrim.R:199:3',
    'test-naive-Bayes_naivebayes.R:194:3', 'test-quad-qda.R:123:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-naive-Bayes.R:36:1'): (code run outside of `test_that()`) ──────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'klaR'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-naive-Bayes.R:36:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-rda.R:7:1'): (code run outside of `test_that()`) ───────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'klaR'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-rda.R:7:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 4 | PASS 434 ]
  Error: Test failures
  Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘0_R6_utils.R’ ‘0_linters.R’ ‘2_FeatureHandler.R’
    ‘3_feature_store_helpers.R’ ‘DiseasystoreBase.R’
    ‘DiseasystoreEcdcRespiratoryViruses.R’ ‘DiseasystoreGoogleCovid19.R’
    ‘DiseasystoreSimulist.R’ ‘drop_diseasystore.R’
    ‘source_conn_helpers.R’ ‘test_diseasystore.R’ ‘truncate_interlace.R’
Error(s) in re-building vignettes:
--- re-building ‘benchmarks.Rmd’ using rmarkdown
fatal: not a git repository (or any of the parent directories): .git
--- finished re-building ‘benchmarks.Rmd’

--- re-building ‘diseasystore-ecdc-respiratory-viruses.Rmd’ using rmarkdown
--- finished re-building ‘diseasystore-ecdc-respiratory-viruses.Rmd’

--- re-building ‘diseasystore-google-covid-19.Rmd’ using rmarkdown
--- finished re-building ‘diseasystore-google-covid-19.Rmd’

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

--- re-building ‘extending-diseasystore-example.Rmd’ using rmarkdown

Quitting from lines 537-540 [stratifications_positive_sex_age_plot] (extending-diseasystore-example.Rmd)
Error: processing vignette 'extending-diseasystore-example.Rmd' failed with diagnostics:
Faceting variables must have at least one value.
--- failed re-building ‘extending-diseasystore-example.Rmd’

--- re-building ‘extending-diseasystore.Rmd’ using rmarkdown
--- finished re-building ‘extending-diseasystore.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘dobin.Rmd’ using rmarkdown

Quitting from lines 22-34 [load2] (dobin.Rmd)
Error: processing vignette 'dobin.Rmd' failed with diagnostics:
Package OutliersO3 is needed for the vignette. Please install it.
--- failed re-building ‘dobin.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘doolkit-Ex.R’ failed
The error most likely occurred in:

> ### Name: dkcrop
> ### Title: crop a mesh
> ### Aliases: dkcrop
> 
> ### ** Examples
> 
> #Crop above a certain threshold:
> mythreshold <- quantile(elev(dkmodel$basin), 0.5)
> mypolynetwork <- poly.network(dkmodel$basin, elev(dkmodel$basin),
+ lwr.limit = mythreshold)
> mynewmesh <- dkcrop(dkmodel$basin, mypolynetwork)
> dkmap(mynewmesh, elev(mynewmesh))
> 
> #Crop the sharpest dental elements:
> sharpmesh <- dkcrop(dkmodel$basin, poly.network(dkmodel$basin,
+ Rvcg::vcgCurve(dkmodel$basin)$meanitmax,
+ lwr.limit = quantile(Rvcg::vcgCurve(dkmodel$basin)$meanitmax, 0.8),
+ min.size = 50))
> dkmap(sharpmesh, arc(sharpmesh), col = "arc", col.levels = 20,
+ min.range = -20, max.range = 20)
> #Map of the sharpest elements' elevation, slope and orientation;
> dkmap(sharpmesh, elev(sharpmesh), col = "elev")
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘dwplot.R’ ‘relabel_predictors.R’
Package vignettes without corresponding tangle output:
  ‘CombiningDratAndTravis.md’
  ‘DratFAQ.md’
  ‘DratForPackageAuthors.md’
  ‘DratForPackageUsers.md’
  ‘DratStepByStep.md’
  ‘WhyDrat.md’
Packages required but not available:
  'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Hsapiens.UCSC.hg38.knownGene'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘dct_check_col_names.R’ ‘dct_check_mapping.R’
    ‘dct_check_mapping_strict.R’ ‘dct_check_sci_name.R’
    ‘dct_check_status_diff.R’ ‘dct_check_tax_status.R’
    ‘dct_check_taxon_id.R’ ‘dct_modify_row.R’ ‘dct_validate.R’ ‘utils.R’
Error(s) in re-building vignettes:
--- re-building ‘eclust.Rmd’ using rmarkdown

Quitting from lines 142-168 [unnamed-chunk-6] (eclust.Rmd)
Error: processing vignette 'eclust.Rmd' failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building ‘eclust.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ggm.R’ ‘lspro.R’ ‘muse.R’ ‘wfdb-annotation.R’ ‘wfdb-io.R’
    ‘wfdb-structures.R’ ‘zzz.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘binary_method_functions.R’ ‘continuous_method_functions.R’
    ‘ordinal_method_functions.R’ ‘utility_functions.R’
Running examples in ‘EmiStatR-Ex.R’ failed
The error most likely occurred in:

> ### Name: CInp2TS
> ### Title: Function to convert Constant Input to Time Series
> ### Aliases: CInp2TS
> ### Keywords: CInp2TS
> 
> ### ** Examples
> 
> library(EmiStatR)
> library(zoo)

