checkRd: (-1) create_unit_tests.Rd:17: Lost braces; missing escapes or markup?
    17 | Create `{testthat}` test cases for the code.
       |         ^
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:
    ‘check_hint.R’ ‘check_hints.R’ ‘check_question.R’ ‘insert_audio.R’
File ‘checkmate/libs/checkmate.so’:
  Found non-API call to R: ‘Rf_isFrame’

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:
  checkpoint.Rd: pkgdepends
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pipe.Rd: magrittr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) C316.amp.Rd:28-32: Lost braces
    28 |     40 x {
       |          ^
checkRd: (-1) C317.amp.Rd:28-32: Lost braces
    28 |     40 x {
       |          ^
checkRd: (-1) C60.amp.Rd:63-67: Lost braces
    63 |     40 x {
       |          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  chkpt_brms.Rd: brms
  make_brmsfit.Rd: brms
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package unavailable to check Rd xrefs: ‘cmdstanr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘closestdist_gcms.Rd’ ‘compare_gcms.R’ ‘compare_gcms.Rd’
    ‘cor_gcms.Rd’ ‘dist_gcms.Rd’ ‘env_gcms.Rd’ ‘flatten_gcms.Rd’
    ‘hclust_gcms.Rd’ ‘kmeans_gcms.R’ ‘kmeans_gcms.Rd’
    ‘montecarlo_gcms.Rd’ ‘optk_gcms.Rd’ ‘summary_gcms.Rd’
    ‘transform_gcms.R’ ‘transform_gcms.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘Ryacas-all.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggpng.Rd: ggsave
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 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_record.Rd’ ‘chronicle.R’ ‘fmap_record.Rd’
    ‘grapes-greater-than-equals-grapes.Rd’ ‘pick.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  insert_chunkwise_into.Rd: tbl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) chunker-methods.Rd:63: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:64: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:70: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ec.datalag.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{prepares Dy y_1 Dy_1 ... Dy_{nlag-1} for estimation}
       |                                    ^
checkRd: (-1) ec.datalag.Rd:15: Lost braces
    15 | ymat contains the folloiwing columns {Dy y_1 Dy_1 ... Dy_{nlag-1}}
       |                                      ^
checkRd: (-1) ec.datalag.Rd:15: Lost braces; missing escapes or markup?
    15 | ymat contains the folloiwing columns {Dy y_1 Dy_1 ... Dy_{nlag-1}}
       |                                                          ^
checkRd: (-1) lagn.Rd:21: Lost braces; missing escapes or markup?
    21 |              REM: alternative to "lead-lag" {dplyr} which applies to vector y
       |                                             ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘long_est.R’
checkRd: (-1) CIplot.Rd:58: Lost braces; missing escapes or markup?
    58 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.
       |                       ^
Missing dependency on R >= 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’
Specified C++11: please drop specification unless essential
checkRd: (-1) rstable.Rd:42: Lost braces
    42 | Lo\"{g}ae\"{v}e, M. (1977). Probability Theory I. (fourth edition) Springer-Verlag, New York.
       |     ^
checkRd: (-1) rstable.Rd:42: Lost braces
    42 | Lo\"{g}ae\"{v}e, M. (1977). Probability Theory I. (fourth edition) Springer-Verlag, New York.
       |            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  circ.plot.Rd: eqscplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘cirls.fit.Rd’ ‘confint.cirls.Rd’
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dbExecQuery.Rd: dbSendQuery, dbClearResult, dbGetQuery
  lbsClear.Rd: dbCommit, dbRollback
  lbsDeleteAllAuthorsDocuments.Rd: dbCommit, dbRollback
  lbsTidy.Rd: dbCommit, dbRollback
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) data_generator.Rd:93: Lost braces; missing escapes or markup?
    93 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                     ^
checkRd: (-1) data_generator.Rd:93: Lost braces; missing escapes or markup?
    93 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                             ^
checkRd: (-1) data_generator.Rd:95: Lost braces; missing escapes or markup?
    95 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++}, S_{*+}
       |                                                                 ^
checkRd: (-1) data_generator.Rd:95: Lost braces; missing escapes or markup?
    95 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++}, S_{*+}
       |                                                                         ^
checkRd: (-1) data_generator_loop.Rd:96: Lost braces; missing escapes or markup?
    96 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                     ^
checkRd: (-1) data_generator_loop.Rd:96: Lost braces; missing escapes or markup?
    96 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                             ^
checkRd: (-1) data_generator_loop.Rd:98: Lost braces; missing escapes or markup?
    98 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++},
       |                                                                 ^
checkRd: (-1) data_generator_loop.Rd:99: Lost braces; missing escapes or markup?
    99 |   S_{*+} and PP estimands}
       |     ^
checkRd: (-1) ciu.ggplot.col.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
checkRd: (-1) ciu.meta.explain.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
checkRd: (-1) ciu.meta.result.new.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
checkRd: (-1) ciu.textual.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CivisFuture.Rd: Future
  civis_platform.Rd: future, plan
  write_civis_file.Rd: plan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 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_cluster_composition.R’ ‘extract_ids_vector.R’
    ‘perform_clustering.R’
File ‘clarabel/libs/clarabel.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
    Object: ‘rust/target/release/libclarabel.a’
  Found ‘abort’, possibly from ‘abort’ (C)
    Object: ‘rust/target/release/libclarabel.a’
  Found ‘exit’, possibly from ‘exit’ (C)
    Object: ‘rust/target/release/libclarabel.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) get_langs.Rd:13: Lost braces
    13 | character vector listing all the languages that tag API call supports. See \code{\link{tag_images}} and code{\link{tag_image_urls}}
       |                                                                                                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  generate_classification_data.Rd: knn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘as_raster.Rd’ ‘clc.R’ ‘clc_category.R’ ‘clc_raster.R’ ‘copy_to.Rd’
    ‘cut_to_extent.Rd’ ‘get_colors.Rd’ ‘get_levels.Rd’ ‘get_raster.Rd’
    ‘plot_clc.Rd’ ‘prepare_plot.Rd’ ‘save_to.Rd’
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ClickHouseHTTPConnection-class.Rd: dbConnect
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fitMarkovChain.Rd: Rsolnp
  frequencies.Rd: transactions
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘horner.Rd’
checkRd: (-1) cf_save_kml.Rd:68: Lost braces
    68 | \code{\link{cf_find_station}} and code{vignette("choose-station")} for
       |                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clinDR-package.Rd: DoseFinding
  emaxsim.Rd: Mods
  emaxsimB.Rd: Mods
  fitEmaxB.Rd: rstan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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_rci.R’
checkRd: (-1) clinsig.Rd:129: Lost braces
   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                   ^
checkRd: (-1) clinsig.Rd:129: Lost braces
   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  knitPrintListObjects.Rd: knitr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘cli/libs/cli.so’:
  Found non-API call to R: ‘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.
checkRd: (-1) print.clogitL1.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.clogitL1.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.clogitL1.Rd:23: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘cloud_drive_download_bulk.Rd’ ‘cloud_drive_read_bulk.Rd’
    ‘cloud_drive_upload_bulk.Rd’ ‘cloud_drive_write_bulk.Rd’
    ‘cloud_s3_download_bulk.Rd’ ‘cloud_s3_read_bulk.Rd’
    ‘cloud_s3_upload_bulk.Rd’ ‘cloud_s3_write_bulk.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cloudml_train.Rd: flags
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) cb_participant_count.Rd:13: Lost braces
    13 | \item{query}{A phenotype query defined using the code{\link{phenotype}} function and logic operators (see example below)}
       |                                                      ^
checkRd: (-1) phenotype.Rd:10: Lost braces
    10 | \item{id}{A single phenotype id. Possible phenotyoes can be explored using the code{\link{cb_search_phenotypes}} function}
       |                                                                                    ^
checkRd: (-1) clr.Rd:24: Lost braces
    24 | the sense that its Karhunen-Lo\`{e}ve decomposition has qx terms only.}
       |                                 ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bias_df_combined.R’ ‘create_table_ep_15.R’
    ‘precision_calculate_aov_info.R’
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.clusEvol.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.clus_lme.Rd: ggexport
  plot.clus_opt_thres3.Rd: ggexport
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dissmutmatrix.Rd: dissplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘clusterhap_reports’
Specified C++11: please drop specification unless essential
checkRd: (-1) HTKmeans.Rd:62: Lost braces
    62 | \item{centers }{A matrix of cluster centres.}
       |      ^
checkRd: (-1) HTKmeans.Rd:62: Lost braces
    62 | \item{centers }{A matrix of cluster centres.}
       |                ^
checkRd: (-1) HTKmeans.Rd:63: Lost braces
    63 | \item{cluster }{A vector of integers (from 1:\code{k}) indicating the cluster to which each point is allocated.}
       |      ^
checkRd: (-1) HTKmeans.Rd:63: Lost braces
    63 | \item{cluster }{A vector of integers (from 1:\code{k}) indicating the cluster to which each point is allocated.}
       |                ^
checkRd: (-1) HTKmeans.Rd:64: Lost braces
    64 | \item{itnb }{The number of iterations executed until convergence}
       |      ^
checkRd: (-1) HTKmeans.Rd:64: Lost braces
    64 | \item{itnb }{The number of iterations executed until convergence}
       |             ^
checkRd: (-1) HTKmeans.Rd:65: Lost braces
    65 | \item{converged }{Whether the algorithm stopped by converging or through reaching the maximum number of itertions.}
       |      ^
checkRd: (-1) HTKmeans.Rd:65: Lost braces
    65 | \item{converged }{Whether the algorithm stopped by converging or through reaching the maximum number of itertions.}
       |                  ^
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kmeansvar.Rd: splitmix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clusvisMixmod.Rd: MixmodCluster-class
  clusvisVarSelLCM.Rd: VSLCMresults-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cluster_stability.Rd: agnes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) CMAPSS.Rd:10: Lost braces
    10 | \item \code{train}{ a list of class "hhsmm.data" as the train dataset}
       |                   ^
checkRd: (-1) CMAPSS.Rd:11: Lost braces
    11 | \item \code{test}{ a list of class "hhsmm.data" as the test dataset}
       |                  ^
checkRd: (-1) CMAPSS.Rd:12: Lost braces
    12 | \item \code{subsets}{ a matrix containig the number of units in each subset of the CMAPSS data set (FD001-FD004) for the train and test datasets}
       |                     ^
checkRd: (-1) cmb.search.Rd:50: Lost braces; missing escapes or markup?
    50 |   \item{order}{applied conditioning order {length p}}
       |                                           ^
'library' or 'require' calls not declared from:
  ‘HDclassif’ ‘MixSim’ ‘mclust’
checkRd: (-1) gp.realize.Rd:20: Lost braces; missing escapes or markup?
    20 | The list \code{l.v} is created by \code{makedistlist()} from a {n x p} design matrix on which to generate the unconditional GP realization.  The correlation parameters take on values in \code{(0,1)} and use the Gaussian correlation model, calculated as \code{rho^d(xi,xj)^2}.  This helper function is used to create the demonstration data used in the example for \code{calibrate()}.
       |                                                                ^
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mlsei.Rd: solve.QP
  mlsun.Rd: solve.QP
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) bvp.Rd:24: Lost braces
    24 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
checkRd: (-1) ivp.Rd:38: Lost braces
    38 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
checkRd: (-1) ivpsys.Rd:29: Lost braces
    29 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘basis.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cnaOpt.Rd: configTable, rreduce, condTbl, cna
  conCovOpt.Rd: configTable, cna
  conCovOpt_utils.Rd: rreduce, condTbl
  ereduce.Rd: full.ct
  findOutcomes.Rd: configTable, cna, selectCases, full.ct
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) cnlt.reg.Rd:43: Lost braces
    43 | \emph{Technometrics}, bold{60} (1), 48-60, DOI 10.1080/00401706.2017.1281846.\cr\cr
       |                           ^
checkRd: (-1) fwtnppermC.Rd:35: Lost braces
    35 | Given \eqn{n} points on a line, \env{x}, each with a corresponding env{f} value this function computes
       |                                                                       ^
checkRd: (-1) educFM.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:28: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘cb_summary_stats_numeric.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  create_codemeta.Rd: write_json
  write_codemeta.Rd: write_json
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coefplot.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
No news entries found.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohensdpLibrary.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:
    ‘CreateCohortExplorerApp.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  boxesLx.Rd: grViz
  mkratetable.Rd: survival, pyears
  plotcuminc.Rd: survival, pyears
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 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’
File ‘collections/libs/collections.so’:
  Found non-API calls to R: ‘PRENV’, ‘SET_CLOENV’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘collinear.R’ ‘cor_cramer_v.R’ ‘cor_df.R’ ‘cor_select.R’ ‘f_auc.Rd’
    ‘f_r2.Rd’ ‘f_r2_counts.Rd’ ‘f_v.Rd’ ‘f_v_rf_categorical.Rd’
    ‘identify.R’ ‘model_formula.R’ ‘preference_order.R’
    ‘preference_order_methods.R’ ‘target_encoding_methods.R’ ‘validate.R’
    ‘vif_df.R’ ‘vif_select.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  roi_select.Rd: imager
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) getHistList.Rd:32: Lost braces; missing escapes or markup?
    32 | ({FALSE})? If a bin is empty, the center of the bin is returned as the
       |  ^
checkRd: (-1) imageClusterPipeline.Rd:82: Lost braces; missing escapes or markup?
    82 | of the bin ({FALSE})? If a bin is empty, the center of the bin is returned
       |             ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘simulate_populations.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_colors_3d.Rd: plotly
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  InterpolateColorFun.Rd: ggplot2
  OrderDataTSP.Rd: TSP
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) colour_values.Rd:143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values.Rd:144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values_rgb.Rd:143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values_rgb.Rd:144: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘c4a.Rd’ ‘c4a_plot_hcl_space.R’ ‘c4a_table.R’
Unexported object imported by a ':::' call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) xsimplex.Rd:6: Lost braces; missing escapes or markup?
     6 |              Generates all points on a {p,n} simplex lattice (i.e. a p-part
       |                                        ^
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
checkRd: (-1) BMD.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add.risk.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add.risk.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) count_pairs.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) score_log_nonparam.Rd:36: Lost braces; missing escapes or markup?
    36 | {0, 1}.
       | ^
checkRd: (-1) score_log_semiparam.Rd:40: Lost braces; missing escapes or markup?
    40 | values in {0, 1}.
       |           ^
checkRd: (-1) sort_pairs.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) hmm.Rd:47-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:56-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:63-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:71-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:79-84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:85-89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:95-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:104-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:108-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:112-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:119-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:130-133: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘compareMCMCs.R’ ‘metrics-addMetrics.R’
checkRd: (-1) glass.Rd:10: Lost braces
    10 | \item{item}{factor}{200 levels - which item the measurements came from}
       |                    ^
checkRd: (-1) glass.Rd:11-12: Lost braces
    11 | \item{fragment}{factor}{4 levels - which of the four fragments from each item the observations were made
       |                        ^
checkRd: (-1) glass.Rd:13: Lost braces
    13 | \item{logNaO}{numeric}{log of sodium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:14: Lost braces
    14 | \item{logMgO}{numeric}{log of magnesium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:15: Lost braces
    15 | \item{logAlO}{numeric}{log of aluminium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:16: Lost braces
    16 | \item{logSiO}{numeric}{log of silicon concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:17: Lost braces
    17 | \item{logKO}{numeric}{log of potassium concentration to oxygen concentration}
       |                      ^
checkRd: (-1) glass.Rd:18: Lost braces
    18 | \item{logCaO}{numeric}{log of calcium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:19: Lost braces
    19 | \item{logFeO}{numeric}{log of iron concentration to oxygen concentration}
       |                       ^
checkRd: (-1) atomdeps.Rd:9: Lost braces
     9 |  \item{"tangle"}: {Dihedral angle defined by atoms A-B-C-D as described below. \code{NA}'s represent the free side chain dihedral angles \emph{chi} for that amino acid.}
       |                   ^
checkRd: (-1) atomdeps.Rd:10: Lost braces; missing escapes or markup?
    10 |  \item{"names"}: {The component atoms of the amino acid side chain.  Represents atom D in the dihedral.}
       |                  ^
checkRd: (-1) atomdeps.Rd:11: Lost braces; missing escapes or markup?
    11 |  \item{"matx"}: {The names of atoms A,B,C in the dihedral, with rows corresponding to the atoms in "names".}
       |                 ^
checkRd: (-1) atomdeps.Rd:12: Lost braces; missing escapes or markup?
    12 |  \item{"bangle"}: {Planar bond angle formed between B-C-D}
       |                   ^
checkRd: (-1) atomdeps.Rd:13: Lost braces; missing escapes or markup?
    13 |  \item{"blength"}: {Bond length between C-D}
       |                    ^
checkRd: (-1) keener.Rd:82: Lost braces; missing escapes or markup?
    82 | a_{ij} = (S_ij + 1) / (S_ij + S_ji + 2). This step should make comparing
       |   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rlm.Rd: lqs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  codadendrogram.Rd: histogram
  pairwisePlot.Rd: lmrob
  pwlrPlot.Rd: lmrob
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘fitmodel.R’
checkRd: (-1) concstats_hhi.Rd:13: Lost braces; missing escapes or markup?
    13 | value is required. Ranges from {0, 1} and often used for comparison over
       |                                ^
checkRd: (-1) KCI.Rd:44: Lost braces
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                ^
checkRd: (-1) KCI.Rd:44: Lost braces
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                      ^
checkRd: (-1) KCI.Rd:44: Lost braces; missing escapes or markup?
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pcmvt.Rd: pmvt, GenzBretz
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'library' or 'require' call not declared from: ‘e1071’
checkRd: (-1) mya.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
Running ‘confintrob_test.R’ [14s/18s]
  Comparing ‘confintrob_test.Rout’ to ‘confintrob_test.Rout.save’ ...64c64
<       AIC       BIC    logLik -2*log(L)  df.resid 
---
>      AIC      BIC   logLik deviance df.resid 
203c203
<       AIC       BIC    logLik -2*log(L)  df.resid 
---
>      AIC      BIC   logLik deviance df.resid 
  Running ‘parallelTest.R’ [5s/12s]
  Running ‘varComprob_createParamSampleFunction.R’ [12s/15s]
  Comparing ‘varComprob_createParamSampleFunction.Rout’ to ‘varComprob_createParamSampleFunction.Rout.save’ ... OK
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  loo_conformal.Rd: predictive_interval
  predictive_interval.conformal.Rd: posterior_predict
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  conformal.multidim.full.Rd: future.apply
  conformal.multidim.msplit.Rd: future.apply
  glmnet.funs.Rd: glmnet
  plot_multidim.Rd: ggplot2, gridExtra, hrbrthemes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  km.outcomes.Rd: survfit
  km.pmf.Rd: survfit
  km.support.Rd: survfit
  km.surv.Rd: survfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) binary_class_cm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
Found the following files/directories:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DBI.Rd: DBIConnection-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘api-get_datalog.R’ ‘api-get_device.R’ ‘api-get_devices.R’
    ‘api-get_element.R’ ‘api-get_elements.R’ ‘api-get_project.R’
    ‘api-get_projects.R’ ‘api-get_users_me.R’ ‘client.R’
checkRd: (-1) Univranks.Rd:69: Lost braces; missing escapes or markup?
    69 | To obtain the preference rankings from the paired comparisons the procedure has been the following: the first row of the raw data is [1  3  2   1   2   1  1  2  1   1   1   2   1    1   2]. London is preferred to Paris, St. Gallen, Barcelona Stockholm (LP, LM, LSg, LB and LSt are always equal to 1), and there is no preference between London and Milan (they are tied); Milan is preferred to Paris (PM = 2), St. Gallen, Barcelona and Stockholm; and so on. The first ordering is then <{L M} Sg St B P> corresponding to a ranking [1,5,1,2,4,3], where the columns indicate L  P  M Sg  B St.  
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ^
Specified C++11: please drop specification unless essential
checkRd: (-1) getConvexHull.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getConvexHull.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getConvexHull.Rd:30: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘cumulative_split_code.Rd’ ‘decompose_contrasts.Rd’
    ‘expand_formulas.R’ ‘factor_coercion_messages.R’
    ‘glimpse_contrasts.R’ ‘make_parameters.R’ ‘orth_polynomial_code.Rd’
    ‘raw_polynomial_code.Rd’ ‘use_contrast.R’ ‘utils_check_labels.R’
    ‘utils_trymatch.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  curve_cont.Rd: riskRegression
  plot_surv_3Dsurface.Rd: riskRegression
  plot_surv_animated.Rd: riskRegression, facet_wrap
  plot_surv_area.Rd: riskRegression, facet_wrap
  plot_surv_at_t.Rd: riskRegression, facet_wrap
  plot_surv_contour.Rd: riskRegression, ggplot2, facet_wrap
  plot_surv_heatmap.Rd: riskRegression, facet_wrap
  plot_surv_lines.Rd: riskRegression, facet_wrap
  plot_surv_matrix.Rd: riskRegression, facet_wrap
  plot_surv_quantiles.Rd: riskRegression, facet_wrap
  plot_surv_rmst.Rd: riskRegression, facet_wrap
  plot_surv_rmtl.Rd: riskRegression, facet_wrap
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) CovrgPlot.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{plotCI}{a vector of up to 4 numbers out of the set {1,2,3,4}, corresponding to which
       |                                                          ^
Specified C++11: please drop specification unless essential
checkRd: (-1) copCAR.Rd:40: Lost braces
    40 |        item{\code{maxit}}{the maximum number of iterations to be used by \code{\link{optim}} when optimizing the objective function. Defaults to \code{1000}.}
       |            ^
checkRd: (-1) copCAR.Rd:40: Lost braces
    40 |        item{\code{maxit}}{the maximum number of iterations to be used by \code{\link{optim}} when optimizing the objective function. Defaults to \code{1000}.}
       |                          ^
checkRd: (-1) condQestCopC.Rd:45: Lost braces; missing escapes or markup?
    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                          ^
checkRd: (-1) condQestCopC.Rd:45: Lost braces; missing escapes or markup?
    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                                      ^
checkRd: (-1) condQestCopC.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                  ^
checkRd: (-1) condQestCopC.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                              ^
checkRd: (-1) ComputeCope.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:57-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DrawContour.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Draws the contour {f=c}.}
       |                          ^
checkRd: (-1) DrawContour.Rd:20: Lost braces; missing escapes or markup?
    20 | Draws the contour {f=c}.
       |                   ^
checkRd: (-1) cope.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:35: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cophe.prepare.dat.susie.Rd: runsusie
  cophe.susie.Rd: check_dataset, runsusie
  cophe.susie.lbf.Rd: runsusie
  cophe_heatmap.Rd: pheatmap
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bcalibrate.Rd: kEstimate, pca
  cal_rv.Rd: kEstimate, pca
  gcalibrate.Rd: kEstimate, pca
  plot_estimates.Rd: theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CoreCollection.Rd: R6Class
  dot-CoreCollectionClass.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) getSurface.Rd:22: Lost braces
    22 | value \code{getSurface} shortens the output of \code{conv} to remove artificial surface layers. The output is thus a subset of the input, and identical in structure to the /code{conv} output.
       |                                                                                                                                                                                  ^
checkRd: (-1) carstats.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:14: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  carstats.Rd: data.table
  rundata.Rd: data.table
  titanic.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘refresh_coronvirus.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tCorpus-cash-annotate_rsyntax.Rd: tquery
  tCorpus-cash-subset.Rd: subset.data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  corrarray.Rd: rcorr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggbplot.Rd: bplot
  tally.Rd: bplot, calibrate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  corrgrapher.Rd: visNetwork
  plot.corrgrapher.Rd: visNetwork
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  polycorr.Rd: polychor
  tetracorr.Rd: polychor
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘corrRect.hclust.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rplot.Rd: geom_point
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘corrBarplot.R’ ‘corrNetwork.R’
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ctmaAllInvFit.Rd: ctStanFit
  ctmaFit.Rd: ctStanFit, ctsem
  ctmaInit.Rd: ctStanFit, ctsem
  ctmaOptimizeFit.Rd: ctStanFit
  ctmaOptimizeInit.Rd: ctStanFit
  ctmaPlotCtsemMod.Rd: ctsem
  ctmaScaleInits.Rd: ctStanFit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) summary_fitlist.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fasttrakg.Rd:18: Lost braces
    18 |     \item{\code{killip}}{Killip level of cardiac event severity (1-4)age75}{1= Age>75; 0=Age<=75}
       |                                                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ml.nb1.Rd: glm.nb
  ml.nb2.Rd: glm.nb
  ml.nbc.Rd: glm.nb
  ml.pois.Rd: glm.nb
  modelfit.Rd: glm.nb
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘covfefe_inauguration.txt’
File ‘covr/libs/covr.so’:
  Found non-API calls to R: ‘BODY’, ‘CLOENV’, ‘FORMALS’, ‘SET_BODY’,
    ‘SET_CLOENV’, ‘SET_FORMALS’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  axis_canvas.Rd: ggplot2, coord_flip
  background_grid.Rd: theme
  draw_line.Rd: geom_path
  draw_text.Rd: geom_label
  ggsave2.Rd: ggsave
  insert_xaxis_grob.Rd: ggplot2
  save_plot.Rd: ggsave
  theme_minimal_grid.Rd: theme_minimal
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coxed.Rd: mgcv, rms
  coxed.gam.Rd: mgcv
  coxed.gam.tvc.Rd: mgcv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘coxphf-tidiers.R’
Specified C++11: please drop specification unless essential
checkRd: (-1) gen_data.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gen_data.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gen_data.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coxr.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) coxph.RT.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) coxph.RT.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) coxph.RT.Rd:59-71: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coxsei-package.Rd: survival
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CPC.Rd: diana, pam, dbscan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘cpp11qpdf/libs/cpp11qpdf.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘libqpdf/libstatqpdf.a’
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘libqpdf/libstatqpdf.a’
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
    Object: ‘libqpdf/libstatqpdf.a’
  Found ‘putchar’, possibly from ‘putchar’ (C)
    Object: ‘libqpdf/libstatqpdf.a’
  Found ‘srandom’, possibly from ‘srandom’ (C)
    Object: ‘libqpdf/libstatqpdf.a’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘libqpdf/libstatqpdf.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) sharedat.Rd:23: Lost braces
    23 | \doi{10.7910/DVN/YXMQZM}{Harvard dataverse}
       |                         ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘cleaning.R’
checkRd: (-1) crwPredict.Rd:54-68: Lost braces
    54 | \item("predTime"){
       |                  ^
checkRd: (-1) crwPredict.Rd:59: Lost braces
    59 |  no longer the default (see \item{return.type}). If the original data were 
       |                                  ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘pick_colors.R’ ‘scale_crayons.Rd’
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:
    ‘CRMetrics.R’ ‘CRMetrics.Rd’ ‘inner_functions.R’
checkRd: (-1) normFit.Rd:39: Lost braces; missing escapes or markup?
    39 | {analytes}}
       | ^
checkRd: (-1) normPred.Rd:27: Lost braces
    27 | ode{standards}, \code{analytes}}
       |    ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘crop.R’ ‘helpers.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_multi_silodata.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running ‘testthat.R’ [33s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(crossmap)
  > 
  > test_check("crossmap")
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 382 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-errors.R:12:3'): require future ──────────────────────────────
  `future_xmap(list(1:3, 1:3), paste)` did not throw an error.
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 382 ]
  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:
    ‘officer.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  filter_slider.Rd: tag, HTML
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Crossword.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) confRegCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                                                                                    ^
checkRd: (-1) confRegCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                                                                                      ^
checkRd: (-1) confRegUCRandUCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  crsra_anonymize.Rd: digest
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: ‘ggplot2’
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:
    ‘helpers.R’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("crunchy")
  Loading required package: crunchy
  Loading required package: crunch
  
  Attaching package: 'crunch'
  
  The following objects are masked from 'package:stats':
  
      filter, rstandard, setNames
  
  The following object is masked from 'package:graphics':
  
      title
  
  The following object is masked from 'package:utils':
  
      write.csv
  
  The following object is masked from 'package:base':
  
      table
  
  Loading required package: shiny
  [ FAIL 1 | WARN 2 | SKIP 1 | PASS 28 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-gadgets.R:56:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-gadgets.R:69:5'): (code run outside of `test_that()`) ──────────
  Error: "test ds" not found
  Backtrace:
       ▆
    1. ├─global with_mock_crunch(...) at test-gadgets.R:63:1
    2. │ ├─base::with(opts, with_mock_api(expr))
    3. │ ├─crunch:::with.contextManager(opts, with_mock_api(expr))
    4. │ │ └─base::eval(substitute(expr), envir = parent.frame())
    5. │ │   └─base::eval(substitute(expr), envir = parent.frame())
    6. │ └─httptest::with_mock_api(expr)
    7. │   └─base::eval.parent(expr)
    8. │     └─base::eval(expr, p)
    9. └─crunch::loadDataset("test ds") at test-gadgets.R:69:5
   10.   └─httpcache::halt(dQuote(dataset), " not found")
  
  [ FAIL 1 | WARN 2 | SKIP 1 | PASS 28 ]
  Error: Test failures
  Execution halted
checkRd: (-1) cruts-package.Rd:21: Lost braces
    21 | section{Dependencies}{
       |        ^
checkRd: (-1) cruts-package.Rd:21-24: Lost braces
    21 | section{Dependencies}{
       |                      ^
checkRd: (-1) cruts-package.Rd:26: Lost braces
    26 | section{Citation}{
       |        ^
checkRd: (-1) cruts-package.Rd:26-28: Lost braces
    26 | section{Citation}{
       |                  ^
checkRd: (-1) cruts-package.Rd:30-32: Lost braces
    30 | references{
       |           ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘crypto_global_quotes.R’ ‘crypto_history.R’ ‘crypto_info.R’
    ‘crypto_listings.R’
checkRd: (-1) calculate_cell_volume.Rd:16: Lost braces; missing escapes or markup?
    16 | V A real number. The volume (in angstroms^3 or angstroms^{-3})
       |                                                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  akde.Rd: res
  as.telemetry.Rd: fread
  ctmm-FAQ.Rd: zoom
  projection.Rd: CRS
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ctpm.fit.Rd: slouch, plot.variogram
  variogram.Rd: plot.variogram
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ctqr-package.Rd: pchreg
  ctqr.Rd: Surv, pchreg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ctFit.Rd: ctModel
  ctModelFromFit.Rd: ctModel
  ctMultigroupFit.Rd: ctLongToWide, ctModel
  ctPostPredict.Rd: ctPlotArray
  ctRefineTo.Rd: ctModel
  ctsemOMX.Rd: ctModel
  summary.ctsemFit.Rd: ctModel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘Hello.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:
    ‘connection-config.R’ ‘read-float.R’ ‘read-hex.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_by_blocks.R’ ‘balance_by_blocks.Rd’ ‘balance_matrix.R’
    ‘balance_matrix.Rd’ ‘make_non_negative.Rd’ ‘round_by_blocks.Rd’
    ‘round_matrix.R’ ‘round_matrix.Rd’ ‘round_vector.Rd’
File ‘cubature/libs/cubature.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
    Objects: ‘Cuba/libcuba.a’, ‘cubature-1.0.4/libcubature.a’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘Cuba/libcuba.a’
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
    Object: ‘Cuba/libcuba.a’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘cubature-1.0.4/libcubature.a’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘Cuba/libcuba.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘accessors.Rd’ ‘as-cubble.R’ ‘as_cubble.Rd’ ‘check-key.R’
    ‘climate-data.Rd’ ‘covid.Rd’ ‘cubble-attrs.R’ ‘cubble-class.R’
    ‘cubble-print.R’ ‘dplyr.R’ ‘dplyr.Rd’ ‘face-spatial-temporal.R’
    ‘face.Rd’ ‘glyph.R’ ‘glyph.Rd’ ‘make_spatial_sf.Rd’
    ‘make_temporal_tsibble.Rd’ ‘matching.R’ ‘matching.Rd’ ‘netcdf.R’
    ‘sf.R’ ‘test-data.Rd’ ‘tsibble.R’ ‘tsibble.Rd’ ‘unfold.R’ ‘unfold.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  jumpoints.Rd: lars
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Survcure.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘create_cure_dataframe.R’ ‘cure_plot.R’ ‘resample_residuals.R’
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
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:
    ‘plot_curriculum_graph.R’
Found the following files/directories:
  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SparseCCA.Rd: CCA, CCA.permute
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  simulate_cycloSurv.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Cramer_vonMises.Rd: Copula-class
  Cylcop.Rd: Copula-class
  ccylcop.Rd: Copula-class
  cyl_copula-class.Rd: Copula-class
  cyl_rect_combine-class.Rd: Copula-class
  cyl_rect_combine.Rd: Copula-class
  cyl_rot_combine-class.Rd: Copula-class
  cyl_rot_combine.Rd: Copula-class
  fit_cylcop_ml.Rd: Copula-class, fitCopula
  full2half_circ.Rd: circular
  half2full_circ.Rd: circular
  joint.Rd: Copula-class
  numerical_conditional_cop.Rd: Copula-class
  numerical_inv_conditional_cop.Rd: Copula-class
  plot_cop_surf.Rd: Copula-class
  wasserstein.Rd: Copula-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) fit.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CytofTree.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RetrievePops.Rd:20-21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RetrievePops.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rnaRaw.Rd: dgCMatrix-class
  rnaVelo.Rd: dgCMatrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ConfMatrix.Rd: R6
  D2MCS.Rd: getModelInfo
  GainRatioHeuristic.Rd: gain.ratio
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘d3TreeFunctions.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  StoragehubManager.Rd: R6Class
  d4storagehub4RLogger.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DAAGtheme.Rd: theEconomist.theme, standard.theme, simpleTheme,
    custom.theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{  A small, positive scalar that determines when iterations
       |               ^
checkRd: (-1) fpiter.Rd:60-61: Lost braces
    60 |     \code{maxiter}{  An integer denoting the maximum limit on the number of
       |                   ^
checkRd: (-1) fpiter.Rd:63-65: Lost braces
    63 |     \code{trace}{  A logical variable denoting whether some of the intermediate
       |                 ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘clean_land_points.R’ ‘join_mpa_data.R’ ‘join_mpa_data.Rd’
    ‘join_ports_locations.R’ ‘model_vms.R’ ‘vms_clean.R’
checkRd: (-1) formatScientificTeX.Rd:33: Lost braces; missing escapes or markup?
    33 | function will return  " 3.0\\\\times 10^{2}"
       |                                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.predict_parts.Rd: break_down, local_attributions,
    local_interactions
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘cla_tune.R’ ‘clu_clusterer.R’ ‘graphics.R’ ‘plot_bar.Rd’
    ‘plot_boxplot_class.Rd’ ‘plot_density.Rd’ ‘plot_density_class.Rd’
    ‘plot_groupedbar.Rd’ ‘plot_hist.Rd’ ‘plot_lollipop.Rd’
    ‘plot_pieplot.Rd’ ‘plot_scatter.Rd’ ‘plot_stackedbar.Rd’ ‘reg_tune.R’
    ‘trans_smoothing.R’ ‘ts_tune.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  link_dam_metadata.Rd: data.table
  read_dam_file.Rd: behavr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  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.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dcr_app.Rd: plotly
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) StartEnd.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) StartEnd.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FillIn.Rd: data.table
  slide.Rd: dplyr
  slideMA.Rd: dplyr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running examples in ‘DataCombine-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MoveFront
> ### Title: Move variables to the front of a data frame.
> ### Aliases: MoveFront
> 
> ### ** Examples
> 
> # Create fake data
> A <- B <- C <- 1:50
> OldOrder <- data.frame(A, B, C)
> 
> # Move C to front
> NewOrder1 <- MoveFront(OldOrder, "C")
> names(NewOrder1)
[1] "C" "A" "B"
> 
> # Move B and A to the front
> NewOrder2 <- MoveFront(OldOrder, c("B", "A"))
> names(NewOrder2)
[1] "B" "A" "C"
> 
> ## Non-exact matching (example from Felix Hass)
>  # Create fake data
>  df <- data.frame(dummy = c(1,0), Name = c("Angola", "Chad"),
+                  DyadName = c("Government of Angola - UNITA",
+                  "Government of Chad - FNT"),
+                  Year = c("2002", "1992"))
> 
>  df <- MoveFront(df, c("Name", "Year"), exact = FALSE)
Error in grep(pattern, x, ignore.case, value, perl, fixed, useBytes, invert) : 
  NA in coercion to boolean
Calls: MoveFront -> OneMove -> grep
Execution halted
checkRd: (-1) processFlow.Rd:14: Lost braces
    14 | \item{roundDigits}{Integer. If NA, numerics are not rounded before comparison. If /code{roundDigits} is specified, numerics are 
       |                                                                                        ^
checkRd: (-1) processFlow.Rd:15: Lost braces
    15 | rounded to /code{roundDigits} decimal places using \link[base]{round}.}
       |                 ^
checkRd: (-1) data_edit.Rd:137: Lost braces
   137 | code{data_edit} is a shiny application built on \code{rhandsontable} that is
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  configure_report.Rd: theme
  create_report.Rd: render
  drop_columns.Rd: data.table
  group_category.Rd: data.table
  plotDataExplorer.Rd: theme
  plotDataExplorer.grid.Rd: theme
  plotDataExplorer.multiple.Rd: theme, facet_wrap
  plotDataExplorer.single.Rd: theme
  plot_bar.Rd: geom_bar, theme_gray, theme
  plot_boxplot.Rd: geom_boxplot, geom_jitter, scale_y_continuous,
    theme_gray, theme
  plot_correlation.Rd: geom_text, theme_gray, theme
  plot_density.Rd: geom_density, scale_x_continuous, theme_gray, theme
  plot_histogram.Rd: geom_histogram, scale_x_continuous, theme_gray,
    theme
  plot_intro.Rd: geom_label, theme_gray, theme
  plot_missing.Rd: geom_label, theme_gray, theme
  plot_prcomp.Rd: geom_label, theme_gray, theme
  plot_qq.Rd: geom_qq, geom_qq_line, theme_gray, theme
  plot_scatterplot.Rd: geom_point, geom_jitter, scale_x_continuous,
    scale_y_continuous, theme_gray, theme
  plot_str.Rd: diagonalNetwork, radialNetwork
  set_missing.Rd: data.table
  split_columns.Rd: data.table
  update_columns.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘DataGraph/libs/DataGraph.so’:
  Found non-API call to R: ‘Rf_isFrame’