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

> 
> data("Esch_Sure2010")
> data("qs_factor")
> 
> cinp            <- 150 # water consumption [m3/h]
> prec            <- Esch_Sure2010[1:1000,] # selecting just the first 1,000 rows
> 
> cinp.daily.file <- qs_factor
> cinp.weekly     <- list(mon=1, tue=.83, wed=.83, thu=.83, fri=1, sat=1.25, sun=1.25)  
> # factors average to 1
> cinp.seasonal   <- list(jan=.79, feb=.79, mar=1.15, apr=1.15, may=1.15, jun=1.15,
+                         jul=1.15, aug=1.15, sep=1.15, oct=1.15, nov=.79, dec=.79) 
> # factors average to 1
> ts1 <- CInp2TS(cinp, prec, cinp.daily.file, cinp.weekly, cinp.seasonal)
Error in `[.xts`(cinp.ts.deltap, 1:nrow(P1), ) : subscript out of bounds
Calls: CInp2TS -> [ -> [.xts
Execution halted
Running ‘EpiILM.network.R’ [4s/8s]
  Comparing ‘EpiILM.network.Rout’ to ‘EpiILM.network.Rout.save’ ...9817c9817
<  [ reached 'max' / getOption("max.print") -- omitted 301 rows ]
---
>  [ reached getOption("max.print") -- omitted 301 rows ]
19695c19695
<  [ reached 'max' / getOption("max.print") -- omitted 301 rows ]
---
>  [ reached getOption("max.print") -- omitted 301 rows ]
  Running ‘EpiILM.spatial.R’ [2s/5s]
  Comparing ‘EpiILM.spatial.Rout’ to ‘EpiILM.spatial.Rout.save’ ... OK
Packages unavailable to check Rd xrefs: ‘FactoMineR’, ‘GDAtools’
Unknown package ‘quanteda.textmodels’ in Rd xrefs
Running examples in ‘FACT-Ex.R’ failed
The error most likely occurred in:

> ### Name: ClustPredictor
> ### Title: Clustering Predictor Object
> ### Aliases: ClustPredictor
> 
> ### ** Examples
> 
> require(factoextra)
Loading required package: factoextra
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘factoextra’
> require(FuzzyDBScan)
Loading required package: FuzzyDBScan
> multishapes <- as.data.frame(multishapes[, 1:2])
Error: object 'multishapes' not found
Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FACT)
  > 
  > test_check("FACT")
  Error in `FUN()`:
  ! In path: "/Volumes/Builds/packages/big-sur-x86_64/results/4.5/FACT.Rcheck/tests/testthat/setup.R"
  Caused by error in `library()`:
  ! there is no package called 'factoextra'
  Backtrace:
       ▆
    1. ├─testthat::test_check("FACT")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library(factoextra) at tests/testthat/setup.R:3:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/fcl.Rcheck/00install.out’ for details.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘caps-diagnostic.R’ ‘caps-plot.R’ ‘compare-caps.R’ ‘fdadbscan.R’
    ‘fdadist.R’ ‘fdahclust.R’ ‘fdakmeans.R’ ‘utils.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘NHD_FUNCTIONS.R’ ‘NLCD_FUNCTIONS.R’ ‘UTILITY_FUNCTIONS.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘00.helpers.R’ ‘01.firm_query.R’ ‘01.firm_register.R’ ‘02.FOandFM.R’
    ‘03.people.R’ ‘04.FF_both.R’ ‘04.FF_either.R’ ‘04.FF_methods.R’
    ‘05.1.graph_methods.R’ ‘05.1.network_methods.R’ ‘05.network&graph.R’
    ‘06.1.Fielder.R’
Package required but not available: ‘RGN’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘Overview.Rmd’ using rmarkdown

Quitting from lines 25-33 [unnamed-chunk-1] (Overview.Rmd)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
there is no package called 'FactoMineR'
--- failed re-building ‘Overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘FuzzyDBScan-Ex.R’ failed
The error most likely occurred in:

> ### Name: Fuzzy_DBScan
> ### Title: Fuzzy DBScan
> ### Aliases: Fuzzy_DBScan FuzzyDBScan
> 
> ### ** Examples
> 
> # load factoextra for data and ggplot for plotting
> library(factoextra)
Error in library(factoextra) : there is no package called ‘factoextra’
Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(FuzzyDBScan)
  > 
  > test_check("FuzzyDBScan")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_initialize.R:23:3'): Output ────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'factoextra'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_initialize.R:23:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘gaawr2.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'EnsDb.Hsapiens.v75''
running: bash  -c "export message=\"Hello, world!\"
echo \"print('\$message')\" > hello.R
R CMD BATCH hello.R
R --no-save -q < hello.R
R --no-save -q <<END
message <- Sys.getenv(\"message\"); print(message)
source(\"hello.R\")
END
echo \${message} | \\
Rscript -e '
message <- scan(\"stdin\", what=\"\", sep=\"\\n\", quiet=TRUE);
write.table(message, col.names=FALSE, row.names=FALSE,
            quote=FALSE)
' | \\
cat
rm hello.*"

Quitting from lines 408-413 [ensdb] (gaawr2.Rmd)
Error: processing vignette 'gaawr2.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'metadata': object 'EnsDb.Hsapiens.v75' not found
--- failed re-building ‘gaawr2.Rmd’

--- re-building ‘web.Rmd’ using rmarkdown
[WARNING] Citeproc: citation tsv not found
--- finished re-building ‘web.Rmd’

SUMMARY: processing the following file failed:
  ‘gaawr2.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘bsch.R’ [1s/2s]
  Comparing ‘bsch.Rout’ to ‘bsch.Rout.save’ ...3a4
> 
  Running ‘penInf.R’ [4s/5s]
  Comparing ‘penInf.Rout’ to ‘penInf.Rout.save’ ...5a6
> 
  Running ‘sh9.2012.R’ [2s/3s]
  Comparing ‘sh9.2012.Rout’ to ‘sh9.2012.Rout.save’ ...3a4
> 
  Running ‘shPUR.R’ [2s/4s]
  Comparing ‘shPUR.Rout’ to ‘shPUR.Rout.save’ ...3a4
> 
  Running ‘test1Fast.R’ [3s/5s]
  Comparing ‘test1Fast.Rout’ to ‘test1Fast.Rout.save’ ...3a4
> 
  Running ‘test1QE.R’ [1s/1s]
  Comparing ‘test1QE.Rout’ to ‘test1QE.Rout.save’ ...3a4
> 
  Running ‘test2Fast.R’ [3s/5s]
  Comparing ‘test2Fast.Rout’ to ‘test2Fast.Rout.save’ ...3a4
> 
  Running ‘test2QE.R’ [1s/1s]
  Comparing ‘test2QE.Rout’ to ‘test2QE.Rout.save’ ...3a4
> 
  Running ‘test3Fast.R’ [4s/5s]
  Comparing ‘test3Fast.Rout’ to ‘test3Fast.Rout.save’ ...3a4
> 
  Running ‘test3QE.R’ [1s/2s]
  Comparing ‘test3QE.Rout’ to ‘test3QE.Rout.save’ ...3a4
> 
  Running ‘test5Fast.R’ [4s/4s]
  Comparing ‘test5Fast.Rout’ to ‘test5Fast.Rout.save’ ...3a4
> 
  Running ‘test7Fast.R’ [4s/5s]
  Comparing ‘test7Fast.Rout’ to ‘test7Fast.Rout.save’ ...3a4
> 
  Running ‘testMyFam.R’ [1s/1s]
  Comparing ‘testMyFam.Rout’ to ‘testMyFam.Rout.save’ ...3a4
>
Error(s) in re-building vignettes:
--- re-building ‘glmtree.Rmd’ using rmarkdown