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:
  ‘my new data set.rds’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dataone-defunct.Rd: getData, getIdentifier, getFormatId,
    setPublicAccess, canRead, addData
  setPublicAccess.Rd: DataObject-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) build_date_factor.Rd:15: Lost braces; missing escapes or markup?
    15 | Map a vector of dates to a factor at one of these levels {"yearmonth", "yearquarter", "quarter", "month"}
       |                                                          ^
checkRd: (-1) build_date_factor.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{type}{One of {"year", "yearquarter", "yearmonth", "quarter", "month"}}
       |                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  aggregate_by_key.Rd: data.table
  build_target_encoding.Rd: data.table
  fast_handle_na.Rd: copy, data.table
  generate_date_diffs.Rd: data.table
  set_col_as_character.Rd: data.table
  set_col_as_date.Rd: data.table
  set_col_as_factor.Rd: data.table
  set_col_as_numeric.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘drwho_directors.Rd’ ‘drwho_episodes.Rd’ ‘drwho_writers.Rd’
    ‘torchwood_directors.Rd’ ‘torchwood_episodes.Rd’
    ‘torchwood_writers.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dataStepClass.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘data.table/libs/data_table.so’:
  Found non-API calls to R: ‘LEVELS’, ‘OBJECT’, ‘Rf_GetOption’,
    ‘Rf_isFrame’, ‘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.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Node.Rd: R6Class
  as.Node.rpart.Rd: rpart, text.rpart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dbcsp-class.Rd: TSDatabaseDistances, parallelDist
  predict.dbcsp.Rd: predict.lda
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) plot.mleBb.Rd:48: Lost braces
    48 |   \ code{size} is extracted from argument \code{x}.
       |         ^
checkRd: (-1) value_missing_table.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) value_missing_table.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CI_mc.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{i}{the row index of the interest entry X_{i,j}}
       |                                                ^
checkRd: (-1) CI_mc.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{j}{the row index of the interest entry X_{i,j}}
       |                                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  arrange.tbl_lazy.Rd: arrange, show_query
  backend-hana.Rd: copy_to
  collapse.tbl_sql.Rd: collapse, compute, collect
  complete.tbl_lazy.Rd: show_query
  copy_inline.Rd: copy_to
  copy_to.src_sql.Rd: copy_to, show_query
  count.tbl_lazy.Rd: count, tally
  db-sql.Rd: copy_to
  dbplyr-slice.Rd: slice_min, slice_max, slice_sample
  distinct.tbl_lazy.Rd: distinct, show_query
  expand.tbl_lazy.Rd: show_query
  filter.tbl_lazy.Rd: show_query
  get_returned_rows.Rd: rows_insert, rows_append, rows_update,
    rows_upsert, rows_delete
  group_by.tbl_lazy.Rd: group_by
  head.tbl_lazy.Rd: show_query
  join.tbl_sql.Rd: join, show_query
  memdb_frame.Rd: !!, !!!, .data, .env
  mutate.tbl_lazy.Rd: mutate, transmute, show_query
  nycflights13.Rd: src_postgres
  pivot_wider.tbl_lazy.Rd: expand
  pull.tbl_sql.Rd: pull
  replace_na.tbl_lazy.Rd: show_query
  rows-db.Rd: rows_insert, rows_append, rows_update, rows_patch,
    rows_upsert, rows_delete, tbl, compute
  select.tbl_lazy.Rd: select, rename, relocate
  summarise.tbl_lazy.Rd: summarise, show_query
  tbl.src_dbi.Rd: compute, collect, show_query, explain, do
  win_over.Rd: group_by, arrange
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dbglm.Rd: daisy
  dblm.Rd: daisy
  dbplsr.Rd: plsr, daisy
  disttoD2.rd: daisy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) data.Rd:11: Lost braces
    11 | \doi{10.1007/s40258-021-00647-3}{DOI}
       |                                 ^
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dcoptions.Rd: gelman.diag
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) CalcStatClusterGivenCenter.Rd:36: Lost braces; missing escapes or markup?
    36 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) CalcStatClusterGivenCenter.Rd:37: Lost braces; missing escapes or markup?
    37 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) CalcStatsAllClusters.Rd:49: Lost braces; missing escapes or markup?
    49 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) CalcStatsAllClusters.Rd:50: Lost braces; missing escapes or markup?
    50 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) DetectClustersModel.Rd:60: Lost braces; missing escapes or markup?
    60 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) DetectClustersModel.Rd:61: Lost braces; missing escapes or markup?
    61 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) glmAndZIP.iscluster.Rd:34: Lost braces; missing escapes or markup?
    34 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) glmAndZIP.iscluster.Rd:35: Lost braces; missing escapes or markup?
    35 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CalcStatClusterGivenCenter.Rd: glmer
  CalcStatsAllClusters.Rd: glmer
  DetectClustersModel.Rd: glmer, SpatialPolygonsDataFrame, STFDF,
    SpatialPolygons
  glmAndZIP.iscluster.Rd: glmer
  knbinary.Rd: SpatialPolygonsDataFrame
  mergeknclusters.Rd: SpatialPolygonsDataFrame
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dcFit-class.Rd: bugs.fit
  gsFit-class.Rd: bugs.fit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) kernel.assign.Rd:27: Lost braces; missing escapes or markup?
    27 |  {q = [0, 1]}. Kernels are of the Müller-Wang type ("MW"), Müller type ("M")
       |  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dNTD.Rd: plotTensor3D
  dNTF.Rd: plotTensor3D
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CUR.Rd: pcor, spcor
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) detectAgeInterval.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Age}, or code{age}.}
       |                                                                              ^
checkRd: (-1) detectSex.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Sex}, or code{sex}.}
       |                                                                              ^
checkRd: (-1) ggbgetAgesFit.Rd:28: Lost braces
    28 | code{\link{ggbChooseAges}}
       |     ^
checkRd: (-1) plot.ddpcr_plate.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ddpcr_plate.Rd:138-139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ddpcr_plate.Rd:140-141: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_cashflow.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  declare_estimator.Rd: lm_robust, estimatr, glance
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  inst.ratio.Rd: pdfDisplay
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) deconv.Rd:85: Lost braces; missing escapes or markup?
    85 |     \code{tg}, std. error of \eqn{g}, \eqn{G} (the cdf of {g}),
       |                                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  recode.variables.Rd: recode
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  deepforest.Rd: rpart.control
  deeptree.Rd: rpart.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) deepNN-package.Rd:18: Lost braces
    18 | section{Dependencies}{
       |        ^
checkRd: (-1) deepNN-package.Rd:18-21: Lost braces
    18 | section{Dependencies}{
       |                      ^
checkRd: (-1) deepNN-package.Rd:23: Lost braces
    23 | section{Citation}{
       |        ^
checkRd: (-1) deepNN-package.Rd:23-25: Lost braces
    23 | section{Citation}{
       |                  ^
checkRd: (-1) deepNN-package.Rd:27-38: Lost braces
    27 | references{
       |           ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘deeptrafo.Rd’ ‘ensembles.R’ ‘methods.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:
    ‘defineOptions-package.Rd’ ‘define_option.Rd’ ‘parse_with_defs.Rd’
    ‘summary.parsed_result.Rd’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘api.R’ ‘category_blur.R’ ‘deident.R’
checkRd: (-1) deltaPlot.Rd:28: Lost braces
    28 |  \item{purify}{logical: should item purification be performed? (Default is code{FALSE}). See \bold{Details}.}
       |                                                                                ^
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘Caswell.R’
Found the following files/directories:
  ‘smd_table.docx’
checkRd: (-1) kin.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:53-61: Lost braces
    53 | {\itemize{
       | ^
checkRd: (-1) kin.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:59-67: Lost braces
    59 | {\itemize{
       | ^
checkRd: (-1) kin2sex.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sim.dpp.modal.fast.Rd: spam
  sim.dpp.modal.fast.seq.Rd: spam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) conifersIP.Rd:9: Lost braces; missing escapes or markup?
     9 | \code{conifersIP} {has following variables:}
       |                   ^
checkRd: (-1) conifersIP.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sync.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dendro.varcov.Rd: varFunc, varIdent, lmeObject
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
'library' or 'require' calls not declared from:
  ‘HSAUR2’ ‘Iyer517’ ‘PairViz’ ‘RColorBrewer’ ‘mvtnorm’ ‘scagnostics’
Missing dependency on R >= 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_slwer_to_tidy.R’ ‘download_pdfwer_srilanka.R’
    ‘get_pdflinks_srilanka.R’ ‘min_max.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  estim_sigma.Rd: estim_ncp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  density_polygons.Rd: sf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  start_bot_for_chat.Rd: telegram.bot
  use_ui.Rd: ui_line, ui_todo, ui_done, ui_oops, ui_info,
    ui_code_block, ui_stop, ui_warn, ui_yeah, ui_nope, ui_field,
    ui_value, ui_path, ui_code
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) responses.Rd:68: Lost braces
    68 |         response.  See code{\link{makeDepmix}} for an example of how to use
       |                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  depmix.fit.Rd: solnp
  response-classes.Rd: nnet
  vcov.Rd: nlme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.N’ ‘.Nmiss’ ‘.Q1’ ‘.Q3’ ‘.factorN’ ‘.factorNmiss’ ‘.factorQ1’
  ‘.factorQ3’ ‘.factormax’ ‘.factormean’ ‘.factormedian’ ‘.factormin’
  ‘.factorsd’ ‘.max’ ‘.mean’ ‘.median’ ‘.min’ ‘.sd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pander.desctable.Rd: pandoc.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘mod_template_srv.R’
'library' or 'require' call not declared from: ‘nlme’
checkRd: (-1) detour-shiny.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{expr}{an expression that generates a {detourr} widget}
       |                                            ^
checkRd: (-1) show_sage.Rd:80: Lost braces; missing escapes or markup?
    80 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
checkRd: (-1) show_scatter.Rd:67: Lost braces; missing escapes or markup?
    67 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
checkRd: (-1) show_scatter_internal.Rd:65: Lost braces; missing escapes or markup?
    65 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
checkRd: (-1) show_slice.Rd:76: Lost braces; missing escapes or markup?
    76 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
checkRd: (-1) tour_aes.Rd:11: Lost braces; missing escapes or markup?
    11 | Variables are evaluated using {tidyselect} syntax.}
       |                               ^
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DetLTS.Rd: h.alpha.n
  OGKCStep.Rd: h.alpha.n
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  check.Rd: compiler_flags
  remote-reexports.Rd: ellipsis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘aov.R’ ‘create_subtree.R’ ‘create_tree.R’ ‘monte_carlo.R’ ‘node.R’
    ‘oat.R’ ‘option.R’ ‘sensitivity_index.R’ ‘synoptique.R’ ‘tree.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:
    ‘differentiate.R’ ‘gradient.R’ ‘simplify.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MA_estimates.Rd: glmer, lmerControl, glmerControl
  REMB-class.Rd: glmer
  glimem.Rd: glmer, lmerControl, glmerControl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) runContrasts.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:82: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘dggridR.R’
checkRd: (-1) AIC.dglars.Rd:47: Lost braces
    47 | \item{comp}{the measures of model complexity used to compute the measure of goodness-of-fit. It is equal to \code{npar} when code{complexity = "df"};}
       |                                                                                                                                  ^
checkRd: (-1) dglars.Rd:258: Lost braces
   258 |                 \item{\code{7}}{maximum number of solution points ('code{np}') reached.}
       |                                                                         ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) dHSIC-package.Rd:32: Lost braces
    32 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dHSIC-package.Rd:36: Lost braces
    36 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dHSIC-package.Rd:36: Lost braces
    36 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
checkRd: (-1) dhsic.Rd:84: Lost braces
    84 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dhsic.Rd:88: Lost braces
    88 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dhsic.Rd:88: Lost braces
    88 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
checkRd: (-1) dhsic.test.Rd:124: Lost braces
   124 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dhsic.test.Rd:128: Lost braces
   128 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dhsic.test.Rd:128: Lost braces
   128 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  class_to_regL1.Rd: rq
  class_to_rq.Rd: rq
  forwardSearch_regL1.Rd: lmsreg, rq, rq.fit.br, rq.fit.fnb
  regL1.Rd: rq, rq.fit.br, rq.fit.fnb
  regL1_het.Rd: rq, rq.fit.br, rq.fit.fnb
  summary.regL1.Rd: summary.rq, boot.rq
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘diario.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  max_qEI.Rd: genoud
  qEGO.nsteps.Rd: genoud
  sampleFromEI.Rd: km
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) DIconvex.Rd:40: Lost braces; missing escapes or markup?
    40 |  {Paul Schneider <paul.schneider@usi.ch>}{}
       |  ^
checkRd: (-1) define.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) did_imputation.Rd:74: Lost braces; missing escapes or markup?
    74 | form average treatment effects for groups of {it}.
       |                                              ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘diem.r’ ‘internal.r’ ‘rank2map.r’ ‘vcf2diem.r’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  diffChr.Rd: style, num_colors
  diffCsv.Rd: style, num_colors
  diffDeparse.Rd: style, num_colors
  diffFile.Rd: style, num_colors
  diffPrint.Rd: style, num_colors
  diffStr.Rd: style, num_colors
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) sensitivitySamplerManual-DPMech-function-numeric-numeric-numeric-method.Rd:25: Lost braces
    25 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
checkRd: (-1) sensitivitySamplerManual-DPMechNumeric-function-numeric-numeric-numeric-method.Rd:25: Lost braces
    25 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
checkRd: (-1) sensitivitySamplerManual.Rd:22: Lost braces
    22 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
checkRd: (-1) simulate_diff_tables.Rd:72: Lost braces; missing escapes or markup?
    72 |   {The Sharma-Song test} {\code{\link[DiffXTables]{sharma.song.test}}}
       |   ^
checkRd: (-1) simulate_diff_tables.Rd:74: Lost braces; missing escapes or markup?
    74 |   {The comparative chi-squared test} {\code{\link[DiffXTables]{cp.chisq.test}}}
       |   ^
checkRd: (-1) simulate_diff_tables.Rd:76: Lost braces; missing escapes or markup?
    76 |   {The heterogeneity test} {\code{\link[DiffXTables]{heterogeneity.test}}}
       |   ^
checkRd: (-1) difTID.Rd:185: Lost braces
   185 |  \code{\link[deltaPlotR]{deltaPlot}}, code{\link[deltaPlotR]{diagPlot}}, \code{\link{dichoDif}}
       |                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  itemPar1PL.rd: rasch
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'::' or ':::' import not declared from: ‘rbenchmark’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘dilp_functions.R’
checkRd: (-1) DIME.Rd:272: Lost braces; missing escapes or markup?
   272 | \item{name}{the name of the model {"GNG", "iNUDGE","NUDGE"} where
       |                                   ^
Specified C++11: please drop specification unless essential
File ‘dipsaus/libs/dipsaus.so’:
  Found non-API calls to R: ‘CLOENV’, ‘ENCLOS’

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:
  DirichletRegModel.Rd: update.Formula
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  expectreg.aft.Rd: rb, cdf.qp, cdf.bundle, summary.expectreg,
    plot.expectreg, predict.expectreg, resid.expectreg,
    fitted.expectreg, effects.expectreg
  modreg.Rd: control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nelsonaalen_npdf.Rd: survfit
  npdf_cox.Rd: Surv
  plot.npdf.Rd: survfit.formula, plot.survfit
  survfit_npdf.Rd: survfit.formula
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  discrim-package.Rd: discrim_flexible
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) mc_attitudes.Rd:52: Lost braces
    52 | P\'{a}ez, A. (2013). Mapping travelers’ attitudes: does space matter?. Journal of Transport Geography, 26, 117-125. (https://doi.org/10.1016/j.jtrangeo.2012.09.002)
       |    ^
checkRd: (-1) mc_commute.csv.Rd:49: Lost braces
    49 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
checkRd: (-1) mc_commute_long.Rd:74: Lost braces
    74 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
checkRd: (-1) mc_commute_wide.Rd:87: Lost braces
    87 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
checkRd: (-1) mc_modality.Rd:50: Lost braces
    50 | Lavery, T., P\'{a}ez, A., & Kanaroglou, P.S. (2013). Driving out of choices: An investigation of transport modality in a university sample. Transportation Research Part A: Policy and Practice, 57:37-46 (https://doi.org/10.1016/j.tra.2013.09.010)
       |                ^
checkRd: (-1) cIndex.Rd:32: Lost braces; missing escapes or markup?
    32 | [a_{q-1}, a_q) are available.
       |    ^
checkRd: (-1) cIndexCompRisks.Rd:31: Lost braces; missing escapes or markup?
    31 | [a_{q-1}, a_q) are available.
       |    ^
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
checkRd: (-1) estMargProb.Rd:23: Lost braces; missing escapes or markup?
    23 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) estMargProbCompRisks.Rd:24: Lost braces; missing escapes or markup?
    24 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) estSurv.Rd:23: Lost braces; missing escapes or markup?
    23 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) estSurvCompRisks.Rd:24: Lost braces; missing escapes or markup?
    24 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) lifeTable.Rd:21: Lost braces; missing escapes or markup?
    21 | [a_0, a_1), [a_1, a_2), ..., [a_{q-1}, a_q) ("character vector")}
       |                                 ^
checkRd: (-1) csv_to_disk.frame.Rd:56: Lost braces; missing escapes or markup?
    56 | strings, and you are encouraged to use {fasttime} to convert the strings to
       |                                        ^
checkRd: (-1) purrr_as_mapper.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{.f}{a normal function or purrr syntax function i.e. `~{ ...code...}`}
       |                                                             ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘dht2.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DistatisR-package.Rd: prettyGraphs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘distcomp/libs/distcomp.so’:
  Found non-API call to R: ‘NAMED’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Running ‘testthat.R’ [233s/149s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(distillML)
  > packageVersion("distillML")
  [1] '0.1.0.13'
  > 
  > test_check("distillML")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 83 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-predictor.R:57:3'): Tests that the predictor wrapper is working ──
  Error in ``[.data.frame`(wrapped_preds, , 1)`: undefined columns selected
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-predictor.R:57:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─base::all.equal(wrapped_preds[, 1], standard_preds, tolerance = 1e-04)
   5. ├─wrapped_preds[, 1]
   6. └─base::`[.data.frame`(wrapped_preds, , 1)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 83 ]
  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:
    ‘dev_package.R’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) dapply.Rd:27-30: Lost braces
    27 | udf <- function(x){
       |                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dists.Rd: betareg
  moments.Rd: betareg, gamlss, bamlss
  plot_dist.Rd: gamlss, bamlss, betareg, ggplot2
  plot_moments.Rd: gamlss, bamlss, betareg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘mixture.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dmrcoef-class.Rd: dgCMatrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mock-db-methods.Rd: dbConnect, dbListFields, dbWriteTable,
    dbRemoveTable, dbGetInfo, dbQuoteIdentifier
  mockdb.Rd: dbConnect
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cr.Rd: smooth.construct.cr.smooth.spec
  ps.Rd: smooth.construct.ps.smooth.spec
  smooth.construct.cb.smooth.spec.Rd: smooth.construct.ps.smooth.spec,
    smooth.construct.cr.smooth.spec,
    smooth.construct.tensor.smooth.spec
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  compare_category.data.frame.Rd: tbl_df
  compare_numeric.data.frame.Rd: tbl_df
  correlate.data.frame.Rd: grouped_df
  describe.data.frame.Rd: tbl_df, grouped_df, group_by
  describe.tbl_dbi.Rd: group_by
  diagnose.data.frame.Rd: tbl_df, grouped_df
  diagnose_category.data.frame.Rd: tbl_df, grouped_df
  diagnose_numeric.data.frame.Rd: tbl_df, grouped_df
  diagnose_outlier.data.frame.Rd: tbl_df, grouped_df
  diagnose_paged_report.data.frame.Rd: tbl_df
  diagnose_report.data.frame.Rd: tbl_df
  diagnose_sparese.data.frame.Rd: tbl_df
  diagnose_web_report.data.frame.Rd: tbl_df
  eda_paged_report.data.frame.Rd: tbl_df
  eda_report.data.frame.Rd: tbl_df
  eda_web_report.data.frame.Rd: tbl_df
  find_na.Rd: tbl_df
  find_outliers.Rd: tbl_df
  find_skewness.Rd: tbl_df
  imputate_na.Rd: tbl_df
  imputate_outlier.Rd: tbl_df
  normality.data.frame.Rd: tbl_df, group_by
  normality.tbl_dbi.Rd: group_by
  overview.Rd: tbl_df
  plot_bar_category.data.frame.Rd: tbl_df, grouped_df
  plot_box_numeric.data.frame.Rd: tbl_df, grouped_df
  plot_correlate.data.frame.Rd: tbl_df
  plot_hist_numeric.data.frame.Rd: tbl_df, grouped_df
  plot_normality.data.frame.Rd: tbl_df
  plot_outlier.data.frame.Rd: tbl_df
  plot_qq_numeric.data.frame.Rd: tbl_df, grouped_df
  target_by.data.frame.Rd: tbl_df, grouped_df
  target_by.tbl_dbi.Rd: grouped_df
  transformation_paged_report.Rd: tbl_df
  transformation_report.Rd: tbl_df
  transformation_web_report.Rd: tbl_df
  univar_category.data.frame.Rd: tbl_df
  univar_numeric.data.frame.Rd: tbl_df
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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(DLSSM)
  > 
  > test_check("DLSSM")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-DLSSM.R:19:3'): Input errors ───────────────────────────────────
  Error in `dimnames(x) <- dn`: length of 'dimnames' [2] not equal to array extent
  Backtrace:
      ▆
   1. ├─testthat::expect_error(...) at test-DLSSM.R:19:3
   2. │ └─testthat:::expect_condition_matching(...)
   3. │   └─testthat:::quasi_capture(...)
   4. │     ├─testthat (local) .capture(...)
   5. │     │ └─base::withCallingHandlers(...)
   6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   7. └─DLSSM::Batched(formula2, data2, time = "t", S = 10)
   8.   └─base::`colnames<-`(`*tmp*`, value = c(var_names, time))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ]
  Error: Test failures
  Execution halted
checkRd: (-1) dma.Rd:47: Lost braces; missing escapes or markup?
    47 | When y_t is controlled, only y_{t-delay-1} and before 
       |                                ^
checkRd: (-1) dma.Rd:64: Lost braces; missing escapes or markup?
    64 |                  estimate of theta_{j-1} for model k at t}
       |                                    ^
checkRd: (-1) dma.Rd:66: Lost braces; missing escapes or markup?
    66 |                  variance of theta_{j-1} for model k at t}
       |                                    ^
checkRd: (-1) dma.Rd:68: Lost braces; missing escapes or markup?
    68 |                  estimate of theta_{j-1} at t}
       |                                    ^
checkRd: (-1) dma.Rd:70: Lost braces; missing escapes or markup?
    70 |                  variance of thetahat_{j-1} at t}
       |                                       ^
checkRd: (-1) dca.Rd:24: Lost braces; missing escapes or markup?
    24 | \eqn{neglinks_{ij} = 1} means chunklet \code{i} and chunklet {j}
       |                                                              ^
checkRd: (-1) dca.Rd:26: Lost braces; missing escapes or markup?
    26 | \eqn{neglinks_{ij} = 0} means chunklet \code{i} and chunklet {j}
       |                                                              ^
checkRd: (-1) rca.Rd:57: Lost braces; missing escapes or markup?
    57 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |            ^
checkRd: (-1) rca.Rd:57: Lost braces; missing escapes or markup?
    57 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |                          ^
checkRd: (-1) scale_color_dMod.Rd:10: Lost braces
    10 | \item{...}{arguments goint to code{scale_color_manual()}}
       |                                   ^
checkRd: (-1) scale_fill_dMod.Rd:10: Lost braces
    10 | \item{...}{arguments goint to code{scale_color_manual()}}
       |                                   ^
checkRd: (-1) trust.Rd:103: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:104: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:107-108: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:109-110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:111-112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:113-114: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:115-122: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:123-126: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:127: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:128-131: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:132-133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:134-135: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:136-138: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:139-141: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EstimateDMQ.rd: DEoptim
  fn.DEoptim.Rd: DEoptim
  fn.solnp.Rd: solnp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' call not declared from: ‘tidyverse’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tractography.Rd: rgl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                 ^
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                             ^
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                                             ^
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                                                         ^
checkRd: (-1) outliers.ranking.Rd:143: Lost braces; missing escapes or markup?
   143 |   where g_{y,i} and g_{x,i} are the two groups involved in the merge at
       |           ^
checkRd: (-1) outliers.ranking.Rd:143: Lost braces; missing escapes or markup?
   143 |   where g_{y,i} and g_{x,i} are the two groups involved in the merge at
       |                       ^
checkRd: (-1) outliers.ranking.Rd:144: Lost braces; missing escapes or markup?
   144 |   step i, and g_{x,i} is the group which X belongs to. Note that if X
       |                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kNN.Rd: knn, knn1, knn.cv
  rpartXse.Rd: rpart, prune.rpart
  rt.prune.Rd: rpart, prune.rpart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) setCPT.O.Rd:85: Lost braces; missing escapes or markup?
    85 | statespace {0,1,2}, which this is *not* checked anywhere. Thus, if
       |            ^
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  deepAFT.Rd: survreg
  deepSurv.Rd: survreg
  dnn-package.Rd: coxph, survival
  print.Rd: survreg
  survfit.deepAFT.Rd: survfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
checkRd: (-1) beetle.Rd:13: Lost braces; missing escapes or markup?
    13 |     \item{\code{x}}{dose (log base 10 CS2mgl^{-1})}
       |                                              ^
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  to_miniature.Rd: image_border, pdf_convert, image_read
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  checks.Rd: rcmdcheck
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  corrPlot.Rd: levelplot
  fac.design.Rd: factorize
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  functionsFromDoEbase.Rd: DoE.base
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) rsmformula.Rd:96: Lost braces
    96 |       URL{http://www.jstatsoft.org/v32/i07/}.
       |          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rsmformula.Rd: rsm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bootAverageDominanceAnalysis.Rd: boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) py_select_interpreter.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Tell {reticulate} to use Python Conda version available on Domino Data Lab.}
       |             ^
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
checkRd: (-1) redisWorker.Rd:56: Lost braces; missing escapes or markup?
    56 | You can increase it by including a {timeout=n} argument value.
       |                                    ^
checkRd: (-1) startLocalWorkers.Rd:54: Lost braces; missing escapes or markup?
    54 | You can increase it by including a {timeout=n} argument value.
       |                                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  redisDelete.Rd: hiredis
  redisGet.Rd: hiredis
  redisSet.Rd: hiredis
  registerDoRedis.Rd: foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New features
Found the following calls to attach():
File ‘doSNOW/R/doSNOW.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dosresmeta-package.Rd: mvmeta, mvmeta-package, mvmeta.fit, blup
  dosresmeta.Rd: mvmeta.fit, mvmeta
  dosresmeta.control.Rd: mvmeta.control
  dosresmetaObject.Rd: mvmetaObject
  mlprof.fun.Rd: mvmeta.control, mvmeta.fit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
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:
    ‘dwplot.R’
checkRd: (-1) downscale.Rd:9: Lost braces; missing escapes or markup?
     9 | \item{occupancies}{Either a data frame containing two columns or an object of class \code{"upgrain"} from the \code{\link{upgrain}} function. If using a data frame the first column must be the grain sizes (cell area in squared units e.g. km^{2}). The second column is the proportion of occupancies at each grain size.}
       |                                                                                                                                                                                                                                                  ^
checkRd: (-1) ensemble.downscale.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
checkRd: (-1) hui.downscale.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{new.areas}{vector of grain sizes as cell area (in same units as cell.width but squared e.g. km^{2}) at fine scales for model prediction.}
       |                                                                                                      ^
checkRd: (-1) predict.downscale.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  downscale.Rd: mpfr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘dpkg_release_gh.R’ ‘read_dpkg.Rd’ ‘stow.R’ ‘stow.Rd’
File ‘dplyr/libs/dplyr.so’:
  Found non-API calls to R: ‘LEVELS’, ‘OBJECT’, ‘PRVALUE’,
    ‘R_shallow_duplicate_attr’, ‘Rf_allocSExp’, ‘SET_PRCODE’,
    ‘SET_PRENV’, ‘SET_PRVALUE’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  datapackage_init.Rd: toJSON, export
  datapackage_install.Rd: import
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' call not declared from: ‘devtools’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘expm1x.Rd’ ‘pnt.Rd’ ‘pt_Witkovsky_Tab1.Rd’
checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gompertz.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) hatvalues.drc.Rd:43: Lost braces
    43 |   emph{Generalized Linear Models}, 
       |       ^
checkRd: (-1) hatvalues.drc.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) llogistic.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) modelFit.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) weibull1.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) excalibur.Rd:18: Lost braces; missing escapes or markup?
    18 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
checkRd: (-1) festuca.Rd:16: Lost braces; missing escapes or markup?
    16 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ED.drcte.Rd: drm
  drmte.Rd: LL.4, LL.5, W1.4, getMeanFunctions, drmc
  drmteControl.Rd: drm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) generate_individual_graphs.Rd:11: Lost braces
    11 | code{\link[DrDimont]{compute_correlation_matrices}}}
       |     ^
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.drf.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:44: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  findRoots.Rd: nleqslv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘goodmap.R’ ‘traits.R’
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) popsize.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dr.weights.Rd: cov.rob
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘dscore.R’ ‘get_age_equivalent.R’
File ‘dsdp/libs/dsdp.so’:
  Found non-API call to R: ‘Rf_allocSExp’