Quitting from lines 31-51 [segmentation_pca1] (glmtree.Rmd)
Error: processing vignette 'glmtree.Rmd' failed with diagnostics:
there is no package called 'FactoMineR'
--- failed re-building ‘glmtree.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘gluvarpro-Ex.R’ failed
The error most likely occurred in:

> ### Name: preprocessgvp
> ### Title: preprocessing raw data from continuous glucose monitoring
> ### Aliases: preprocessgvp
> 
> ### ** Examples
> 
> data("datagvp4")
> preprocessgvp(datagvp4)
Error in preprocessgvp(datagvp4) : 
  Variable date and time must have yyyy/mm/dd and hh:mm:ss format.
Execution halted
Running ‘testthat.R’ [6s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(GPfit)
  > 
  > test_check("GPfit", reporter = "summary")
  GP_deviance: 
  GP_deviance: ...
  GPfit: 
  GP_fit creates GP model: ..............
  corr_matrix: 
  corr_matrix: ......
  predict.GP: 
  GP model for predictions: ......1..2......
  
  ══ Failed ══════════════════════════════════════════════════════════════════════
  ── 1. Failure ('test_predict.GP.R:64:9'): check predict.GP ─────────────────────
  smse2 >= 0 & smse2 < 30 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── 2. Failure ('test_predict.GP.R:81:9'): check predict.GP ─────────────────────
  sum(gpp2$complete_data[, 5] - ms2 < 1e-05) >= 10 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘MultiSpat.Rmd’ using rmarkdown

Quitting from lines 41-47 [unnamed-chunk-1] (MultiSpat.Rmd)
Error: processing vignette 'MultiSpat.Rmd' failed with diagnostics:
there is no package called 'adespatial'
--- failed re-building ‘MultiSpat.Rmd’

--- re-building ‘guerry-multivariate.Rmd’ using rmarkdown
--- finished re-building ‘guerry-multivariate.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘hetGP_vignette.Rnw’ using knitr


Quitting from lines 1122-1124 [sirfit] (hetGP_vignette.Rnw)
Execution halted

* checking PDF version of manual ...* using check arguments '--no-clean-on-error '
Error(s) in re-building vignettes:
--- re-building ‘germinar.Rmd’ using rmarkdown

Quitting from lines 14-16 [setup] (germinar.Rmd)
Error: processing vignette 'germinar.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building ‘germinar.Rmd’

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

Quitting from lines 21-23 [setup] (huito.Rmd)
Error: processing vignette 'huito.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building ‘huito.Rmd’

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

Quitting from lines 14-15 [setup] (labels.Rmd)
Error: processing vignette 'labels.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building ‘labels.Rmd’

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

Quitting from lines 14-15 [setup] (stickers.Rmd)
Error: processing vignette 'stickers.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building ‘stickers.Rmd’

SUMMARY: processing the following files failed:
  ‘germinar.Rmd’ ‘huito.Rmd’ ‘labels.Rmd’ ‘stickers.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘allexercises.R’ [3s/4s]
  Comparing ‘allexercises.Rout’ to ‘allexercises.Rout.save’ ... OK
  Running ‘allscripts.R’ [3s/3s]
  Comparing ‘allscripts.Rout’ to ‘allscripts.Rout.save’ ...1821,1824c1821,1822
<     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
<    0.000    8.000   28.000  225.723  268.500 1836.000 
< attr(,"NAs")
< [1] 338
---
>   Length    Class     Mode 
>      829 difftime  numeric 
2846c2844
<  Mean   :1.373   Mean   :164325   Mean   :23.00  
---
>  Mean   :1.373   Mean   :164326   Mean   :23.00  
2855c2853
<           Mean   :164325   Mean   :23.00  
---
>           Mean   :164326   Mean   :23.00
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘checks.R’ ‘dplyr-joins.R’ ‘freq_table.R’ ‘info_display.R’ ‘is_id.R’
    ‘joyn-merge.R’ ‘joyn_workhorse.R’ ‘merge-data.table.R’
    ‘possible_ids.R’ ‘update_na_vals.R’ ‘utils.R’ ‘zzz.R’
Error(s) in re-building vignettes:
--- re-building ‘labelled.Rmd’ using rmarkdown

Quitting from lines 537-541 [unnamed-chunk-44] (labelled.Rmd)
Error: processing vignette 'labelled.Rmd' failed with diagnostics:
there is no package called 'questionr'
--- failed re-building ‘labelled.Rmd’

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

Quitting from lines 31-33 [unnamed-chunk-3] (look_for.Rmd)
Error: processing vignette 'look_for.Rmd' failed with diagnostics:
there is no package called 'questionr'
--- failed re-building ‘look_for.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘labelled.Rmd’ ‘look_for.Rmd’

Error: Vignette re-building failed.
Execution halted
Package vignettes without corresponding tangle output:
  ‘littler-examples.md’
  ‘littler-faq.md’
Error(s) in re-building vignettes:
--- re-building ‘analysis_workflow.Rmd’ using rmarkdown