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:
    ‘mice_weights.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘QeFairHelpers.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DSLiteConnection-class.Rd: DSConnection-class
  DSLiteDriver-class.Rd: DSDriver-class
  DSLiteResult-class.Rd: DSResult-class
  getDSLiteData.Rd: DSConnection-class
  setupCNSIMTest.Rd: datashield.login
  setupDASIMTest.Rd: datashield.login
  setupDATASETTest.Rd: datashield.login
  setupDISCORDANTTest.Rd: datashield.login
  setupDSLiteServer.Rd: datashield.login
  setupSURVIVALTest.Rd: datashield.login
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) dsm_varprop.Rd:67: Lost braces
    67 | parameter uncertainty. See Wood, Pya & S{\"a}fken (2016) for more
       |                                         ^
checkRd: (-1) dsm_varprop.Rd:100: Lost braces
   100 | Wood, S.N., Pya, N. and S{\"a}fken, B. (2016) Smoothing parameter and model
       |                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  check.cols.Rd: mrds
  dsm.cor.Rd: residuals.gam
  dsm_cor.Rd: residuals.gam
  dsm_varprop.Rd: gamObject
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  OpalConnection-class.Rd: DSConnection-class
  OpalDriver-class.Rd: DSDriver-class
  OpalResult-class.Rd: DSResult-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘v_fmt_to_type.R’
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Onoue.Friberg.Rd: pomp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) DTDAcif.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) efron.petrosian.Rd:22: Lost braces
    22 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
checkRd: (-1) lynden.Rd:21: Lost braces
    21 |    \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                                ^
checkRd: (-1) shen.Rd:24: Lost braces
    24 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
Specified C++11: please drop specification unless essential
checkRd: (-1) applied_crm.Rd:64: Lost braces; missing escapes or markup?
    64 | The empiric model is specified as F(d, beta) = d^{exp(beta)}. The logistic model is
       |                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  arrange.dtplyr_step.Rd: arrange
  count.dtplyr_step.Rd: count
  distinct.dtplyr_step.Rd: distinct
  filter.dtplyr_step.Rd: arrange
  group_by.dtplyr_step.Rd: group_by, ungroup
  group_modify.dtplyr_step.Rd: group_map, group_modify
  intersect.dtplyr_step.Rd: union_all
  lazy_dt.Rd: collect, pull, select
  left_join.dtplyr_step.Rd: left_join, right_join, inner_join,
    full_join, anti_join, semi_join
  mutate.dtplyr_step.Rd: mutate
  relocate.dtplyr_step.Rd: relocate
  rename.dtplyr_step.Rd: rename, rename_with
  select.dtplyr_step.Rd: select
  slice.dtplyr_step.Rd: slice
  summarise.dtplyr_step.Rd: summarise
  transmute.dtplyr_step.Rd: transmute
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Mena.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:19: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dataTableOutput.Rd: shinyWidgetOutput
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘Ahat.R’ ‘DTRreg.R’ ‘DWsurv.R’ ‘dtrProcedure.R’ ‘gest.R’
    ‘inputProcessing.R’ ‘interactive.R’ ‘treatmentClasses.R’ ‘utils.R’
    ‘varest.R’
checkRd: (-1) DTWUMI_1gap_imputation.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTWUMI_1gap_imputation.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTWUMI_1gap_imputation.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTWUMI_1gap_imputation.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTWUMI_1gap_imputation.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘scale_duke_color_discrete.Rd’ ‘scale_duke_fill_discrete.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DurgaPlot.Rd: RColorBrewer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
No news entries found.
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:
    ‘utils.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cfaHB.Rd: lavaan, cfa, model.syntax
  cfaOne.Rd: lavaan, cfa, model.syntax
  equivTest.Rd: lavaan
  exactFit.Rd: lavaan, cfa, model.syntax
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) dyadic_similarity.Rd:27: Lost braces; missing escapes or markup?
    27 |      For example, the order {a, b, c} implies that a > b, a  > c, and b > c.
       |                             ^
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘simulateRTConf.Rd’
checkRd: (-1) generate_kinetics.Rd:57: Lost braces; missing escapes or markup?
    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                          ^
checkRd: (-1) generate_kinetics.Rd:57: Lost braces; missing escapes or markup?
    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                                                     ^
checkRd: (-1) new_log_level.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{log_style}{is a {crayon::style()} that will colorize
       |                       ^
checkRd: (-1) new_log_level.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{msg_style}{is a {crayon::style()} style that will gray scale the
       |                       ^
checkRd: (-1) sys_context.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{"sysname"} : {The operating system name.}
       |                    ^
checkRd: (-1) sys_context.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{"release"} : {The OS release.}
       |                    ^
checkRd: (-1) sys_context.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{"version"} : {The OS version.}
       |                    ^
checkRd: (-1) sys_context.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{"nodename"} : {A name by which the machine is known on the network (if any).}
       |                     ^
checkRd: (-1) sys_context.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{"machine"} : {A concise description of the hardware, often the CPU type.}
       |                    ^
checkRd: (-1) sys_context.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{"login"} : {The user's login name, or "unknown" if it cannot be ascertained.}
       |                  ^
checkRd: (-1) sys_context.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{"user"} : {The name of the real user ID, or "unknown" if it cannot be ascertained.}
       |                 ^
checkRd: (-1) sys_context.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{"r-ver"} : {R Version in (major).(minor) format.}
       |                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  new_fmt_layout.Rd: crayon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Produc.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dynr.cook.Rd: autoplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) dynsim.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:57-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dynsimGG.Rd: scale_colour_brewer, discrete_scale
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mapdf.Rd: map
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘getConstraintTests.R’ ‘getInvarCompTable.R’ ‘outputConstraintTab.R’
    ‘outputInvarCompTab.R’
Specified C++11: please drop specification unless essential
checkRd: (-1) monitor_long_1d.Rd:33: Lost braces
    33 | If \code{side="upward"}{apply control charts that aim to detect upward shifts.} \cr
       |                        ^
checkRd: (-1) monitor_long_1d.Rd:34: Lost braces
    34 | If \code{side="downward"}{apply control charts that aim to detect downward shifts.} \cr
       |                          ^
checkRd: (-1) monitor_long_1d.Rd:35: Lost braces
    35 | If \code{side="both"}{apply control charts that aim to detect shifts in both sides}}
       |                      ^
checkRd: (-1) monitor_long_1d.Rd:38: Lost braces
    38 | If \code{chart="CUSUM"}{apply CUSUM charts.} \cr
       |                        ^
checkRd: (-1) monitor_long_1d.Rd:39: Lost braces
    39 | If \code{chart="EWMA"}{apply EWMA charts.}}
       |                       ^
checkRd: (-1) AM.Rd:95-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:99-102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:123-125: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:126-133: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:134-135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:163-165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:166-173: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:174-176: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:177-178: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:179-180: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:55-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:75: Lost braces; missing escapes or markup?
    75 | From the initial values, \code{B0} and {S0}, \code{\link{MHLS}} draws \code{beta} and \code{subgrad} samples.
       |                                        ^
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
    34 | if (require(incidence)) {
       |                         ^
checkRd: (-1) surrogates_ews.Rd:31: Lost braces
    31 | \item{span}{parameter that controls the degree of smoothing (numeric between 0 and 100, Default 25). see more on loess{stats}}
       |                                                                                                                       ^
checkRd: (-1) surrogates_ews.Rd:33: Lost braces
    33 | \item{degree}{the degree of polynomial to be used for when loess fitting is applied, normally 1 or 2 (Default). see more on loess{stats}}
       |                                                                                                                                  ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘edl_set_token.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:
    ‘plottingfunctions.bgms.R’ ‘plottingfunctions.easybgm.R’
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’
'library' or 'require' call not declared from: ‘lavaan’
checkRd: (-1) ArrayToNc.Rd:30-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ArrayToNc.Rd:39-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ArrayToNc.Rd:51-76: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  boot.Rd: paircomp
  envirosound.Rd: paircomp
  soundquality.Rd: paircomp
  winetaste.Rd: paircomp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ebase_plot.R’ ‘ebase_prep.R’
checkRd: (-1) OCC1950.Rd:64: Lost braces
    64 |     \doi{10.18128/D010.V10.0}{IPUMS USA: Version 10.0 [dataset]. Minneapolis, MN: IPUMS}. 
       |                              ^
checkRd: (-1) Oil.Rd:45: Lost braces
    45 |       code{pt-pt-1} on a constant
       |           ^
checkRd: (-1) breaches.Rd:70-74: Lost braces
    70 |     \code{breach_end}{
       |                      ^
checkRd: (-1) breaches.Rd:75-78: Lost braces
    75 |     \code{year}{
       |                ^
checkRd: (-1) nuclearWeaponStates.Rd:82-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:93-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:104-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:128-140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:141-150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:151-161: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:162-172: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:173-191: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:192-219: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  USFinanceIndustry.Rd: readNIPA
  USstateAbbreviations.Rd: readUSstateAbbreviations,
    grepNonStandardCharacters, subNonStandardCharacters
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) e_pictorial.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) e_pictorial.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nesting.Rd:48: Lost braces
    48 | `{itemStyle: {color: 'red', fontBold: 'bold'}}`.
       |  ^
checkRd: (-1) nesting.Rd:48: Lost braces; missing escapes or markup?
    48 | `{itemStyle: {color: 'red', fontBold: 'bold'}}`.
       |              ^
checkRd: (-1) nesting.Rd:51: Lost braces; missing escapes or markup?
    51 | `{symbolSize: 4}`.
       |  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  echartsNJSON.Rd: jsonlite
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ecipex.Rd: count.elements
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cgr.Rd: glasso
  plot.cgr.Rd: gplot
  stackedsdm.Rd: mvabund
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ecolRxC.Rd:161-166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:167-175: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:176-178: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:179-185: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:186-192: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:193-201: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:202-208: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:209-216: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:217-221: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calcres.Rd: ode
  ecosim-package.Rd: calc.stoich.coef, ode
  process-class.Rd: calc.stoich.coef
  system-class.Rd: ode
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘ECOSolveR/libs/ECOSolveR.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects: ‘ecos/libecos.a’, ‘ecos/libecos_bb.a’
  Found ‘putchar’, possibly from ‘putchar’ (C)
    Objects: ‘ecos/libecos.a’, ‘ecos/libecos_bb.a’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Objects: ‘ecos/libecos.a’, ‘ecos/libecos_bb.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  glenan.Rd: envelope
  glomel.Rd: envelope
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coef.ecpc.Rd: Surv
  cv.ecpc.Rd: Surv
  ecpc.Rd: Surv
  postSelect.Rd: Surv
  predict.ecpc.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) transformFitness.Rd:25: Lost braces; missing escapes or markup?
    25 | minimization (most others). This function computes a factor from {-1, 1} for
       |                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  filter_case_condition.Rd: dplyr_data_masking
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) read.edf.Rd:30: Lost braces
    30 | Kemp B., V\"{a}rri, A., Rosa, A.C., Nielsen, K.D. and Gade, J. (1992).
       |             ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO:
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘indicator_volunteers.R’
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  eval_posterior_eDITH.Rd: aggregate_river
  posterior_pred_sim_eDITH.Rd: aggregate_river, DHARMa
  run_eDITH_BT.Rd: aggregate_river, river_to_AEM, runMCMC,
    createBayesianSetup, dtrunc, MAP, getCredibleIntervals,
    gelmanDiagnostics
  run_eDITH_BT_joint.Rd: aggregate_river, river_to_AEM, runMCMC,
    createBayesianSetup, dtrunc, MAP, getCredibleIntervals,
    gelmanDiagnostics
  run_eDITH_optim.Rd: aggregate_river, river_to_AEM
  run_eDITH_optim_joint.Rd: aggregate_river, river_to_AEM
  run_eDITH_single.Rd: aggregate_river
  sampling_strategy_direct.Rd: aggregate_river
  sampling_strategy_eDNA.Rd: paths_river
  wigger.Rd: extract_river
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.lp.mip.Rd: make.lp
  editrules.plotting.Rd: as.igraph
  editrules_package.Rd: as.igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  USData.Rd: xts
  USRecessions.Rd: zoo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  crosstabplot.Rd: mosaic
  gelmansim.Rd: sim
  moves_calc.Rd: data.table
  profpoly.Rd: geom_polygon
  profpoly.data.Rd: geom_polygon
  theme_dpi.Rd: theme_bw
  theme_dpi_map.Rd: theme_bw
  theme_dpi_map2.Rd: theme_bw
  theme_dpi_mapPNG.Rd: theme_bw
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) eesim.Rd:148-151: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) eesim.Rd:152-155: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) eesim.Rd:156-158: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EESPCACV.Rd: PMA
  RifleInit.Rd: rifle
  RiflePCACV.Rd: rifle, PMA
  TpowerPCACV.Rd: PMA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  regex.search.Rd: read.fasta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  effCoef.Rd: get_parameters
  effect.Rd: gls, multinom, polr, lmer, glmer, svyglm, xyplot,
    densityplot, barchart
  effectsTheme.Rd: trellis.device, trellis.par.set
  plot.effect.Rd: sequential_hcl, lattice, xyplot, densityplot,
    print.trellis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  acor.Rd: zoo
  egcm-package.Rd: adf.test, pp.test
  egcm.Rd: zoo, rlm, adf.test, pp.test
  egcm.set.default.i1test.Rd: adf.test, pp.test
  pgff.test.Rd: adf.test
  ur_power.Rd: adf.test, pp.test
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotCounts.Rd: xyplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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:
    ‘ggm.R’ ‘wfdb-structures.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:
    ‘clustered.graphs.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as_tibble.egor.Rd: tbl_svy, as_tibble, as_survey
  egor.Rd: as_tibble, tibble, tbl_svy
  rowlist.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotFluxHistBoot.Rd: printFluxUnitCheatSheet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  join_vars_to_ontol.Rd: tidygraph
  metavariable_agg.Rd: tidygraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘backfile.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:
    ‘directory.R’ ‘facets.R’ ‘metadata.R’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) fit_mean.Rd:54: Lost braces
    54 | \code{t_optims}{optimal parametrizations}
       |                ^
checkRd: (-1) fit_mean.Rd:55: Lost braces
    55 | \code{G_optims}{optimal rotations}
       |                ^
checkRd: (-1) fit_mean.Rd:56: Lost braces
    56 | \code{b_optims}{optimal scalings}
       |                ^
checkRd: (-1) fit_mean.Rd:57: Lost braces
    57 | \code{n_optims}{optimal re-normalization}
       |                ^
checkRd: (-1) fit_mean.Rd:58: Lost braces
    58 | \code{n_iter}{number of iterations until convergence}
       |              ^
checkRd: (-1) docs_delete_by_query.Rd:47: Lost braces; missing escapes or markup?
    47 | as a document at .tasks/task/${taskId}. This is yours to keep or remove
       |                               ^
checkRd: (-1) docs_update_by_query.Rd:48: Lost braces; missing escapes or markup?
    48 | as a document at .tasks/task/${taskId}. This is yours to keep or remove
       |                               ^
checkRd: (-1) AuditErrors.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) compute.audit.errors.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) compute.stark.t.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) find.q.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) find.q.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) stark.test.Rd:50: Escaped LaTeX specials: \$
checkRd: (-1) stark.test.Rd:101: Escaped LaTeX specials: \$ \$
checkRd: (-1) tri.audit.sim.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) tri.calc.sample.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) tri.sample.Rd:34: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) weight.function.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) electData.Rd:16: Lost braces; missing escapes or markup?
    16 | Variables: \code{id}  = {identification number},
       |                         ^
checkRd: (-1) electData.Rd:17: Lost braces; missing escapes or markup?
    17 | \code{state} = {state}, \code{age} = age in years on a shifted scale (current age minus 70),
       |                ^
checkRd: (-1) summary.elect.Rd:25: Lost braces; missing escapes or markup?
    25 |  TRUE for output on start-state totals e_{r.} (for \code{S}>0)
       |                                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_aws_terrain.Rd: st_crs
  get_elev_point.Rd: st_crs
  get_elev_raster.Rd: st_crs
  get_opentopo.Rd: st_crs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
File ‘ellipsis/libs/ellipsis.so’:
  Found non-API calls to R: ‘PRVALUE’, ‘Rf_findVarInFrame3’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) elliptic-package.Rd:92: Lost braces
    92 |     J. Kotus and M. Urb\'{a}nski 2003.  \emph{Hausdorff dimension and Hausdorff
       |                          ^
Specified C++11: please drop specification unless essential
checkRd: (-1) elo.run.Rd:80: Lost braces
    80 | \code{\link{score}}, \link{elo.run.helpers}{elo.run helpers}, \code{\link{elo.calc}},
       |                                            ^
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.
checkRd: (-1) NEWS.Rd:194: Lost braces; missing escapes or markup?
   194 |             \item added {d,r}betabinom
       |                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  apply2d.Rd: create_progress_bar
  curve3d.Rd: create_progress_bar
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  write.excel.Rd: openxlsx
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
License stub is invalid DCF.
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:
    ‘binary_method_functions.R’ ‘ordinal_method_functions.R’
    ‘utility_functions.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  em.prec.Rd: glassoFast
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hfit.Rd: maxLik
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) minimize.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:33: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  write_eml.Rd: write_xml
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) macacaModels.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) macacaModels.Rd:10-11: 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:
    ‘as.character.emphatic.Rd’ ‘as_emphatic.Rd’ ‘as_html.Rd’
    ‘as_latex.Rd’ ‘as_svg.Rd’ ‘as_svg_anim.Rd’ ‘as_svg_group.Rd’
    ‘as_typst.Rd’ ‘hl.Rd’ ‘hl_adjust.Rd’ ‘is_emphatic.Rd’
    ‘knit_print.emphatic.Rd’ ‘print.emphatic.Rd’ ‘show_html.Rd’
    ‘write_xlsx.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  empChurn.Rd: prediction
  empCreditScoring.Rd: prediction
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) em.Rd:25: Lost braces
    25 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.clogit.Rd:65: Lost braces
    65 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.default.Rd:65: Lost braces
    65 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.fitdist.Rd:49: Lost braces
    49 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.glmerMod.Rd:50: Lost braces
    50 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.panelmodel.Rd:49: Lost braces
    49 |  \code{terms} the code{terms} object used.
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_trackdata.Rd: wrasspOutputInfos, tibble
  query.Rd: tibble
  requery_hier.Rd: tibble
  requery_seq.Rd: tibble
  serve.Rd: stopAllServers, httpuv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) droso.Rd:8: Lost braces; missing escapes or markup?
     8 | The dataset contains 400 true donor sites, 400 false donor sites and 50 false sites as test set. Each sequence is of 40 nucleotides long. The conserved di-nucleotides GT are present at $21^{st}$ and $22^{nd}$ positions respectively.
       |                                                                                                                                                                                              ^
checkRd: (-1) droso.Rd:8: Lost braces; missing escapes or markup?
     8 | The dataset contains 400 true donor sites, 400 false donor sites and 50 false sites as test set. Each sequence is of 40 nucleotides long. The conserved di-nucleotides GT are present at $21^{st}$ and $22^{nd}$ positions respectively.
       |                                                                                                                                                                                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  APR.Feature.Rd: DNAStringSet
  Bayes.Feature.Rd: DNAStringSet
  Density.Feature.Rd: DNAStringSet
  MM1.Feature.Rd: DNAStringSet
  MM2.Feature.Rd: DNAStringSet
  MN.Fdtf.Feature.Rd: DNAStringSet
  Maldoss.Feature.Rd: DNAStringSet
  PN.Fdtf.Feature.Rd: DNAStringSet
  POS.Feature.Rd: DNAStringSet
  Predoss.Feature.Rd: DNAStringSet
  SAE.Feature.Rd: DNAStringSet
  Sparse.Feature.Rd: DNAStringSet
  Trint.Dist.Feature.Rd: DNAStringSet
  WAM.Feature.Rd: DNAStringSet
  WMM.Feature.Rd: DNAStringSet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  genkeys.Rd: openssl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘file.path(temp_dir, gp2.csv)’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  endoSwitch.Rd: maxLik
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) enetLTS-package.Rd:41: Lost braces; missing escapes or markup?
    41 |   \code{family="binomial"} should be a factor with two levels which is coded as \code{0} and {1}.
       |                                                                                              ^
Running examples in ‘enrichR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: listEnrichrDbs
> ### Title: Look up available databases on Enrichr
> ### Aliases: listEnrichrDbs
> 
> ### ** Examples
> 
> dbs <- listEnrichrDbs()
Error in (function (..., deparse.level = 1, make.row.names = TRUE, stringsAsFactors = FALSE,  : 
  numbers of columns of arguments do not match
Calls: listEnrichrDbs -> do.call -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘enrichR.Rmd’ using rmarkdown

Quitting from enrichR.Rmd:59-64 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! numbers of columns of arguments do not match
---
Backtrace:
    ▆
 1. └─enrichR::listEnrichrDbs()
 2.   ├─base::do.call(rbind.data.frame, dbs)
 3.   └─base (local) `<fn>`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'enrichR.Rmd' failed with diagnostics:
numbers of columns of arguments do not match
--- failed re-building ‘enrichR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) CTN.Rd:22: Lost braces; missing escapes or markup?
    22 | less memory. Genetic data consists of nucleotide data {A,T,C,G} and are usually saved
       |                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Regression.Integrator.PCR.SelMin.Config-class.Rd:
    Regression.Integrator.Config-class
  Regression.Integrator.PCR.SelMin.FitObj-class.Rd:
    Regression.Integrator.FitObj-class
  epcreg.Rd: Instance.List-class, Regression.CV.Batch.FitObj-class,
    Regression.Batch.FitObj-class
  epcreg.baselearner.control.Rd: rmse.error
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘HeatMap.R’
File ‘enviPat/libs/enviPat.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) metrics.Rd:124: Lost braces
   124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
       |                                  ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘network.Rd’ ‘types.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘dividends.R’ ‘financials.R’ ‘ipos.R’ ‘news.R’ ‘prices.R’ ‘splits.R’
Found the following files/directories:
  ‘Net1-fromR.inp’
checkRd: (-1) misClustRate.Rd:18: Lost braces; missing escapes or markup?
    18 | Compute the empirical MCR, assuming that #{cluster} = #{block},
       |                                           ^
checkRd: (-1) misClustRate.Rd:18: Lost braces; missing escapes or markup?
    18 | Compute the empirical MCR, assuming that #{cluster} = #{block},
       |                                                        ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘clean_admin_names.R’ ‘consistency_check.R’ ‘get_admin_names.R’
    ‘handle_outliers.R’ ‘missing_plot.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clean_admin_names.Rd: countrycode
  clean_names_strings.Rd: janitor
  consistency_check.Rd: ggplot2
  export.Rd: rio
  import.Rd: rio
  missing_plot.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
checkRd: (-1) estimate_R.Rd:59-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:64-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:70-72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:76-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:79-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:84-86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:48-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:56-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  estimate_R.Rd: incidence
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sub-.epiflows.Rd: [.epicontacts
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DiscreteCovariatesToOneHot.Rd: dplyr_tidy_select
  charlson_score.Rd: dplyr_data_masking
  flatten_date_intervals.Rd: dplyr_tidy_select, dplyr_data_masking
  lms.Rd: dplyr_data_masking
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.epictmcmc.Rd: mcmc, plot.mcmc
  summary.epictmcmc.Rd: mcmc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  epimcmc.Rd: MCMC, adaptMCMC
  plot.epimcmc.Rd: mcmc, plot.mcmc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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’ [3s/3s]
  Comparing ‘EpiILM.spatial.Rout’ to ‘EpiILM.spatial.Rout.save’ ... OK
checkRd: (-1) runSim.Rd:111: Lost braces
   111 | \ifelse{html}{\out{<i>r</i><sub>1</sub> = 1}}{{\eqn{r_1 = 1}}{r_1 = 1}} while the individual with the lowest phenotypic value
       |                                                              ^
checkRd: (-1) runSim.Rd:112: Lost braces
   112 | is given the rank \ifelse{html}{\out{<i>r<sub>n</sub></i> = <i>n</i>}}{{\eqn{r_n = n}}{r_n = n}}), the probability of an individual
       |                                                                                       ^
checkRd: (-1) runSim.Rd:120-122: Lost braces
   120 | }{
       |  ^
checkRd: (-1) getAgeGender.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAgeGender.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAgeGender.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAgeGender.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getMap.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getMap.Rd:46-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getMap.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTableByMS.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTableByMS.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTableByMS.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTrend.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTrend.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAgeGender.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAgeGender.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAgeGender.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTS12MAvg.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTS12MAvg.Rd:28: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getAgeGender.Rd: ggplot2, officer
  getMap.Rd: officer
  getSeason.Rd: ggplot2, officer
  getTableByMS.Rd: flextable, officer
  getTrend.Rd: ggplot2, officer
  plotAge.Rd: ggplot2
  plotAgeGender.Rd: ggplot2
  plotBar.Rd: ggplot2
  plotBarGrouped.Rd: ggplot2
  plotBarGroupedH.Rd: ggplot2
  plotBarH.Rd: ggplot2
  plotPie.Rd: ggplot2
  plotSeasonality.Rd: ggplot2
  plotTS.Rd: ggplot2
  plotTS12MAvg.Rd: ggplot2
  plotTSGrouped.Rd: ggplot2
  shapeECDCFlexTable.Rd: set_header_df, flextable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  boot.bias.Rd: boot
  plot.episensr.booted.Rd: boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fit_disc_gamma.Rd: distcrete
  gamma_tools.Rd: distcrete
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 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’ ‘functions-server.R’ ‘functions-ui.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Cmip6Dict.Rd: data.table
  summary_database.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  equiv.boot.Rd: boot
  equivalence.xyplot.Rd: xyplot
  rtost.Rd: yuen.t.test
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Tm.Rd:46-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:49-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:52-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:55-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:58-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:36-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:40-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:43-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:47-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:57-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:60-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:63-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:66-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:69-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:75-77: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘render_erd.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Binomial-ergmReference-cdff43a4.Rd: ergmTerm, ergmReference
  CMB-ergmTerm-5a51afe9.Rd: ergmTerm
  CMP-ergmTerm-4d501174.Rd: ergmTerm
  Disc-ergmProposal-b6c6e5ca.Rd: DiscUnif-ergmReference, ergmProposal
  DiscTNT-ergmProposal-c3c2e8cb.Rd: DiscUnif-ergmReference,
    ergmProposal, TNT-ergmProposal
  Geometric-ergmReference-1ee5c5ac.Rd: sum-ergmTerm, ergmReference
  Poisson-ergmReference-40df5ec8.Rd: ergmTerm, ergmReference
  ZIPoisson-ergmProposal-bba55a81.Rd: ergmProposal
  ergm.count-package.Rd: ergm-package, ergmReference, ergmTerm, ergm,
    control.ergm
  zach.Rd: network
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nvertex.Rd: network
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AlterSwap-ergmProposal-7e827ae4.Rd: ergmProposal
  CompleteOrder-ergmReference-f40141c3.Rd: ergmReference
  ergm.rank-package.Rd: ergm-package, ergm
  rankdeference-ergmTerm-73181c43.Rd: ergmTerm
  rankedgecov-ergmTerm-5905bc22.Rd: ergmTerm
  rankinconsistency-ergmTerm-b232ab56.Rd: network, ergmTerm
  ranknodeicov-ergmTerm-856bed59.Rd: ergmTerm
  ranknonconformity-ergmTerm-a4593778.Rd: ergmTerm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘erlang_c_app.R’
checkRd: (-1) ifa.Rd:16: Lost braces; missing escapes or markup?
    16 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then Sigma^{-1} 
       |                                                                         ^
checkRd: (-1) ifa.Rd:17: Lost braces; missing escapes or markup?
    17 | has the corresponding q-factor decomposition Sigma^{-1}=diag(phi)(I-theta theta')diag(phi), where theta is a mxq matrix and phi the vector of 
       |                                                    ^
checkRd: (-1) ifa.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{iSB}{m x q matrix (diag(Psi)+BB')^{-1}B.}
       |                                         ^
checkRd: (-1) isqrtfa.Rd:15: Lost braces; missing escapes or markup?
    15 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then the function returns a matrix Omega such that Sigma^{-1} = Omega Omega'. Equivalently,
       |                                                                                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  elastic.Rd: glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  errorist_init.Rd: searcher
  shims.Rd: searcher
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MipRules-class.Rd: validator
  errorlocate-package.Rd: validate
  errorlocation.Rd: values
  is_linear.Rd: validator
  replace_errors.Rd: validator
  translate_mip_lp.Rd: lp.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) enp.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enp.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evolat.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evolat.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psns.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psns.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘esem_cfa_syntax.R’
checkRd: (-1) festRidge.Rd:80: Lost braces; missing escapes or markup?
    80 | \item{XtXlamIinv}{explicit value of (X'X + diag(penalty))^{-1}.  Useful
       |                                                           ^
checkRd: (-1) USA_state_N.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) USA_state_N.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) confirmed.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) confirmed.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) death.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) death.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recovered.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recovered.Rd:11: Lost braces in \itemize; meant \describe ?
File ‘essentials/libs/essentials.so’:
  Found non-API calls to R: ‘IS_S4_OBJECT’, ‘OBJECT’, ‘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.
Specified C++11: please drop specification unless essential
checkRd: (-1) momento.central.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{orden}{Es un valor numérico que representa el orden del momento central (orden = {1,2,3,4,...})}
       |                                                                                        ^
checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) aic.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:64: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  W_sampler.Rd: R6Class
  beta_sampler.Rd: R6Class
  rho_sampler.Rd: R6Class
  sigma_sampler.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) integration.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) integration.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) integration.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) integration.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loess.options.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loess.options.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maxlogLreg.Rd:138: Lost braces; missing escapes or markup?
   138 | $j^{th}$ for all the observations.
       |    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  maxlogL.Rd: DEoptim
  maxlogLreg.Rd: DEoptim, DEoptim.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  simulate_background_earthquakes.Rd: etas
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  catalog.Rd: inside.owin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ETC-package.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ETC-package.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ETC-package.Rd:32: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dbWipe.Rd: DBIConnection-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) data_cls.Rd:24: Lost braces
    24 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability 0.10 for
       |                    ^
checkRd: (-1) data_cls.Rd:24: Lost braces
    24 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability 0.10 for
       |                            ^
checkRd: (-1) data_reg.Rd:21: Lost braces
    21 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability given by
       |                    ^
checkRd: (-1) data_reg.Rd:21: Lost braces
    21 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability given by
       |                            ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘elx_run_query.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  set_key.Rd: setkey
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) FuzzyCluster.Rd:15: Lost braces; missing escapes or markup?
    15 | A list of cluster labels and a R object of class "fcm {ppclust}"
       |                                                       ^
checkRd: (-1) pamCluster.Rd:15: Lost braces; missing escapes or markup?
    15 | A list of cluster labels and a R object of class "pam {cluster}"
       |                                                       ^
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
checkRd: (-1) colplot.Rd:52: Lost braces
    52 | \item{legend}{should a legend be added? Defaults to code{FALSE}}
       |                                                         ^
checkRd: (-1) colplot.Rd:56: Lost braces
    56 | \item{legend.pretty}{logical: should the legend values produced by \[base]{pretty}? Othewrwise they are exact. Defaults to \code{TRUE}}
       |                                                                           ^
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) glr.Rd:5: Lost braces
     5 |   Conducts a generalized likelihood ratio test testing whether {\eqn{\beta \in}  (-\code{c},\code{c})}. Covariates can be accommodated.
       |                                                                ^
checkRd: (-1) glr.Rd:34: Lost braces
    34 |   This is a similar function to the main function \code{evian}. Instead of testing H0: \eqn{\beta}=0, it tests for whether H0:{\eqn{\beta \in} (-\code{c},\code{c})}.
       |                                                                                                                               ^
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
'library' or 'require' call not declared from: ‘ggplot2’
checkRd: (-1) fmgammagpd.Rd:183: Lost braces; missing escapes or markup?
   183 |  \item {nlumgammagpd} and {proflumgammagpd} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], sigmau, xi)}
       |                           ^
checkRd: (-1) fmgammagpdcon.Rd:181: Lost braces; missing escapes or markup?
   181 |  \item {nlumgammagpdcon} and {proflumgammagpdcon} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], xi)}
       |                              ^
checkRd: (-1) kernels.Rd:87: Lost braces
    87 | code{\link[evmix:kernels]{kd*}}  and \code{\link[evmix:kernels]{kp*}} give the
       |     ^
Found the following files/directories:
  ‘sample .nwk’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MantelCor.Rd: mantel
  MantelModTest.Rd: mantel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Almer.Rd: lme4, lmer, merMod
  Almer_SE.Rd: lmer, merMod
  Almer_sim.Rd: simulate.merMod
  rate_gls.Rd: phylo
  simulate_rate.Rd: phylo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ShapeDist.Rd:18: Lost braces; missing escapes or markup?
    18 | Procrustes distance provides a measure of coincidence of two point sets {xi} and {yi}, i=1..N. For this purpose the variance of point deviations is calculated at the optimal superposition of the sets. It allows to characterize the shape proximity of a given simplex to shape of a reference one.
       |                                                                         ^
checkRd: (-1) ShapeDist.Rd:18: Lost braces; missing escapes or markup?
    18 | Procrustes distance provides a measure of coincidence of two point sets {xi} and {yi}, i=1..N. For this purpose the variance of point deviations is calculated at the optimal superposition of the sets. It allows to characterize the shape proximity of a given simplex to shape of a reference one.
       |                                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clockrate_dens_plot.Rd: facet_wrap, geom_density
  clockrate_reg_plot.Rd: geom_smooth, geom_point
  plot_treerates_sgn.Rd: scale_color_steps2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) stop_rule.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stop_rule.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stop_rule.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stop_rule.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  power2x2.Rd: uniroot.integer, ss.nonadh
  unirootGrid.Rd: uniroot.integer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  powerBinom.Rd: uniroot.integer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++14: please drop specification unless essential
File ‘excursions/libs/excursions.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Object: ‘CAMD.a’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘CAMD.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:42: Lost braces
    42 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
checkRd: (-1) ccF.Rd:41: Lost braces
    41 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  expectreg-package.Rd: BayesX-package, mboost-package
  india.bnd.Rd: BayesX-package
  northger.bnd.Rd: BayesX-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘compare_benchmark_event.R’ ‘compare_benchmark_time.R’
File ‘expint/libs/expint.so’:
  Found non-API call to R: ‘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:
  ExplainPrediction-package.Rd: CORElearn, CoreModel, predict.CoreModel
  explanation.Rd: CoreModel, discretize, semiArtificial-package,
    CORElearn, predict.CoreModel, attrEval
  wrap4Explanation.Rd: nnet, CORElearn-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  graph2office.Rd: emf
  table2office.Rd: tidy
  table2spreadsheet.Rd: tidy
  table2tex.Rd: tidy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mrset.Rd: text_expand
  vars.Rd: text_expand
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 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_fct_adjs.R’ ‘compute_fct_adjs.Rd’ ‘guess_measure_sets.R’
    ‘mutate_expecvar.R’ ‘mutate_expecvar.Rd’ ‘mutate_metrics.R’
    ‘mutate_metrics.Rd’ ‘summarise_measures.R’ ‘summarise_measures.Rd’
    ‘validators.R’
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) MatIn.Rd:6: Lost braces
     6 | Computation of aggregation matrices for generalized interactions that are used in code{\link{extRC}} to estimate extended RC models.
       |                                                                                       ^
checkRd: (-1) plot.Rd:5: Lost braces
     5 | \description{It plots the output of code{\link{extRC}} function for a vector of lambda values.}
       |                                         ^
checkRd: (-1) print.Rd:5: Lost braces
     5 | \description{Given the output of code{\link{extRC}} function, it is written in a readable form.}
       |                                      ^
checkRd: (-1) summary.Rd:5: Lost braces
     5 | \description{Summary method for the output of code{\link{extRC}} function.}
       |                                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  distLquantile.Rd: quantileMean
  distLweights.Rd: dist.list
  plotLexBoot.Rd: ciBand
  plotLextreme.Rd: logAxis
  plotLfit.Rd: logAxis
  printL.Rd: rainbow2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  autoplot.ds_radf.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) va.Rd:80: Lost braces
    80 | \doi{10.1016/s0002-9394(02)01825-1}{Beck et al.}, and
       |                                    ^
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
checkRd: (-1) EEzGP_fit.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EEzGP_fit.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EEzGP_predict.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EEzGP_predict.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_fit.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_fit.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_predict.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_predict.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LEzGP_fit.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LEzGP_fit.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LLF_gradients.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LLF_gradients.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ez-package.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:33: Lost braces in \itemize; meant \describe ?
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:
    ‘GLARMA.R’ ‘GLARMA.Rd’ ‘INGARCH.R’ ‘INGARCH.Rd’ ‘fitted.GLARMA.Rd’
    ‘fitted.INGARCH.Rd’ ‘forecast.GLARMA.Rd’ ‘forecast.INGARCH.Rd’
    ‘glance.GLARMA.Rd’ ‘glance.INGARCH.Rd’ ‘residuals.GLARMA.Rd’
    ‘residuals.INGARCH.Rd’ ‘tidy.GLARMA.Rd’ ‘tidy.INGARCH.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pspline.Rd: gam, mgcv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) fmCov.Rd:37: Lost braces; missing escapes or markup?
    37 | where, \code{alpha(i)} is the intercept, \code{f(t)} is a {K x 1} vector of 
       |                                                           ^