Quitting from lines 19-28 [setup] (analysis_workflow.Rmd)
Error: processing vignette 'analysis_workflow.Rmd' failed with diagnostics:
there is no package called 'FactoMineR'
--- failed re-building ‘analysis_workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘MARVEL-Ex.R’ failed
The error most likely occurred in:

> ### Name: RunPCA.Exp
> ### Title: Principle component analysis for gene Data
> ### Aliases: RunPCA.Exp
> 
> ### ** Examples
> 
> marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))
> 
> # Define genes for analysis
> gene_ids <- marvel.demo$Exp$gene_id
> 
> # PCA
> marvel.demo <- RunPCA.Exp(MarvelObject=marvel.demo,
+                           sample.ids=marvel.demo$SplicePheno$sample.id,
+                           cell.group.column="cell.type",
+                           cell.group.order=c("iPSC", "Endoderm"),
+                           min.cells=5,
+                           features=gene_ids,
+                           point.size=2
+                           )
Error in loadNamespace(x) : there is no package called ‘FactoMineR’
Calls: RunPCA.Exp ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘MARVEL.Rmd’ using rmarkdown

Quitting from lines 60-71 [unnamed-chunk-4] (MARVEL.Rmd)
Error: processing vignette 'MARVEL.Rmd' failed with diagnostics:
there is no package called 'FactoMineR'
--- failed re-building ‘MARVEL.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘latexMatrix.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘col_to_lst_col.R’ ‘lst_col_na_to_empty.R’
    ‘read_gene_model_coord_rpt.R’ ‘read_gtgup_rpt.R’
    ‘read_mgi_biotype_conflict_rpt.R’ ‘read_mgi_inter_pro_domains_rpt.R’
    ‘read_mrk_coord_rpt.R’ ‘read_mrk_ensembl_rpt.R’
    ‘read_mrk_genetrap_rpt.R’ ‘read_mrk_list1_rpt.R’
    ‘read_mrk_list2_rpt.R’ ‘read_mrk_sequence_rpt.R’
    ‘read_mrk_swissprot_rpt.R’ ‘read_mrk_swissprot_tr_embl_rpt.R’
    ‘read_prb_primerseq_rpt.R’ ‘report_source.R’ ‘reports.R’
    ‘variable_types.R’
Package required but not available: ‘InteractiveComplexHeatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘internals.R’ ‘s3methods.R’
Packages required but not available: 'plyranges', 'ggbio'

Packages suggested but not available for checking:
  'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene',
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'BSgenome.Hsapiens.UCSC.hg19',
  'chromVAR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bigram.R’ ‘clean_up.R’ ‘make_group.R’ ‘moranajp.R’ ‘utils_id.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘get_individual_algebra_results.R’ ‘mxsem_group_by.R’
Packages required but not available:
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'TCGAbiolinks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘PartialNetwork_vignette.Rmd’ using rmarkdown

Quitting from lines 39-72 [IV1] (PartialNetwork_vignette.Rmd)
Error: processing vignette 'PartialNetwork_vignette.Rmd' failed with diagnostics:
there is no package called 'CDatanet'
--- failed re-building ‘PartialNetwork_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/PerMallows.Rcheck/00install.out’ for details.
Note: skipping ‘fisheries.Rmd’ due to unavailable dependencies:
  'phylosignal'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘pipeline.R’ ‘pkgname.R’ ‘utils.R’
To use viewer = 'mapview', first install the required packages:mapview, mapedit

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Error(s) in re-building vignettes:
--- re-building ‘Import_data.Rmd’ using rmarkdown
--- finished re-building ‘Import_data.Rmd’

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

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

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

Quitting from lines 35-39 [requirement] (PLNPCA.Rmd)
Error: processing vignette 'PLNPCA.Rmd' failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building ‘PLNPCA.Rmd’

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

Quitting from lines 38-40 [requirement] (PLNmixture.Rmd)
Error: processing vignette 'PLNmixture.Rmd' failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building ‘PLNmixture.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘PLNPCA.Rmd’ ‘PLNmixture.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘fcm.Rmd’ using rmarkdown

Quitting from lines 45-48 [unnamed-chunk-3] (fcm.Rmd)
Error: processing vignette 'fcm.Rmd' failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building ‘fcm.Rmd’

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

Quitting from lines 46-49 [unnamed-chunk-3] (upfc.Rmd)
Error: processing vignette 'upfc.Rmd' failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building ‘upfc.Rmd’