checkRd: (-1) plot.ffm.Rd:82: Lost braces; missing escapes or markup?
    82 | \item{las}{one of {0, 1, 2, 3} to set the direction of axis labels, same as
       |                   ^
checkRd: (-1) summary.ffm.Rd:39: Lost braces; missing escapes or markup?
    39 | Returned object is of class {summary.ffm}.
       |                             ^
checkRd: (-1) fviz_nbclust.Rd:75: Lost braces; missing escapes or markup?
    75 | (2001) proposed: "the smallest k such that gap(k) >= gap(k+1) - s_{k+1}". 
       |                                                                   ^
checkRd: (-1) fviz_nbclust.Rd:77: Lost braces; missing escapes or markup?
    77 | SE.factor*s_{k+1}" where SE.factor is a numeric value which can be 1
       |             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Investigate.Rd: CA
  classif.Rd: HCPC
  description.Rd: CA
  factoGraph.Rd: CA
  graphHab.Rd: CA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  HCPC.Rd: agnes
  plotellipses.Rd: xyplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    minor changes
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  factorplot.Rd: glht, summary.glht
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SMART.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) FADPclust.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) happy.Rd:14: Lost braces
    14 |                  code{Pretty happy} <  \code{Very happy}}
       |                      ^
checkRd: (-1) fra_sf.Rd:22: Lost braces; missing escapes or markup?
    22 | A map of France as {sf} object. Can be used as dataset or for maps
       |                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getFormula.Rd: createLipidDB, assignDB
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) pi0FAMT.Rd:18: Lost braces
    18 | \code{pi0}{The estimated proportion \code{pi0} of null hypotheses.}}
       |           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.FAMTdata.Rd: impute.knn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kmPredictWrapper.Rd: predict.km, fast99
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' calls not declared from:
  ‘RColorBrewer’ ‘colorspace’ ‘zoo’
File ‘fansi/libs/fansi.so’:
  Found non-API call to R: ‘R_nchar’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘aggregate_gt.R’ ‘aux_funcs.R’ ‘double_did.R’ ‘estimate_gtatt.R’
    ‘generics.R’ ‘sim_did.R’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fastJT-package.Rd: Rcpp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) KITdesign.Rd:36: Lost braces; missing escapes or markup?
    36 |  \item{trait}{One of {'c','d','s',NULL} indicating the type
       |                      ^
checkRd: (-1) KITkernel.Rd:51: Lost braces; missing escapes or markup?
    51 |  \item{trait}{One of {'c','d','s',NULL} indicating the type
       |                      ^
checkRd: (-1) geno.Rd:19: Lost braces; missing escapes or markup?
    19 |                 Must be one of {'ibs', 'linear', 'quadratic'}.
       |                                ^
checkRd: (-1) geno.Rd:31: Lost braces; missing escapes or markup?
    31 |                      {'add', 'dom', 'rec'} indicating additive,
       |                      ^
checkRd: (-1) nongeno.Rd:14: Lost braces; missing escapes or markup?
    14 |                 Must be one of {'interactive', 'linear', 'quadratic'}.
       |                                ^
checkRd: (-1) eigen_compute_single_entry_of_diagonal_matrix.Rd:17: Lost braces; missing escapes or markup?
    17 | The value of m^{-1}_{j,j}
       |                ^
checkRd: (-1) eigen_compute_single_entry_of_diagonal_matrix.Rd:17: Lost braces; missing escapes or markup?
    17 | The value of m^{-1}_{j,j}
       |                     ^
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API calls to R: ‘DATAPTR’, ‘EXTPTR_PTR’, ‘NAMED’, ‘OBJECT’,
    ‘SETLENGTH’, ‘SET_NAMED’, ‘STRING_PTR’, ‘VECTOR_PTR’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SSplot.Rd: rand
  col.fastR.Rd: trellis.par.set, show.settings
  maxLik2.Rd: maxLik
  plot.maxLik2.Rd: maxLik
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  directed_erdos_renyi.Rd: Matrix
  directed_factor_model.Rd: Matrix
  erdos_renyi.Rd: Matrix
  undirected_factor_model.Rd: Matrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) update_nhl_db.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_nhl_db.Rd:54-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_phf_db.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_phf_db.Rd:54-57: Lost braces in \itemize; meant \describe ?
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  WebPlot.Rd: Cairo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Note: information on .o files is not available
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fat2Lpoly.Rd: kinship
  fat2Lpoly.withinR.Rd: kinship
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Error-Classes.Rd:107-119: Lost braces
   107 |   \item \code{do_verbose(response, template)} {
       |                                               ^
checkRd: (-1) Error.Rd:33-45: Lost braces
    33 |   \item \code{do(response, mssg)} {
       |                                   ^
checkRd: (-1) FBN.histogramMaxima.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fbad_copy_ad.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_ad.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) fbad_copy_adset.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_adset.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) fbad_copy_campaign.Rd:31: Lost braces; missing escapes or markup?
    31 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_campaign.Rd:33: Lost braces; missing escapes or markup?
    33 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) plot.fbroc.conf.Rd:5: Lost braces
     5 | \title{Plots function for object of class{fbroc.conf}}
       |                                          ^
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
checkRd: (-1) fcr-package.Rd:15: Lost braces; missing escapes or markup?
    15 | Let $y_{ij}$ denote some outcome measured at
       |        ^
checkRd: (-1) fcr-package.Rd:16: Lost braces; missing escapes or markup?
    16 | $t_{ij}$ on the functional domain (e.g. time) for subject $i$ at observation
       |    ^
checkRd: (-1) fcr-package.Rd:29: Lost braces; missing escapes or markup?
    29 | Initially, a model is fit without $b_i(t_{ij})$. Using the residuals from this initial fit,
       |                                          ^
checkRd: (-1) fcr.Rd:13: Lost braces; missing escapes or markup?
    13 | The formula should only include terms not associated with the random function intercept b_i(t_{ij}). See Examples.}
       |                                                                                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fcr.Rd: gam, bam, face.sparse
  plot.fcr.Rd: plot.gam
  predict.fcr.Rd: predict.gam, predict.bam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘.Rprofile’
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:
    ‘caps-plot.R’ ‘utils.R’
checkRd: (-1) simulation_model9.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                              ^
checkRd: (-1) simulation_model9.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                                           ^
checkRd: (-1) NASAtemp.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NASAtemp.Rd:15: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FDboost.Rd: mboost
  FDboostLSS.Rd: Families, GaussianLSS, boost_control
  bootstrapCI.Rd: cvrisk
  cvrisk.FDboostLSS.Rd: cvrisk.mboostLSS
  predict.FDboost_fac.Rd: predict.mboost
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘vert.txt’
checkRd: (-1) p.fdr.Rd:30: Lost braces
    30 | \item{adjust.method}{A string used to identify the p-value and false discovery rate adjustment method. Defaults to \code{BH}. Options are \code{BH}, \code{BY}, code{Bon},\code{Holm}, \code{Hoch}, and \code{Sidak}.}
       |                                                                                                                                                                     ^
Specified C++11: please drop specification unless essential
File ‘feather/libs/feather.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘libfeather.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) mutlicol_terminator.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Missing dependency on R >= 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’ ‘comments.R’ ‘create.R’ ‘delete.R’ ‘finish_upload.R’ ‘map.R’
    ‘map_elements.R’ ‘proc.R’ ‘style.R’ ‘user.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-squintability.R’ ‘get.R’ ‘pipe-sine-boa.Rd’ ‘plot-projection.R’
    ‘projection.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘change_column_types.Rd’ ‘create_alter_attr.Rd’ ‘create_edgelist.Rd’
    ‘create_nw.Rd’ ‘create_relation_labels.Rd’ ‘create_tidygraph.Rd’
    ‘fix_errors.Rd’ ‘produce_data.R’ ‘translate.Rd’
Unexported object imported by a ':::' call: ‘bit:::R_bit_as_hi’
  See the note in ?`:::` about the use of this operator.
Missing dependency on R >= 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_cplx.Rd’ ‘add_l2nm.Rd’ ‘can_repr.Rd’ ‘cross.R’ ‘fft.R’
    ‘fftab.Rd’ ‘fourier_frequencies.Rd’ ‘frequency.R’ ‘get.R’ ‘get_fx.Rd’
    ‘get_rect.Rd’ ‘has_cplx.Rd’ ‘internal.R’ ‘plot.R’ ‘repr.R’
    ‘to_cplx.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  classtable.Rd: confusionMatrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) contemParametros.Rd:19: Lost braces
    19 | \item{exclui3pontos}{verify por ... ? in f<-function(a, ...){ }}
       |                                                             ^
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  instrument.auto.Rd: setSymbolLookup
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  collect_predictions.Rd: collect_metrics, tune
  show_best.Rd: show_best
  tune_sim_anneal.Rd: tune_grid, tune_bayes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
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:
    ‘00.helpers.R’ ‘01.firm_register.R’ ‘02.FOandFM.R’ ‘03.people.R’
    ‘04.FF_either.R’ ‘05.network&graph.R’
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) FiSh-package.Rd:19: Lost braces
    19 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
checkRd: (-1) FiSh-package.Rd:32: Lost braces
    32 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
checkRd: (-1) SEP_FIM.Rd:46: Lost braces
    46 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
checkRd: (-1) fitConic.Rd:66-73: Lost braces
    66 | \code{parA }{vector of the six "ABCDEF" coefficients
       |             ^
checkRd: (-1) fitConic.Rd:67: Lost braces
    67 | \code{RSS }{'root sum square' figure of merit describing the relative fit quality}
       |            ^
checkRd: (-1) fitConic.Rd:68: Lost braces
    68 | \code{iters }{number of iterations at convergence}
       |              ^
checkRd: (-1) fitConic.Rd:69-71: Lost braces
    69 | \code{exitCode }{1 means ellipse, 2 means hyperbola, 3 means parabola.
       |                 ^
checkRd: (-1) rotateA.Rd:59: Lost braces; missing escapes or markup?
    59 | For \code{xyrot} {a Nx2 array of the x,y coordinates of the rotated data set. }
       |                  ^
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Missing dependency on R >= 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’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fitode-class.Rd: mle2-class
  fitode.Rd: ode, ginv, mle2
  fitodeMCMC.Rd: ode
  logLik.sensitivity.Rd: ode
  ode.sensitivity.Rd: ode
  summary-fitodeMCMC-method.Rd: effectiveSize, gelman.diag
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fitplc.Rd: nlme, lme, intervals.lme, deltaMethod
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘readData.R’
Specified C++11: please drop specification unless essential
checkRd: (-1) food_world_cup.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:75: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fpAnova.Rd: anovaBF
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  feNmlm.Rd: jacobian, genD
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) distribution_vector.Rd:14: Lost braces; missing escapes or markup?
    14 | All standard distributions from {stats} package are covered. For a list
       |                                 ^
checkRd: (-1) convertInitDesignToGrid.Rd:11: Lost braces; missing escapes or markup?
    11 | The initial design, consisting of \code{d + 1} columns ({d} dimensions and
       |                                                         ^
Specified C++11: please drop specification unless essential
checkRd: (-1) ModelMixHMM-class.Rd:31: Lost braces; missing escapes or markup?
    31 |         \code{smoothed} of class {StatMixHMM}).
       |                                  ^
checkRd: (-1) ModelMixHMMR-class.Rd:31: Lost braces; missing escapes or markup?
    31 |         \code{smoothed} of class {StatMixHMMR}).
       |                                  ^
checkRd: (-1) summary.flamcv.rd:8: Lost braces
     8 | This function summarizes a call to code{\link{flamCV}} and identifies the tuning parameter chosen by cross-validation.
       |                                        ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘projection.R’
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
checkRd: (-1) flashlight.Rd:53: Lost braces; missing escapes or markup?
    53 | like those in package {MetricsWeighted}.}
       |                       ^
checkRd: (-1) grouped_stats.Rd:49: Lost braces; missing escapes or markup?
    49 | {MetricsWeighted}.}
       | ^
checkRd: (-1) plot_counts.Rd:45: Lost braces; missing escapes or markup?
    45 | Experimental. Uses package {ggpubr} to rearrange the figure.
       |                            ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘flashcard.R’ ‘list_decks.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:
    ‘define_labels.Rd’ ‘divide.Rd’ ‘extract_labels.Rd’ ‘fill_labels.Rd’
    ‘fill_values.Rd’ ‘flatten_table_list.Rd’ ‘ft_ex.Rd’ ‘ft_ex_v2.Rd’
    ‘ft_set.Rd’ ‘get_col_values.Rd’ ‘get_page.Rd’ ‘pf_ex_compact.Rd’
    ‘remove_agg.Rd’ ‘remove_bottom.Rd’ ‘remove_cols.Rd’ ‘remove_empty.Rd’
    ‘remove_k.Rd’ ‘remove_left.Rd’ ‘remove_right.Rd’ ‘remove_rows.Rd’
    ‘remove_top.Rd’ ‘replace_dec.Rd’ ‘set_page.Rd’ ‘unpivot.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_top_level_commits.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) flex_dashboard.Rd:96: Lost braces; missing escapes or markup?
    96 | the `{.storyboard}` attribute to individual pages rather than using the
       |      ^
checkRd: (-1) fmp.Rd:45: Lost braces; missing escapes or markup?
    45 | If k = 0: (xi_1, ..., x_{C_i - 1}, omega)
       |                         ^
checkRd: (-1) fmp.Rd:47: Lost braces; missing escapes or markup?
    47 | If k = 1: (xi_1, ..., x_{C_i - 1}, omega, alpha1, tau1)
       |                         ^
checkRd: (-1) fmp.Rd:49: Lost braces; missing escapes or markup?
    49 | If k = 2: (xi_1, ..., x_{C_i - 1}, omega, alpha1, tau1, alpha2, tau2)
       |                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FLXMRnlm.Rd: gnm, flexmix
  flexmixNL-package.Rd: flexmix, gnm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AICc.Rd: gam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FlexParamCurve-package.Rd: nlsList, nlme
  SSposnegRichards.Rd: nlsList, nlme
  extraF.Rd: nlsList
  logist.data.Rd: nlme
  pn.mod.compare.Rd: nlsList
  pn.modselect.step.Rd: nlsList
  posneg.data.Rd: nlme
  posnegRichards.calls.Rd: nlsList
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘gen_grob.Rd’ ‘paginate.Rd’ ‘tab_settings.Rd’
Missing dependency on R >= 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’ ‘utils_aircrafts.R’ ‘utils_airfares.R’
    ‘utils_airport_movement.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  scramblase_assay_plot.Rd: facet_wrap, ggplot, nlsLM, geom_line,
    geom_segment, geom_point
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 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_flowmap.R’ ‘add_flowmap.Rd’ ‘hca_flowdat.R’
checkRd: (-1) flow_embed.Rd:30: Lost braces; missing escapes or markup?
    30 | \item Don't forget to add {flow} to Suggests in your DESCRIPTION file.
       |                           ^
checkRd: (-1) flowdata.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{Flow}{Water flow, in m^{3}/s}
       |                              ^
Malformed Description field: should contain one or more complete sentences.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addPredictions.Rd: crosspred
  metaFluMoDL.Rd: mvmeta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘flux.CH4.txt’
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  obsplot.Rd: print.deSolve, ode, deSolve
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Running examples in ‘FMM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FMM-methods
> ### Title: Methods for objects of class "FMM"
> ### Aliases: FMM-methods summary coef fitted resid summary,FMM-method
> ###   coef,FMM-method fitted,FMM-method resid,FMM-method
> 
> ### ** Examples
> 
> ## Generate example data:
> fmm2.data <- generateFMM(0, rep(2, 2), c(1.5, 3.4), c(0.2, 2.3), c(0.1, 0.2),
+                     plot = FALSE, outvalues = TRUE,
+                     sigmaNoise = 0.5) # add a gaussian noise with sigma = 0.5
> 
> ## Fit the FMM model with nback = 2 component
> ## fit is an object of S4 class 'FMM'
> fit <- fitFMM(vData = fmm2.data$y,timePoints = fmm2.data$t,nback = 2,
+               lengthAlphaGrid = 24,lengthOmegaGrid = 10)
Error in `rlang::env_unlock()`:
! `env_unlock()` is defunct as of rlang 1.1.5
Backtrace:
    ▆
 1. └─FMM::fitFMM(...)
 2.   └─FMM:::addShowMethod()
 3.     └─rlang::env_unlock(env = asNamespace("FMM"))
 4.       └─rlang::abort(msg)
Execution halted
checkRd: (-1) FMP.Rd:30: Lost braces; missing escapes or markup?
    30 | \eqn{m(\theta) = b_0 + b_1 \theta + b_2 \theta^2 + b_3 \theta^3}. Acceptable values of k = {0,1,2,3}. According to 
       |                                                                                            ^
checkRd: (-1) autoFMradio.Rd:46: Lost braces; missing escapes or markup?
    46 | Step 1 (regularized correlation matrix estimation) is performed using the \code{X}, \code{t}, and {fold} arguments.
       |                                                                                                   ^
checkRd: (-1) Estable.Rd:40: Lost braces
    40 |   \code{dEstable}{ gives the density function;}
       |                  ^
checkRd: (-1) Estable.Rd:41: Lost braces
    41 |   \code{pEstable}{ gives the distribution function or its complement;}
       |                  ^
checkRd: (-1) Estable.Rd:42: Lost braces
    42 |   \code{qEstable}{ gives quantiles;}
       |                  ^
checkRd: (-1) Estable.Rd:43-56: Lost braces
    43 |   \code{tailsEstable}{ returns a list with the following components
       |                      ^
checkRd: (-1) FMstable.Rd:50: Lost braces
    50 |   \code{dFMstable}{ gives the density function;}
       |                   ^
checkRd: (-1) FMstable.Rd:51: Lost braces
    51 |   \code{pFMstable}{ gives the distribution function or its complement;}
       |                   ^
checkRd: (-1) FMstable.Rd:52: Lost braces
    52 |   \code{qFMstable}{ gives quantiles;}
       |                   ^
checkRd: (-1) FMstable.Rd:53-66: Lost braces
    53 |   \code{tailsFMstable}{  returns a list with the following components
       |                       ^
checkRd: (-1) navbar_page.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) navbar_page.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) navbar_page.Rd:38: Lost braces in \itemize; meant \describe ?
Malformed Description field: should contain one or more complete sentences.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  foodingraph.Rd: igraph, ggraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘airport_footprint.R’ ‘airport_footprint.Rd’ ‘latlong_footprint.R’
    ‘latlong_footprint.Rd’
checkRd: (-1) foreca.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:78-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:84-87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:88-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:91-92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) initialize_weightvector.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:64-65: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  comb_EIG2.Rd: accuracy
  comb_SA.Rd: accuracy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘mod_carga_datos.R’ ‘mod_comparacion.R’ ‘mod_descom.R’
    ‘mod_descom_utils.R’ ‘mod_desvio.R’ ‘mod_model_arima_utils.R’
    ‘mod_normal_utils.R’ ‘mod_nuevos.R’ ‘mod_periodograma.R’
    ‘mod_periodograma_utils_.R’ ‘mod_t_c.R’ ‘mod_t_c_utils.R’
    ‘mod_train_test.R’ ‘ts_utils.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cvts.Rd: forecast
  fitted.hybridModel.Rd: accuracy
  plot.hybridModel.Rd: autoplot
  plotFitted.Rd: autoplot
  plotModelObjects.Rd: autoplot
  residuals.hybridModel.Rd: accuracy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  analyze.windanomaly.Rd: lpacf.plot
  forecastlpacf.Rd: lpacf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) errorMetricFunctions.Rd:48: Lost braces
    48 |         The metric MdAE is obtained using code{type = "AE"} and  \code{statistic = "Md"}
       |                                               ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
checkRd: (-1) species_bw.Rd:23: Lost braces
    23 | between trees." \doi{10.1371/journal.pone.0229930}{PLOS One 15: e0229930}.
       |                                                   ^
checkRd: (-1) process_pcl.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{pavd}{logical input to include Plant Area Volume Density Plot from {plot_pavd},
       |                                                                          ^
checkRd: (-1) depth.Rd:17: Lost braces; missing escapes or markup?
    17 |   \item {file} : {filename}
       |                  ^
checkRd: (-1) depth.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item {z_depth} : {measured focus range depth (z)}}
       |                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bio.volume.Rd: volume
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘str_extract_part.R’
checkRd: (-1) FGf.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FourgameteP.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:38: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) plot_lines.Rd:66: Lost braces