SUMMARY: processing the following files failed:
  ‘fcm.Rmd’ ‘upfc.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘test01-utility.R’ [1s/1s]
  Comparing ‘test01-utility.Rout’ to ‘test01-utility.Rout.save’ ... OK
  Running ‘test03-channel-type.R’ [0s/0s]
  Comparing ‘test03-channel-type.Rout’ to ‘test03-channel-type.Rout.save’ ... OK
  Running ‘test04-channel.R’ [1s/1s]
  Comparing ‘test04-channel.Rout’ to ‘test04-channel.Rout.save’ ...42c42
<    0.2436  280.0141  675.7335  987.6435 1355.5114 9630.5918 
---
>    0.244  280.014  675.734  987.643 1355.511 9630.592 
  Running ‘test05-processor.R’ [1s/1s]
  Comparing ‘test05-processor.Rout’ to ‘test05-processor.Rout.save’ ... OK
  Running ‘test06-pipeline.R’ [1s/1s]
  Comparing ‘test06-pipeline.Rout’ to ‘test06-pipeline.Rout.save’ ... OK
  Running ‘test07-complete-channel.R’ [1s/1s]
  Comparing ‘test07-complete-channel.Rout’ to ‘test07-complete-channel.Rout.save’ ...22,27c22,27
<  Min.   :6.560e-02   Min.   :33.61   Min.   :    0.0  
<  1st Qu.:2.855e+02   1st Qu.:55.95   1st Qu.:  225.7  
<  Median :6.874e+02   Median :60.01   Median :  626.7  
<  Mean   :1.003e+03   Mean   :59.99   Mean   :  944.6  
<  3rd Qu.:1.396e+03   3rd Qu.:64.07   3rd Qu.: 1336.5  
<  Max.   :1.178e+04   Max.   :85.24   Max.   :11718.9  
---
>  Min.   :    0.066   Min.   :33.61   Min.   :    0.0  
>  1st Qu.:  285.474   1st Qu.:55.95   1st Qu.:  225.7  
>  Median :  687.351   Median :60.01   Median :  626.7  
>  Mean   : 1002.718   Mean   :59.99   Mean   :  944.6  
>  3rd Qu.: 1395.736   3rd Qu.:64.07   3rd Qu.: 1336.5  
>  Max.   :11776.787   Max.   :85.24   Max.   :11718.9
Running ‘basic.R’ [22s/34s]
  Comparing ‘basic.Rout’ to ‘basic.Rout.save’ ...294,307c294,307
<       YYYY         MM          DD      timestamp           Qobs   deseaonalized
<  Min.   :0   Min.   :0   Min.   :0   Min.   :0 secs   Min.   :0   Min.   :0    
<  1st Qu.:0   1st Qu.:0   1st Qu.:0   1st Qu.:0 secs   1st Qu.:0   1st Qu.:0    
<  Median :0   Median :0   Median :0   Median :0 secs   Median :0   Median :0    
<  Mean   :0   Mean   :0   Mean   :0   Mean   :0 secs   Mean   :0   Mean   :0    
<  3rd Qu.:0   3rd Qu.:0   3rd Qu.:0   3rd Qu.:0 secs   3rd Qu.:0   3rd Qu.:0    
<  Max.   :0   Max.   :0   Max.   :0   Max.   :0 secs   Max.   :0   Max.   :0    
<        r1   
<  Min.   :0  
<  1st Qu.:0  
<  Median :0  
<  Mean   :0  
<  3rd Qu.:0  
<  Max.   :0  
---
>       YYYY         MM          DD     timestamp             Qobs  
>  Min.   :0   Min.   :0   Min.   :0   Length:1825       Min.   :0  
>  1st Qu.:0   1st Qu.:0   1st Qu.:0   Class :difftime   1st Qu.:0  
>  Median :0   Median :0   Median :0   Mode  :numeric    Median :0  
>  Mean   :0   Mean   :0   Mean   :0                     Mean   :0  
>  3rd Qu.:0   3rd Qu.:0   3rd Qu.:0                     3rd Qu.:0  
>  Max.   :0   Max.   :0   Max.   :0                     Max.   :0  
>  deseaonalized       r1   
>  Min.   :0     Min.   :0  
>  1st Qu.:0     1st Qu.:0  
>  Median :0     Median :0  
>  Mean   :0     Mean   :0  
>  3rd Qu.:0     3rd Qu.:0  
>  Max.   :0     Max.   :0
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/Rblpapi.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/Rcplex.Rcheck/00install.out’ for details.
Package vignette without corresponding tangle output:
  ‘binnmuAfterR340.md’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/RcppMeCab.Rcheck/00install.out’ for details.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘00_console.R’ ‘01_checks.R’ ‘02_helpers.R’ ‘exports.R’
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg38’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [68s/62s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Rforestry)
  ## 
  ##  Rforestry (Version 0.10.0, Build Date: R 4.5.0; x86_64-apple-darwin20; 2025-01-31 02:40:22 UTC; unix)
  ##  See https://github.com/forestry-labs for additional documentation.
  ##  Please cite software as:
  ##    Soren R. Kunzel, Theo F. Saarinen, Edward W. Liu, Jasjeet S. Sekhon. 2019.
  ##    ''Linear Aggregation in Tree-based Estimators.'' arXiv preprint 
  ##    arXiv:1906.06463. https://arxiv.org/abs/1906.06463 
  ##
  > 
  > test_check("Rforestry")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1422 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-forestry.R:48:3'): Tests that random forest is working correctly ──
  `rf <- forestry(x = iris[, -1], y = iris[, 1], seed = seed_i)` threw an error with unexpected message.
  Expected match: "A parameter passed is not assigned: object 'seed_i' not found\n"
  Actual message: "A parameter passed is not assigned: Error in eval(code, test_env): object 'seed_i' not found\n"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test-forestry.R:48:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─Rforestry::forestry(x = iris[, -1], y = iris[, 1], seed = seed_i)
    7.   └─base::tryCatch(...)
    8.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10.         └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1422 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/RGN.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/RMark.Rcheck/00install.out’ for details.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘replace_doi.R’
Running examples in ‘rmdformats-Ex.R’ failed
The error most likely occurred in:

> ### Name: pilltabs
> ### Title: Given a cross-table, outputs HTML code to display several views
> ###   of with a tabbed interface
> ### Aliases: pilltabs
> 
> ### ** Examples
> 
> 
> data(airquality)
> tab <- table(airquality$Month, airquality$Ozone > 25)
> pilltabs(tab)
Error: the questionr package is needed for the pilltabs() function to work. Please install it.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/RmecabKo.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/Rmpi.Rcheck/00install.out’ for details.
Note: skipping ‘rnrfa-vignette.Rmd’ due to unavailable dependencies: 'DT'
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/ROracle.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_Outputfile’,
    ‘R_TempDir’, ‘R_Visible’, ‘R_curErrorBuf’, ‘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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Invalid citation information in ‘inst/CITATION’:
  Error in if (any(ind <- (names(comment) == "ROR"))) {    ids <- comment[ind]    bad <- which(!tools:::.ROR_ID_is_valid(ids))    if (length(bad)) {        warning(sprintf(ngettext(length(bad), "Invalid ROR ID: %s.",             "Invalid ROR IDs: %s."), paste(sQuote(ids[bad]),             collapse = ", ")), domain = NA)    }}: missing value where TRUE/FALSE needed
Package required but not available: ‘GSVAdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘Mroz87SelectionTest.R’ [3s/4s]
  Comparing ‘Mroz87SelectionTest.Rout’ to ‘Mroz87SelectionTest.Rout.save’ ... OK
  Running ‘binarySelectionOutcome.R’ [7s/10s]
  Comparing ‘binarySelectionOutcome.Rout’ to ‘binarySelectionOutcome.Rout.save’ ... OK
  Running ‘fail.R’ [1s/2s]
  Comparing ‘fail.Rout’ to ‘fail.Rout.save’ ... OK
  Running ‘heckitIvTest.R’ [2s/2s]
  Comparing ‘heckitIvTest.Rout’ to ‘heckitIvTest.Rout.save’ ... OK
  Running ‘intervalTest.R’ [10s/13s]
  Comparing ‘intervalTest.Rout’ to ‘intervalTest.Rout.save’ ... OK
  Running ‘invMillsRatioTest.R’ [12s/17s]
  Comparing ‘invMillsRatioTest.Rout’ to ‘invMillsRatioTest.Rout.save’ ...60a61
> 
  Running ‘probit.R’ [2s/3s]
  Comparing ‘probit.Rout’ to ‘probit.Rout.save’ ... OK
  Running ‘selection.R’ [9s/13s]
  Comparing ‘selection.Rout’ to ‘selection.Rout.save’ ... OK
Found the following significant warnings:
  SingleChromosomeVCFIndex.cpp:109:51: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat]
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/seqminer.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.sdk’
Running ‘testthat.R’ [5s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shinystan)
  Loading required package: shiny
  
  This is shinystan version 2.6.0
  
  > 
  > test_check("shinystan")
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 125 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test_creating_sso.R:197:3'
  • {rstanarm} is not installed (5): 'test_creating_sso.R:45:3',
    'test_creating_sso.R:60:3', 'test_creating_sso.R:135:3',
    'test_creating_sso.R:150:3', 'test_creating_sso.R:161:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_misc.R:2:1'): (code run outside of `test_that()`) ──────────────
  <packageNotFoundError/error/condition>
  Error in `library(rstanarm)`: there is no package called 'rstanarm'
  Backtrace:
      ▆
   1. └─base::library(rstanarm) at test_misc.R:2:1
  
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 125 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > shinytest2::test_app()
  Error in loadNamespace(x) : there is no package called 'shinytest2'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Running examples in ‘Sim.DiffProc-Ex.R’ failed
The error most likely occurred in:

> ### Name: rsde1d
> ### Title: Approximate transitional densities and random generation for 1-D
> ###   SDE
> ### Aliases: rsde1d rsde1d.default dsde1d dsde1d.default print.dsde1d
> ###   plot.dsde1d
> ### Keywords: sde ts mts random generators transition density
> 
> ### ** Examples
> 
> 
> ## Example 1:  
> ## dX(t) = (-2*(X(t)<=0)+2*(X(t)>=0)) *dt + 0.5 * dW(t)
> set.seed(1234)
> 
> f <- expression(-2*(x<=0)+2*(x>=0))
> g <- expression(0.5)
> res1 <- snssde1d(drift=f,diffusion=g,M=5000)
> x <- rsde1d(res1, at = 1)
> summary(x)
     Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
-4.075421 -2.064221  0.838452  0.006097  2.067562  3.892380 
> dens1 <-  dsde1d(res1, at = 1)
> dens1

 Density of X(t-t0)|X(t0) = 0 at time t = 1

Data: x (5000 obs.);	Bandwidth 'bw' = 0.348

Error in zapsmall(x[finite], digits = digits + zdigits) : 
  invalid 'digits'
Calls: <Anonymous> ... summary.data.frame -> format -> format.summaryDefault -> zapsmall
Execution halted
Running ‘TEX.r’ [1s/1s]
  Running ‘bridgesde.R’ [4s/8s]
  Running ‘fitsde.R’ [0s/1s]
  Running ‘fptsde.R’ [3s/6s]
  Running ‘rsde.R’ [1s/1s]
Running the tests in ‘tests/rsde.R’ failed.
Complete output:
  > library(Sim.DiffProc)
  Package 'Sim.DiffProc', version 4.9
  browseVignettes('Sim.DiffProc') for more informations.
  > 
  > ## 2-dim SDE
  > set.seed(1234)
  > 
  > # SDE's 2d
  > fx <- expression(3*(2-y),2*x)
  > gx <- expression(1,y)
  > mod2d <- snssde2d(drift=fx,diffusion=gx,x0=c(1,2),M=1000)
  > 
  > # random 
  > r2d <- rsde2d(mod2d,at=0.5)
  > summary(r2d)
         x                 y          
   Min.   :-5.6639   Min.   : 0.4349  
   1st Qu.:-0.3902   1st Qu.: 1.7160  
   Median : 0.5497   Median : 2.4000  
   Mean   : 0.3265   Mean   : 2.7618  
   3rd Qu.: 1.2958   3rd Qu.: 3.3156  
   Max.   : 3.3886   Max.   :12.1161  
  > 
  > # Marginal density 
  > 
  > denM <- dsde2d(mod2d,pdf="M", at=0.5)
  > denM
  
   Marginal density of X(t-t0)|X(t0)=1 at time t = 0.5
  
  Data: x (1000 obs.);	Bandwidth 'bw' = 0.2844
  
  Error in zapsmall(x[finite], digits = digits + zdigits) : 
    invalid 'digits'
  Calls: <Anonymous> ... summary.data.frame -> format -> format.summaryDefault -> zapsmall
  Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/smer.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [0m/14m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(snvecR)
  > 
  > test_check("snvecR")
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 38 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-get_solution.R:22:3', 'test-snvec.R:34:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-get_solution.R:13:3'): get_solution() can load eccentricity solutions ──
  Error in `open.connection(con, "rb")`: cannot open the connection
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-get_solution.R:13:3
   2.   └─rlang::cnd_signal(state$error)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 38 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/spaths.Rcheck/00install.out’ for details.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘addlearn_local.R’
Error(s) in re-building vignettes:
--- re-building ‘classification.Rmd’ using rmarkdown
--- finished re-building ‘classification.Rmd’