    66 | moderator. By default it is equal to \8code{c(19, 17, 15, 8, 5, 4, 3, 1)}.}
       |                                            ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |     ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                        ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                              ^
checkRd: (-1) Fpop.Rd:9: Lost braces; missing escapes or markup?
     9 | m_{i+1}), where the indicator function I counts the number of
       |   ^
Specified C++11: please drop specification unless essential
checkRd: (-1) emfrail_control.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) summary.frbs.Rd:32: Lost braces
    32 |                           \code{"GAUSSIAN"}, code{"TRIANGLE"}, \code{"TRAPEZOID"}, \code{"SIGMOID"}, and \code{"BELL"}.
       |                                                  ^
checkRd: (-1) summary.frbs.Rd:60: Lost braces; missing escapes or markup?
    60 |          {4.0, 0.23, 0.43, 0.53, 0.73} on its column. It means that the label a.2 of variable v.1 
       |          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  checkmnc-methods.Rd: checkimg
  fs_cmd.Rd: readnii
  readmgz.Rd: readnii
  readmnc.Rd: readnii
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fts.freqdom.Rd: freqdom
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' call not declared from: ‘tseries’
Specified C++11: please drop specification unless essential
checkRd: (-1) maximin.Rd:197: Lost braces
   197 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Catalogues.Rd: FrF2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FrF2Large.Rd: Letters
  makecatlg.Rd: Letters
  pb.Rd: generalized.word.length, length3, length4
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' call not declared from: ‘gridExtra’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘as_data_frame.Rd’ ‘as_list.Rd’ ‘dplyr_methods.Rd’ ‘fr_schema.R’
    ‘fr_tdr.R’ ‘read_fr_tdr.R’ ‘update_field.R’ ‘update_field.Rd’
checkRd: (-1) FSelector-package.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) report.Rd:18: Lost braces; missing escapes or markup?
    18 |         \item{las}{numeric in {0,1,2,3}; the style of axis labels (see \code{\link{par}}).}
       |                               ^
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  check_file.Rd: checkimg
  fast.Rd: readnii
  flirt.Rd: readnii
  flirt_apply.Rd: readnii
  fnirt.Rd: readnii
  fnirt_with_affine.Rd: readnii
  fnirt_with_affine_apply.Rd: readnii
  fsl_anat.Rd: checkimg
  fsl_applywarp.Rd: readnii
  fsl_biascorrect.Rd: readnii
  fsl_cluster.Rd: readnii
  fsl_deface.Rd: readnii
  fsl_resample.Rd: readnii
  fslabs.Rd: readnii
  fslacos.Rd: readnii
  fsladd.Rd: readnii
  fslasin.Rd: readnii
  fslatan.Rd: readnii
  fslbet.Rd: readnii
  fslbin.Rd: readnii
  fslbinv.Rd: readnii
  fslchfiletype.Rd: readnii
  fslcmd.Rd: readnii
  fslcos.Rd: readnii
  fslcpgeom.Rd: readnii
  fsldilate.Rd: readnii
  fsldiv.Rd: readnii
  fsledge.Rd: readnii
  fslepi_reg.Rd: readnii
  fslerode.Rd: readnii
  fslexp.Rd: readnii
  fslfill.Rd: readnii
  fslfill2.Rd: readnii
  fslhd.Rd: checkimg
  fslindex.Rd: readnii
  fsllog.Rd: readnii
  fslmask.Rd: readnii
  fslmaths.Rd: readnii
  fslmerge.Rd: readnii
  fslmul.Rd: readnii
  fslnan.Rd: readnii
  fslnanm.Rd: readnii
  fslor.Rd: readnii
  fslorient.Rd: readnii
  fslrand.Rd: readnii
  fslrandn.Rd: readnii
  fslrange.Rd: checkimg
  fslrecip.Rd: readnii
  fslrem.Rd: readnii
  fslreorient2std.Rd: readnii
  fslrobustfov.Rd: readnii
  fslroi.Rd: readnii
  fslsin.Rd: readnii
  fslslicetimer.Rd: readnii
  fslsmooth.Rd: readnii
  fslsplit.Rd: readnii
  fslsqr.Rd: readnii
  fslsqrt.Rd: readnii
  fslstats.Rd: checkimg
  fslsub.Rd: readnii
  fslsub2.Rd: readnii
  fslswapdim.Rd: readnii
  fsltan.Rd: readnii
  fslthresh.Rd: readnii
  fslval.Rd: checkimg
  fslview.Rd: checkimg
  fslvol.Rd: voxdim
  fslxor.Rd: readnii
  getForms.Rd: checkimg
  mcflirt.Rd: readnii
  melodic.Rd: checkimg
  mni_img.Rd: nifti
  readrpi.Rd: readnii
  susan.Rd: readnii
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fso.Rd: dsvdis
  mfso.Rd: dsvdis
  plot.mfso.Rd: dsvdis
  step.mfso.Rd: dsvdis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘utility_fSACF.R’
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: 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:
    ‘combine_fude.R’ ‘extract_fude.R’ ‘get_boundary.R’ ‘ls_fude.R’
    ‘read_fude.R’ ‘rename_fude.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘find_connected_components.R’
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:
    ‘Ravgr.Rd’ ‘TaylorRussell.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  promaxQ.Rd: GPForth
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) plot.fd.Rd:69-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.fd.Rd:72-77: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.fd.Rd: lines.fd, plotfit.fd
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' calls not declared from:
  ‘rgl’ ‘tuneR’
Found the following files/directories:
  ‘completeTrial_byArm_eventPriorRateC3=0.001_eventPriorRateT1=0_eventPriorRateT2=0_eventPriorWt=0.5.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.2.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.4.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.6.RData’
  ‘completeTrial_pooled_eventPriorRate=0.001_eventPriorWt=0.5.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.2.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.4.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.6.RData’
  ‘rcdf_byArm_arm=T1_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03.pdf’
  ‘rcdf_pooled_eventPriorRate=0.06.pdf’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nbrOfWorkers.batchtools.Rd: plan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Fuzzy_DBScan.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) misspellings.Rd:18: Lost braces
    18 | This is a code{tbl_df} mapping misspellings of their words, compiled by
       |               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  regex_join.Rd: str_detect
  stringdist_join.Rd: stringdist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                             ^
checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                                                     ^
checkRd: (-1) genmf.Rd:26: Lost braces; missing escapes or markup?
    26 | \item 'gbellmf' is c(\code{a, b, c}), where \code{a} denotes the width, \code{b} is usually positive and {c} locates the center of the curve.
       |                                                                                                          ^
Specified C++11: please drop specification unless essential
'::' or ':::' import not declared from: ‘here’
'library' or 'require' calls not declared from:
  ‘dplyr’ ‘here’ ‘scales’ ‘tidyverse’
File ‘gafit/libs/gafit.so’:
  Found non-API calls to R: ‘FRAME’, ‘HASHTAB’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) min_hpd_inc_area_df.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) min_hpd_inc_area_df.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) min_hpd_inc_area_df.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) vza_mean_and_var_rasters.Rd:20: Lost braces
    20 | of the paper on Wilson's warbler, this function computes $tilde{T}^{(mu)}$ (returned as
       |                                                                ^
checkRd: (-1) vza_mean_and_var_rasters.Rd:20: Lost braces; missing escapes or markup?
    20 | of the paper on Wilson's warbler, this function computes $tilde{T}^{(mu)}$ (returned as
       |                                                                    ^
checkRd: (-1) vza_mean_and_var_rasters.Rd:21: Lost braces; missing escapes or markup?
    21 | list component \code{mean.raster}) and $R^{(sigma^2)}$ (returned as list component
       |                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gamboostMSM-package.Rd: mboost
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CVgam.Rd: gam
  addhlines.Rd: rpart, predict.rpart
  gamRF.Rd: gam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) naref.Rd:13: Lost braces
    13 | \details{ For every \code{factor} or \code{character} column in \code{x}, \code{naref} sets \code{NA} as the reference level for a \code{factor} variable. Columns coded as \code{character} class are first converted to factors via \R{factor(x)}.  If \code{impute=TRUE} then the numeric columns are converted to two columns, one appended \code{.x} that contains imputed values and another appended \code{.miss} which is a binary variable indicating whether the original value was missing.  Numeric columns are returned without change if \code{impute=FALSE} or if they do not contain any missing values.  
       |                                                                                                                                                                                                                                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  centilesTwo.Rd: centiles
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  KIBNB.Rd: gamlss.family
  KIDEL.Rd: gamlss.family
  KIDPO.Rd: gamlss.family
  KIGEOM.Rd: gamlss.family
  KIGEOMo.Rd: gamlss.family
  KIGPO.Rd: gamlss.family
  KILG.Rd: gamlss.family
  KINBF.Rd: gamlss.family
  KINBI.Rd: gamlss.family
  KINBII.Rd: gamlss.family
  KIPIG.Rd: gamlss.family
  KIPO.Rd: gamlss.family
  KISI.Rd: gamlss.family
  KISICHEL.Rd: gamlss.family
  KIWARING.Rd: gamlss.family
  KIYULE.Rd: gamlss.family
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) pc.Rd:17: Lost braces
    17 | The functions \code{gamlss.pcr()} and \code{gamlss.pc()} are supporting functions. The  are not intended to be called directly by users. The function \code{gamlss.pc()} is using the linear model function \code{lm()} to fit the first principal components while the function code{gamlss.pcr()} uses \code{fitPCR()}.
       |                                                                                                                                                                                                                                                                                      ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘Bucket_plot.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  family_pdf.Rd: gamlss
  fitted_cdf.Rd: gamlss
  fitted_devianceIncr.Rd: gamlss
  model_pca.Rd: gamlss
  resid_plot.Rd: gamlss, plot.gamlss
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LR.test.Rd: dropterm
  gamlss.ps.Rd: ridge
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following significant warnings:
  Warning: replacing previous import ‘gamlss::lp’ by ‘mgcv::lp’ when loading ‘gamlss.spatial’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gamlss.spatial.Rcheck/00install.out’ for details.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MRF.Rd: mrf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gamm4.Rd: lmer, glmer, lmerControl, glmerControl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Gapfill.Rd:66-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:69-70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:71-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ndvi.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ndvi.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ndvi.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ndvi.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) glag.Rd:7: Lost braces; missing escapes or markup?
     7 | Similar to the \code{\link{lag}} function from the \code{stats} package, but \code{glag} enables padding (e.g. {NA}s or 0s) of the lost entries. Contrary to the \code{\link{lag}} function in the stats package, however, the default in \code{glag} is to pad (with \code{NA}s). The \code{glag} is particularly suited for \code{\link{zoo}} objects, since their indexing is retained
       |                                                                                                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coef.garchx.Rd: zoo
  garchx.Rd: zoo, na.trim
  garchxSim.Rd: zoo
  gdiff.Rd: zoo
  glag.Rd: zoo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gargle_oauth_client_from_json.Rd: oauth_app
  request_make.Rd: httr
  request_retry.Rd: httr
  response_process.Rd: httr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) read.ctable.Rd:19: Lost braces; missing escapes or markup?
    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                      ^
checkRd: (-1) read.ctable.Rd:19: Lost braces; missing escapes or markup?
    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                                      ^
checkRd: (-1) read.ctable.Rd:29: Lost braces; missing escapes or markup?
    29 | output array, {row,col}.names are not necessary \code{dimnames[[1]]} and
       |               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Goals.Rd: zoo
  MultiGASFit.Rd: hessian
  UniGASFit.Rd: hessian
  cpichg.Rd: xts
  fn.solnp.Rd: solnp
  sp500ret.Rd: xts
  sp500rv.Rd: xts
  usunp.Rd: xts
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gateR-package.Rd: sparr, spatstat.geom, terra
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) CompoundDensPlot.Rd:18: Lost braces
    18 |   \item{shape1, scale ,shape2, shape3}{numeric; positive parameters of the GB2 distribution. On the plot they are denotes as \code{a}, code{b}, \code{p}, \code{q} and \code{pl0} respectively.}
       |                                                                                                                                            ^
checkRd: (-1) CompoundVarest.Rd:58: Lost braces
    58 | \code{scoreU.cgb2} returns a \eqn{N \times (L-1)} matrix of scores <code{U}.
       |                                                                         ^
checkRd: (-1) Fisk.Rd:26: Lost braces
    26 | \value{\code{fisk} and \code{fiskh} return vectors of length 4 containing the estimated parameters \eqn{a}, eqn{b}, as well as \eqn{p=1} and \eqn{q=1}. 
       |                                                                                                                ^
checkRd: (-1) MLfullGB2.Rd:23: Lost braces
    23 |   \item{method}{numeric; the method to be used by \code{optim}. By default, code{method = }1 and the used method is BFGS. If \code{method = }2, method L-BFGS-B is used.}
       |                                                                                 ^
checkRd: (-1) MLprofGB2.Rd:16: Lost braces
    16 |   \item{method}{numeric; the method to be used by \code{optim}. By default, code{method = }1 and the used method is BFGS. If \code{method = }2, method L-BFGS-B is used.}
       |                                                                                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CompoundAuxVarest.Rd: survey
  CompoundVarest.Rd: survey
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘gbm.factorplot.R’ ‘gbm.mapsf.R’
'library' or 'require' call not declared from: ‘MASS’
Specified C++11: please drop specification unless essential
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) listInverseBlocks.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                           ^
checkRd: (-1) listInverseBlocks.Rd:17: Lost braces; missing escapes or markup?
    17 | List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                    ^
checkRd: (-1) matern.cormat.Rd:17: Lost braces; missing escapes or markup?
    17 | value of the shape parameter of the Matern correlation class. The default {alpha = 0.5} corresponds to an exponential correlation model. 
       |                                                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cluster.cormat.Rd: nlme
  gcmr.Rd: betareg, Formula
  gs.marg.Rd: betareg
  plot.gcmr.Rd: qqPlot
  summary.gcmr.Rd: bread, estfun, sandwich
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) gconsensus.Rd:48-54: Lost braces
    48 | {\code{display.signif.digits} an integer representing the number of significant digits to be obtained in the adaptative approach of the Monte Carlo simulation,
       | ^
Specified C++11: please drop specification unless essential
checkRd: (-1) GCTF.Rd:56: Lost braces; missing escapes or markup?
    56 |   U : A matrix which has N-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) GCTF.Rd:57: Lost braces; missing escapes or markup?
    57 |   V : A matrix which has M-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) GCTF.Rd:58: Lost braces; missing escapes or markup?
    58 |   J : The number of dimension (J < {N, M}).
       |                                    ^
checkRd: (-1) nearblack.Rd:30: Lost braces
    30 | code{infile=}, indicating that the input file should be
       |     ^
Found the following calls to attach():
File ‘g.data/R/g.data.attach.R’:
  attach(NULL, pos, basename(dir))
See section ‘Good practice’ in ‘?attach’.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  angles.csa.Rd: MCA
  dimdescr.Rd: dimdesc
  medoids.Rd: cluster, pam
  modif.rate.Rd: MCA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) GMSCDM.Rd:25: Lost braces; missing escapes or markup?
    25 | representing restricted GMS-DINA and GMS-DINO models where delta_{jm1} are equal for all strategies. Note that only a single model can be used
       |                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Transition-classes.Rd: Raster-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) GDSARM.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) GDSARM.Rd:10: Lost braces
    10 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
checkRd: (-1) GDS_givencols.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) GDS_givencols.Rd:10: Lost braces
    10 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
checkRd: (-1) dantzig.delta.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) dantzigS.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) dataCompoundExt.Rd:6: Lost braces
     6 | \title{Compound Extraction experiment of Dopico-Garc{\' i}a et al. (2007)}
       |                                                     ^
checkRd: (-1) dataCompoundExt.Rd:35: Lost braces
    35 | An analytical experiment conducted by Dopico-Garc{\' i}a et al. (2007) to
       |                                                  ^
checkRd: (-1) dataCompoundExt.Rd:22: Lost braces
    22 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geelm.Rd: geese
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) dental.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gelnet.logreg.obj.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{y}{n-by-1 binary response vector sampled from {0,1}}
       |                                                     ^
checkRd: (-1) parkinson.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parkinson.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parkinson.Rd:11: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_raster_single.Rd: raster
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) GeneF-internal.Rd:40: Lost braces; missing escapes or markup?
    40 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
checkRd: (-1) flexorhtest.Rd:57: Lost braces; missing escapes or markup?
    57 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
checkRd: (-1) flexorhtest.pvalue.Rd:57: Lost braces; missing escapes or markup?
    57 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  factory-mleFactory.Rd: optimParallel
  factory-optimFactory.Rd: optimParallel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geneSLOPE.Rd: SLOPE, bigmemory
  selectionResult.Rd: SLOPE
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) cpm.Rd:70: Lost braces; missing escapes or markup?
    70 | covariates included in \code{formula_l} or {formula_s} (required).}
       |                                            ^
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:
    ‘crossover.R’ ‘initialize_population.R’ ‘mutation.R’
checkRd: (-1) LD.Rd:37-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:47-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:66-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:82-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:84-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:86-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:48-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:59-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:78-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:93-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:95-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:97-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:124: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:126-128: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:129: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
checkRd: (-1) simulate_admixture.Rd:36: Lost braces
    36 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
checkRd: (-1) simulate_ancestry.Rd:49: Lost braces
    49 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
checkRd: (-1) simulate_ancestry_migration.Rd:59: Lost braces
    59 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
checkRd: (-1) simulate_sequence.Rd:51: Lost braces
    51 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
checkRd: (-1) simulate_sequence_migration.Rd:58: Lost braces
    58 | \code{location}{ location of the marker under selection (in Morgan) }
       |                ^
checkRd: (-1) barto.Rd:15-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) barto.Rd:19-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) barto.Rd:23-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chrY_subseg.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chrY_subseg.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mauve_bbone.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mauve_bbone.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) three_genes.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) three_genes.Rd:19-20: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
'library' or 'require' call not declared from: ‘gridExtra’
Missing dependency on R >= 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.precision.Rd’ ‘ridge.R’
File ‘GenSA/libs/GenSA.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) cfunc.new.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gensvm.grid.Rd:125: Lost braces