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

Quitting from lines 70-73 [clusters] (clustering.Rmd)
Error: processing vignette 'clustering.Rmd' failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building ‘clustering.Rmd’

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘textra.R’
Package vignette without corresponding tangle output:
  ‘motivation.md’
Package vignettes without corresponding tangle output:
  ‘data-ingestion-from-sql.md’
  ‘documentation.md’
  ‘installation-options.md’
  ‘introduction.md’
  ‘tiledb-mariadb-examples.md’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bar_chart_counts.R’ ‘date_to_sy.R’ ‘factorize.R’
    ‘position_diverge.R’ ‘setup_repo.R’ ‘sp_.R’ ‘survey_utils.R’
    ‘tntp_colors.R’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/triptych.Rcheck/00install.out’ for details.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘available_version.R’ ‘inform_load.R’ ‘package_installation_info.R’
    ‘updateme_sources_set.R’
Error(s) in re-building vignettes:
--- re-building ‘wrGraphVignette1.Rmd’ using rmarkdown

Quitting from lines 44-50 [setup] (wrGraphVignette1.Rmd)
Error: processing vignette 'wrGraphVignette1.Rmd' failed with diagnostics:
there is no package called 'FactoMineR'
--- failed re-building ‘wrGraphVignette1.Rmd’

SUMMARY: processing the following file failed:
  ‘wrGraphVignette1.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/zoomerjoin.Rcheck/00install.out’ for details.
Problems with news in 'NEWS.md':
No news entries found.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'acep_token_plot.R' 'acep_token_table.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'acoRn.R' 'clean_input.R' 'create_mock_dataset.R'
    'exclude_duplicates.R' 'find_parents.R' 'identify_duplicates.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'compute_accumulation_metrics.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'factorial_plan.R' 'stats.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'analyze.R' 'estimators.R' 'evaluate_estimator.R'
    'fisher_information.R' 'integrate_over_sample_space.R'
    'mle_distribution.R' 'n2c2_helpers.R' 'plot.R' 'print.R'
    'reference_implementation.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'blocks.R' 'compress.R' 'connect_adf.R' 'demo.R' 'device_create.R'
    'entry_info.R' 'helpers.R' 'move.R' 's3_conn.R' 's3_methods.R'
    'virtual_path.R'
Found the following significant warnings:
  adlift.c:719:15: warning: argument 1 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
See 'd:/Rcompile/CRANpkg/local/4.5/adlift.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'cm_formula.R' 'tag_add.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'report_basic.R' 'report_cum_plots.R' 'report_log_mass.R'
    'report_plots.R' 'set_params_2.R'
Running 'Ch-Basics.R' [2s]
  Comparing 'Ch-Basics.Rout' to 'Ch-Basics.Rout.save' ... OK
  Running 'Ch-Intro.R' [2s]
  Comparing 'Ch-Intro.Rout' to 'Ch-Intro.Rout.save' ... OK
  Running 'Ch-LinearRegression.R' [6s]
  Comparing 'Ch-LinearRegression.Rout' to 'Ch-LinearRegression.Rout.save' ...46,51c46,51
<  Min.   :   2   Min.   :  20   Min.   : 0.00522  
<  1st Qu.:  52   1st Qu.: 134   1st Qu.: 0.46449  
<  Median : 122   Median : 282   Median : 1.32051  
<  Mean   : 197   Mean   : 418   Mean   : 2.54846  
<  3rd Qu.: 268   3rd Qu.: 541   3rd Qu.: 3.44017  
<  Max.   :1098   Max.   :2120   Max.   :24.45946  
---
>  Min.   :   2   Min.   :  20   Min.   : 0.005  
>  1st Qu.:  52   1st Qu.: 134   1st Qu.: 0.464  
>  Median : 122   Median : 282   Median : 1.321  
>  Mean   : 197   Mean   : 418   Mean   : 2.548  
>  3rd Qu.: 268   3rd Qu.: 541   3rd Qu.: 3.440  
>  Max.   :1098   Max.   :2120   Max.   :24.459  
886c886
< -0.619068 -0.025568  0.000000 -0.000134  0.033201  0.641027 
---
> -0.6191 -0.0256  0.0000 -0.0001  0.0332  0.6410 
  Running 'Ch-Microeconometrics.R' [3s]
  Comparing 'Ch-Microeconometrics.Rout' to 'Ch-Microeconometrics.Rout.save' ... OK
  Running 'Ch-Programming.R' [22s]
  Comparing 'Ch-Programming.Rout' to 'Ch-Programming.Rout.save' ... OK
  Running 'Ch-TimeSeries.R' [5s]
  Comparing 'Ch-TimeSeries.Rout' to 'Ch-TimeSeries.Rout.save' ... OK
  Running 'Ch-Validation.R' [75s]
  Comparing 'Ch-Validation.Rout' to 'Ch-Validation.Rout.save' ... OK
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'colour_table.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'akaike_adjusted_rsq.R' 'filter_vif.R' 'fit_models.R'
    'select_models.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'ability_agreement.R' 'ability_ai.R' 'ability_compute_bounds.R'
    'ability_compute_stats.R' 'ability_human.R'
    'ability_human_override.R' 'ability_preference.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'plot.GRiwrm.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'gateway_keyring.R' 'gateway_openai.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'airship.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'calc_plan_stats.R'
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'calc_ale.R' 'model_bootstrap.R' 'stats.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'lambda_functions.R' 'likelihood-space.R' 'snc.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'inference.R' 'transformers.R' 'variance.R'
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'calculate_covariates.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'app.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'anim-animate.R' 'anim-prep-cat.R' 'anim-prep.R' 'funnel-web-data.R'
    'kangaroo-data.R' 'kangaroo-plot.R' 'proportional-shade.R'
    'wallaby-data.R' 'wallaby-plot.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'utils.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'ANOFA-contrastFrequencies.R' 'ANOFA-emFrequencies.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'ANOPA-anopa.R' 'ANOPA-contrastProportions.R' 'ANOPA-convert.R'
    'ANOPA-random.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'Af_edge_RMSD.R' 'VDJ_3d_properties.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'apollo_avgInterDraws.R' 'apollo_classAlloc.R' 'apollo_mdcev.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'adb_archive.R' 'adb_backup.R' 'adb_querry.R' 'helpers.R'
    'normGeometry.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'sample_ARMA_coef.R'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SmoothMultiarrayModel.Rd: ChromosomalModel,
    CopyNumberSegmentationModel
  byPath.AffymetrixFileSet.Rd: GenericDataFile
  calculateBaseline.ChipEffectSet.Rd: getAverageFile
  doCRMAv1.Rd: Verbose
  doCRMAv2.Rd: Verbose
  doFIRMA.Rd: Verbose
  doGCRMA.Rd: Verbose
  doRMA.Rd: Verbose
  justRMA.Rd: Verbose
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'main.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'art_pals.R' 'circle_data.R' 'grid_maker.R' 'group_numbers.R'
    'packer.R' 'rotator.R' 'square_data.R' 'wave_data.R'
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'calc_sun.R'
Running 'testthat.R' [46s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ARUtools)
  > 
  > test_check("ARUtools")
  ERROR: Unknown command "TMPDIR=D:/temp/2025_02_15_01_50_01_12291/RtmpicOluc/file2f98c250d7884". Did you mean command "preview"?
  ERROR: Unknown command "TMPDIR=D:/temp/2025_02_15_01_50_01_12291/RtmpicOluc/file2f98c162531f". Did you mean command "preview"?
  Extracting Dates and Times...
  ! Omitted 1 extra, non-json/GPS files
  ! Detected 2 log files
  [ FAIL 2 | WARN 0 | SKIP 6 | PASS 566 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-08_selections.R:27:3', 'test-08_selections.R:91:3',
    'test-08_selections.R:198:3', 'test-10_clean_logs.R:29:3',
    'test-10_clean_logs.R:61:3'
  • SoX not available (1): 'test-07_wave_files.R:193:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-09_create_dirs.R:35:3'): create_dirs() ───────────────────────
  `... <- NULL` produced warnings.
  ── Failure ('test-09_create_dirs.R:78:3'): create_dirs() ───────────────────────
  `... <- NULL` produced warnings.
  
  [ FAIL 2 | WARN 0 | SKIP 6 | PASS 566 ]
  Deleting unused snapshots:
  • 08_selections/sim-selection-weights2.svg
  • 08_selections/sim-selection-weights3.svg
  Error: Test failures
  Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'atpol_grids.R' 'miscRscript.r' 'plot_points_on_atpol.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'catchment_sim.R' 'elementary_pop.R'
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'convert.r'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'autogam.R' 'smooth_formula_string.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'aloocv.R' 'cohortODX.R' 'computeEndpoints.R' 'fit_baclava.R'
    'predictODX.R' 's3_methods.R' 'utilities.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'round_rect.r' 'waffle.r'
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'baf.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'get_cyclone.R'
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'dexpfit.R' 'expfit.R' 'icarfit.R' 'logisticfit.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'acceptenceRate.R' 'extractTreeData.R' 'generic_functions.R'
    'permVint.R' 'plot_all_trees.R' 'splitDensity.R' 'treeBarPlot.R'
    'treeDataframe.R' 'treeList.R' 'vintPlot.R'
File 'base64enc/libs/x64/base64enc.dll':
  Found non-API call to R: 'SETLENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'chadwick_installation.R'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Earlier versions
File 'BAS/libs/x64/BAS.dll':
  Found non-API call to R: 'SETLENGTH'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'batchLLM.R' 'batchLLM_shiny.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'bayes_colors.R' 'bayes_label.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'plot_cutoff.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'helper_functions.R'
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'boot_bw.R' 'boot_bw_estimate.R' 'post_strat_estimation.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'ceac_plot_graph.R' 'ceef_plot_graph.R' 'ceplane_plot_graph.R'
    'contour_graph.R' 'eib_plot_graph.R' 'evppi.default.R'
    'evppi_plot_ggplot.R' 'info_rank_graph.R' 'plot.bcea.R'
    'prep_ceplane_params.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'post.R' 'ps.R' 'pwr_prior.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'apply_contrast.R' 'estimate_varcov.R' 'get_marginal_effect.R'
    'predict_counterfactuals.R'
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'fitting.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'bfs_get_catalog_data.R' 'bfs_get_catalog_tables.R'
File 'Binarize/libs/x64/Binarize.dll':
  Found non-API call to R: 'SET_TYPEOF'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'bbassets.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'install_asreml.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'poisson.ci.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'PCAbiplot_Helper.R' 'TDAbiplot.R' 'TDAbiplot_helper.R'
    'insertAxDeets.R' 'insertDataTable.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'biplot.R' 'translate_axes.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'bisg.R' 'model_cat_dir.R' 'model_lm.R' 'stanmodels.R'
File 'BiTrinA/libs/x64/BiTrinA.dll':
  Found non-API call to R: 'SET_TYPEOF'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'bitstream-ints.R' 'bitstream-uints-exp-golomb.R'
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'assg2xBalance.R'
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'bnns.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'plot.R' 'utils.R'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/BonEV.Rcheck/00install.out' for details.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'summary_to_gt.R'
File 'box/libs/x64/box.dll':
  Found non-API calls to R: 'ENVFLAGS', 'SET_ENVFLAGS'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'sim_dat_one_trial_exp_covar.R' 'sim_dat_one_trial_exp_nocovar.R'
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'AddXMLInternal.R' 'BrowseSVG.R' 'MakeAccessibleSVGInternal.R'
    'RewriteSVG.R' 'ViewSVG.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'BranchGLM.R' 'BranchGLMTable.R' 'VariableImportance.R'
    'VariableImportance.boot.R' 'summaryBranchGLMVS.R'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'get_sinesp_data.R' 'get_sinesp_vde_data.R'