   125 | "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                                ^
checkRd: (-1) gensvm.grid.Rd:125: Lost braces
   125 | "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                                    ^
checkRd: (-1) gensvm.grid.Rd:127: Lost braces
   127 | GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                    ^
checkRd: (-1) gensvm.grid.Rd:127: Lost braces
   127 | GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                        ^
checkRd: (-1) gensvm.grid.Rd:129: Lost braces
   129 | section "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more 
       |                                        ^
checkRd: (-1) gensvm.grid.Rd:129: Lost braces
   129 | section "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more 
       |                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geoarrow_handle.Rd: as_nanoarrow_array
  infer_geoarrow_schema.Rd: as_nanoarrow_schema
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'::' or ':::' import not declared from: ‘geoR’
'library' or 'require' calls not declared from:
  ‘geoR’ ‘mcmcplots’
Missing dependency on R >= 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_geometry.Rd’ ‘add_level.Rd’ ‘common.R’
    ‘complete_point_geometry.Rd’ ‘complete_relation_by_geography.Rd’
    ‘coordinates_to_geometry.Rd’ ‘explotation.R’ ‘geodimension.R’
    ‘geolevel.R’ ‘get_empty_geometry_instances.Rd’
    ‘get_higher_level_names.Rd’ ‘get_level_data.Rd’
    ‘get_level_data_geo.Rd’ ‘get_level_geometries.Rd’
    ‘get_level_layer.Rd’ ‘get_level_names.Rd’
    ‘get_unrelated_instances.Rd’ ‘relate_levels.Rd’ ‘relations.R’
    ‘select_levels.Rd’ ‘set_level_data.Rd’ ‘transform_crs.Rd’
checkRd: (-1) calvaria.Rd:8: Lost braces; missing escapes or markup?
     8 | A named list containing \code{x} {a vector containing the ages}
       |                                  ^
checkRd: (-1) calvaria.Rd:9: Lost braces; missing escapes or markup?
     9 |   \code{y} {a matrix where each column is a preshape.} The 23rd, 101st,
       |            ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geoGAM.Rd: grpreg, cv.grpreg, gamboost, mboost, cvrisk, gam, polr,
    cv, mgcv
  methods.geoGAM.Rd: summary.gam, plot.gam, gam, predict.gam
  predict.geoGAM.Rd: predict.gam, gam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘acs_5yr_geo.R’ ‘acs_5yr_rolap.R’ ‘acs_5yr_topic.R’
    ‘anrc_2021_x01.Rd’ ‘as_GeoPackage.Rd’ ‘as_acs_5yr_geo.Rd’
    ‘as_acs_5yr_topic.Rd’ ‘as_flat_table.Rd’ ‘as_geomultistar.Rd’
    ‘as_star_database.Rd’ ‘download_selected_files.Rd’
    ‘get_area_file_names.Rd’ ‘get_area_groups.Rd’ ‘get_area_years.Rd’
    ‘get_areas.Rd’ ‘get_available_area_topics.Rd’
    ‘get_available_area_years.Rd’ ‘get_available_areas.Rd’
    ‘get_code_from_area_name.Rd’ ‘get_geo_attribute_names.Rd’
    ‘get_geo_layer.Rd’ ‘get_metadata.Rd’ ‘get_name_from_area_code.Rd’
    ‘get_names_of_other_topics.Rd’ ‘get_report_names.Rd’
    ‘get_selected_file_names.Rd’ ‘get_subreport_names.Rd’
    ‘get_too_heavy_file_names.Rd’ ‘get_topic_name.Rd’
    ‘select_area_files.Rd’ ‘select_report.Rd’ ‘select_subreport.Rd’
    ‘select_topic.Rd’ ‘set_metadata.Rd’ ‘unzip_files.Rd’
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘dra_vtd.R’ ‘heda.R’ ‘lewis.R’ ‘regionalize.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  comb_EIG2.Rd: accuracy
  comb_SA.Rd: accuracy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘geometries/libs/geometries.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:
    ‘add_dimension.Rd’ ‘add_facts.Rd’ ‘define_geoattribute.Rd’
    ‘dimensional_query_run_geoquery.R’ ‘filter_dimension.Rd’
    ‘geomultistar_define_geoattribute.R’ ‘get_empty_geoinstances.Rd’
    ‘multistar_as_flat_table.Rd’ ‘relate_dimension.Rd’ ‘run_geoquery.Rd’
    ‘run_query.Rd’ ‘save_as_geopackage.Rd’ ‘select_dimension.Rd’
    ‘select_fact.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.geonetwork.Rd: plot_sf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GeoNodeManager.Rd: R6Class
  GeoNodeUtils.Rd: R6Class
  GeoNodeVersion.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘impacts.R’ ‘posterior_predict.R’
Malformed Description field: should contain one or more complete sentences.
Found the following calls to data() loading into the global environment:
File ‘geotools/R/zzz.R’:
  data(fr_geo_rad)
See section ‘Good practice’ in ‘?data’.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GeotopRasterBrick-class.Rd: Raster-class
  KML-methods.Rd: projectRaster
  bondone.Rd: zoo
  brick-methods.Rd: RasterBrick-class, raster
  brick.decimal.formatter.Rd: raster, RasterBrick-class
  brickFromOutputSoil3DTensor.Rd: RasterLayer-class, RasterBrick-class,
    Raster-class
  geotopbrick.Rd: RasterBrick-class
  get.geotop.inpts.keyword.value.Rd: Raster-class, raster, zoo
  get.geotop.points.Rd: sf
  get.geotop.recovery.state.Rd: raster
  read.ascii.vectorized.brick.Rd: raster, RasterBrick-class
  read.raster.from.url.Rd: raster
  read.vectorized.geotop.recovery.Rd: raster
  write.ascii.vectorized.brick.Rd: RasterBrick-class, writeRaster
  write.vectorized.geotop.recovery.Rd: writeRaster
  writeRasterxGEOtop.Rd: writeRaster, RasterBrick-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geoTS-package.Rd: reclassify
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘gemTemporaryEquilibriumPath.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘query_gesla.R’ ‘query_gesla.Rd’ ‘write_gesla.Rd’
Specified C++11: please drop specification unless essential
checkRd: (-1) gesso.cv.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gesso.cv.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gesso.cv.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gesso.cv.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gesso.cv.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gestMultiple.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestMultiple.Rd:81-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestMultiple.Rd:84-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestMultiple.Rd:87-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestSingle.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestSingle.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestSingle.Rd:79-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestSingle.Rd:81-84: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘gld_read_lattes_zip.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  extract_gfc.Rd: writeRaster
  scale_by_pixel_area.Rd: dataType
  scale_toar.Rd: writeRaster
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) QANOVA.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) QANOVA.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) QANOVA.Rd:64-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) QANOVA.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gfonts.Rd:8: Lost braces; missing escapes or markup?
     8 | Download Google fonts and generate CSS to use in {rmarkdown} documents and
       |                                                  ^
checkRd: (-1) gfonts.Rd:9: Lost braces; missing escapes or markup?
     9 | {shiny} applications. Some popular fonts are included and ready to use.
       | ^
checkRd: (-1) use_pkg_gfont.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Use a Google Font included in {gfonts}}
       |                                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  glag.Rd: zoo, lag.zoo
  gsummary.Rd: vcovHC, NeweyWest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_bkde.Rd: aes, aes_, ggplot, fortify, borders, layer,
    geom_histogram, geom_freqpoly, geom_violin
  geom_bkde2d.Rd: aes, aes_, ggplot, fortify, borders, layer,
    stat_contour, geom_contour, stat_sum
  geom_cartogram.Rd: aes, aes_, ggplot, fortify, layer, borders
  geom_dumbbell.Rd: aes, aes_, ggplot, fortify, layer, borders
  geom_lollipop.Rd: aes, aes_, ggplot, fortify, layer, borders
  geom_stateface.Rd: aes, aes_, ggplot, fortify, layer, borders
  geom_xspline.Rd: aes, aes_, ggplot, fortify, borders, layer
  geom_xspline2.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_ash.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_stepribbon.Rd: aes, aes_, ggplot, fortify, borders, layer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_arrowsegment.Rd: geom_segment
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_arrow.Rd: aes_position, aes_colour_fill_alpha, aes_group_order,
    aes_linetype_size_shape
  geom_arrow_chain.Rd: aes_position, aes_colour_fill_alpha,
    aes_group_order, aes_linetype_size_shape
  geom_arrow_curve.Rd: aes_position, aes_colour_fill_alpha,
    aes_group_order, aes_linetype_size_shape
  geom_arrow_segment.Rd: aes_position, aes_colour_fill_alpha,
    aes_group_order, aes_linetype_size_shape
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  stat_automap.Rd: cartographer
  stat_automap_coords.Rd: cartographer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_quasirandom.Rd: geom_boxplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘crime.Rd’ ‘get_SVD.Rd’ ‘ggscreeplot.Rd’ ‘reflect.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggblend-package.Rd: ggplot
  layer_list.Rd: ggplot2
  partition.Rd: vars
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  brick.Rd: aes, ggplot, fortify, borders
  waffle.Rd: aes, ggplot, fortify, borders
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘girder_experiment.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘labs2.R’
Found the following assignments to the global environment:
File ‘ggExtra/R/ggMarginalGadget.R’:
  assign(plotname, eval(parse(text = origPlot)), envir = .GlobalEnv)
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘geometrical_data_analysis.R’ ‘ggmca.Rd’ ‘ggmca_with_base_ref.Rd’
    ‘ggpca_3d.Rd’ ‘ggpca_cor_circle.Rd’ ‘pca_interpret.Rd’ ‘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:
    ‘lib.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:
    ‘ggcoefplot.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_spline.Rd: geom_smooth, aes, aes_string
  gf_ash.Rd: aes, aes_, facet_wrap, facet_grid, geom_histogram
  gf_bar.Rd: facet_wrap, facet_grid
  gf_bin2d.Rd: facet_wrap, facet_grid
  gf_blank.Rd: facet_wrap, facet_grid
  gf_boxplot.Rd: facet_wrap, facet_grid
  gf_col.Rd: facet_wrap, facet_grid
  gf_contour.Rd: facet_wrap, facet_grid
  gf_count.Rd: facet_wrap, facet_grid
  gf_crossbar.Rd: facet_wrap, facet_grid
  gf_curve.Rd: facet_wrap, facet_grid
  gf_density.Rd: facet_wrap, facet_grid
  gf_density_2d.Rd: facet_wrap, facet_grid
  gf_dotplot.Rd: facet_wrap, facet_grid
  gf_facet_grid.Rd: facet_wrap, facet_grid
  gf_fitdistr.Rd: facet_wrap, facet_grid
  gf_freqpoly.Rd: facet_wrap, facet_grid
  gf_hex.Rd: facet_wrap, facet_grid
  gf_histogram.Rd: facet_wrap, facet_grid
  gf_jitter.Rd: facet_wrap, facet_grid
  gf_line.Rd: facet_wrap, facet_grid
  gf_point.Rd: facet_wrap, facet_grid
  gf_polygon.Rd: facet_wrap, facet_grid
  gf_qq.Rd: facet_wrap, facet_grid
  gf_quantile.Rd: facet_wrap, facet_grid
  gf_raster.Rd: facet_wrap, facet_grid
  gf_rect.Rd: facet_wrap, facet_grid
  gf_rug.Rd: facet_wrap, facet_grid
  gf_segment.Rd: facet_wrap, facet_grid
  gf_sf.Rd: facet_wrap, facet_grid
  gf_sina.Rd: facet_wrap, facet_grid
  gf_smooth.Rd: facet_wrap, facet_grid
  gf_spline.Rd: facet_wrap, facet_grid
  gf_spoke.Rd: facet_wrap, facet_grid
  gf_step.Rd: facet_wrap, facet_grid
  gf_text.Rd: facet_wrap, facet_grid
  gf_theme.Rd: theme_minimal
  gf_tile.Rd: facet_wrap, facet_grid
  gf_violin.Rd: facet_wrap, facet_grid
  ggformula-ggproto.Rd: stat_qq
  ggformula.Rd: facet_wrap, facet_grid
  stat_qqline.Rd: aes, aes_string
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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:
    ‘utilities.R’
checkRd: (-1) render_context.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{xmin, ymin, xmax, ymax}{Boundaries of the area in pixels. {0,0} is the
       |                                                                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  object_support.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘aaa.R’ ‘flip.R’ ‘geom_link.Rd’ ‘geom_seq.Rd’ ‘geom_seq_break.Rd’
    ‘shift.Rd’ ‘track_info.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggheatmap_theme.Rd: theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Missing dependency on R >= 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_phylopic.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:
    ‘inset_shape_circle.R’ ‘inset_shape_rectangle.R’ ‘inset_shape_sf.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  theme_mice.Rd: mice, ggplot2
  theme_minimice.Rd: mice, ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
possible bashism in configure.ac line 36 (should be 'b = a'):
  if test x"${RSysinfoName}" == x"Darwin"; then
  possible bashism in configure.ac line 47 (should be 'b = a'):
  if test x"${hasOpenMP}" == x""; then
checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
':::' call which should be '::': ‘scales:::censor’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘productplots:::bound’
  See the note in ?`:::` about the use of this operator.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AG.Rd: igraph
  MAG.Rd: igraph
  MRG.Rd: igraph
  MSG.Rd: igraph
  MarkEqMag.Rd: igraph
  MarkEqRcg.Rd: igraph
  Max.Rd: igraph
  RG.Rd: igraph
  RepMarBG.Rd: igraph
  RepMarDAG.Rd: igraph
  RepMarUG.Rd: igraph
  SG.Rd: igraph
  ggm.Rd: cliques
  grMAT.Rd: igraph
  msep.Rd: igraph
  null.Rd: Null
  plotGraph.Rd: igraph, tkplot, plot.igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running ‘bsch.R’ [1s/2s]
  Comparing ‘bsch.Rout’ to ‘bsch.Rout.save’ ...3a4
> 
  Running ‘penInf.R’ [5s/5s]
  Comparing ‘penInf.Rout’ to ‘penInf.Rout.save’ ...5a6
> 
  Running ‘sh9.2012.R’ [3s/3s]
  Comparing ‘sh9.2012.Rout’ to ‘sh9.2012.Rout.save’ ...3a4
> 
  Running ‘shPUR.R’ [3s/4s]
  Comparing ‘shPUR.Rout’ to ‘shPUR.Rout.save’ ...3a4
> 
  Running ‘test1Fast.R’ [4s/6s]
  Comparing ‘test1Fast.Rout’ to ‘test1Fast.Rout.save’ ...3a4
> 
  Running ‘test1QE.R’ [2s/3s]
  Comparing ‘test1QE.Rout’ to ‘test1QE.Rout.save’ ...3a4
> 
  Running ‘test2Fast.R’ [4s/6s]
  Comparing ‘test2Fast.Rout’ to ‘test2Fast.Rout.save’ ...3a4
> 
  Running ‘test2QE.R’ [2s/2s]
  Comparing ‘test2QE.Rout’ to ‘test2QE.Rout.save’ ...3a4
> 
  Running ‘test3Fast.R’ [5s/6s]
  Comparing ‘test3Fast.Rout’ to ‘test3Fast.Rout.save’ ...3a4
> 
  Running ‘test3QE.R’ [2s/2s]
  Comparing ‘test3QE.Rout’ to ‘test3QE.Rout.save’ ...3a4
> 
  Running ‘test5Fast.R’ [5s/6s]
  Comparing ‘test5Fast.Rout’ to ‘test5Fast.Rout.save’ ...3a4
> 
  Running ‘test7Fast.R’ [5s/6s]
  Comparing ‘test7Fast.Rout’ to ‘test7Fast.Rout.save’ ...3a4
> 
  Running ‘testMyFam.R’ [1s/1s]
  Comparing ‘testMyFam.Rout’ to ‘testMyFam.Rout.save’ ...3a4
>
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ggmugs.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_density_.Rd: geom_density
  geom_hist_.Rd: geom_histogram
  position_dodge_.Rd: position_dodge
  position_stack_.Rd: position_stack
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_edgetext.Rd: geom_text, geom_label
  geom_edgetext_repel.Rd: geom_text_repel, geom_label_repel
  theme_blank.Rd: theme
  theme_facet.Rd: theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_edge.Rd: layer, geom_segment
  geom_edge_label.Rd: geom_label
  geom_node_label.Rd: ggplot, fortify, borders
  geom_node_plot.Rd: facet_wrap
  ggparty.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) pcp_scale.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:54-55: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggdonut.Rd: geom_text_repel
  ggnestedpie.Rd: geom_text_repel
  ggpie.Rd: geom_text_repel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  n_pages.Rd: facet_wrap_paginate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_pointdensity.Rd: aes, aes_, ggplot, fortify, layer, borders
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_polypath.Rd: geom_polygon, geom_map, geom_path, geom_ribbon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_bracket.Rd: layer
  geom_pwc.Rd: layer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  stat_QC.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_QC_CAPA.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_QC_cap_hlabels.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_QC_cap_hlines.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_QC_cap_summary.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_QC_cap_vlabels.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_QC_cap_vlines.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_QC_labels.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_mR.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_pareto.Rd: aes, aes_, ggplot, fortify, borders, layer
  stat_qc_violations.Rd: aes, aes_, ggplot, fortify, borders, layer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  stat_km.Rd: trans_new
  stat_kmticks.Rd: trans_new, plot.survfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggplot2-ggproto.Rd: geom_jitter, geom_count, geom_bin2d, layer,
    geom_smooth, geom_quantile, geom_density_2d, geom_boxplot,
    geom_hex, geom_density2d
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  StatCityRoad.Rd: aes
  StatDistrict.Rd: aes
  StatDistrictCoordinates.Rd: aes
  StatPlaces.Rd: aes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘reveal_aes.Rd’ ‘reveal_axis.Rd’ ‘reveal_groups.Rd’
    ‘reveal_layers.Rd’ ‘reveal_panels.Rd’ ‘reveal_save.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_density_line.Rd: geom_density
  geom_density_ridges.Rd: aes, aes_, ggplot, layer, stat_density
  geom_ridgeline.Rd: aes, aes_, ggplot, layer
  geom_ridgeline_gradient.Rd: aes, aes_, ggplot, layer
  geom_vridgeline.Rd: aes, aes_, ggplot, layer
  position_points_jitter.Rd: position_jitter
  scale_cyclical.Rd: discrete_scale
  scale_point.Rd: scale_discrete_manual
  scale_vline.Rd: scale_discrete_manual
  stat_density_ridges.Rd: stat_density, aes, aes_, ggplot, layer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘Scatter_ridges_function.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggsdc.Rd: seas
  stat_decomp.Rd: aes, aes_, ggplot, fortify, borders
  stat_index.Rd: aes, aes_, ggplot, fortify, borders
  stat_rollapplyr.Rd: aes, aes_, ggplot, fortify, borders
  stat_seas.Rd: aes, aes_, ggplot, fortify, borders, seas
  stat_stl.Rd: aes, aes_, ggplot, fortify, borders
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    * Changes all data options to .data to decrease possibility of column naming overlap
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggseqlogo.Rd: facet_wrap
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘scales-sides-.R’ ‘side-layout-.r’ ‘utils-calls.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_xsideabline.Rd: aes
  ggside-ggproto-facets.Rd: ggplot2
  xside.Rd: ggplot2
  yside.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  layer_spatial.Raster.Rd: geom_raster
  layer_spatial.SpatRaster.Rd: geom_raster
  layer_spatial.stars.Rd: geom_raster
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘cnet.r’ ‘graph.r’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  annotation_raster_tern.Rd: geom_raster
  approved_layers.Rd: geom_point, geom_path, geom_line, geom_label,
    geom_text, geom_jitter, geom_polygon, geom_segment, geom_count,
    geom_curve, geom_blank, geom_rect, stat_identity, stat_sum,
    stat_unique, position_identity
  coord_tern.Rd: geom_segment
  geom_Xline.Rd: geom_hline, geom_vline
  geom_confidence_tern.Rd: ilr, stat_contour
  geom_hex_tern.Rd: aes_position, aes_colour_fill_alpha,
    aes_group_order, aes_linetype_size_shape
  geom_mean_ellipse.Rd: compositions, stat_contour
  geom_tri_tern.Rd: aes_position, aes_colour_fill_alpha,
    aes_group_order, aes_linetype_size_shape
  ggplot_build.Rd: benchplot
  ggplot_gtable.Rd: gtable
  ggtern_labels.Rd: xlab, ylab, latex2exp
  ggtern_package.Rd: proto
  kde2d.weighted.Rd: kde2d
  theme_elements.Rd: element_rect
  theme_latex.Rd: latex2exp, TeX
  theme_showgrid.Rd: element_line, element_blank
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_tufteboxplot.Rd: stat_boxplot, geom_boxplot
  scale_color_tableau.Rd: discrete_scale
  scale_colour_canva.Rd: discrete_scale
  theme_solid.Rd: theme
  theme_tufte.Rd: geom_rug
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
Missing dependency on R >= 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_donut.Rd’ ‘geom_donut_slice.Rd’ ‘geom_pie.Rd’
    ‘geom_series_circles.Rd’ ‘geom_series_text.Rd’ ‘geom_slice.Rd’
    ‘stat-series-circles.R’
checkRd: (-1) MODFIT.Rd:33: Lost braces; missing escapes or markup?
    33 |   {chisq_i = sum( (O_iz - E_iz)^2 / E_iz; z = 0, ..., C ), }
       |   ^
checkRd: (-1) probs.GGUM.Rd:27: Lost braces; missing escapes or markup?
    27 |   GUM-based probabilities just constrain alpha to a unit vector of length {I}
       |                                                                           ^
'library' or 'require' calls not declared from:
  ‘nasaweather’ ‘tourr’
'data(package=)' call not declared from: ‘ggplot2’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ancsvm.Rd: svm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘annual.R’ ‘anomaly.R’ ‘coverage.R’ ‘daily.R’ ‘flags.R’
    ‘get-country-shapefile.R’ ‘monthly.R’ ‘quarterly.R’ ‘s3_classes.R’
    ‘stations.R’ ‘utils.R’
checkRd: (-1) gigg.Rd:70-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) significantTau.Rd:48-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) significantTau.Rd:52-53: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  monthlyComposite.Rd: stackApply, writeRaster
  oldNaming.Rd: writeFormats, ncvar_get, nc_open
  qualityControl.Rd: overlay, writeRaster
  rasterizeGimms.Rd: writeRaster
  significantTau.Rd: zyp.trend.vector, writeRaster, beginCluster,
    MannKendall
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘rtgin1.R’
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gh_install_packages.Rd: install_github
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) gjamCensorY.Rd:27: Lost braces; missing escapes or markup?
    27 |   \item{\code{y}}{n by S matrix updated with censored {values} substituted for
       |                                                       ^
checkRd: (-1) gjamFillMissingTimes.Rd:32: Lost braces
    32 | Missing times in the data occur where there are gaps in \code{timeCol} column of \code{xdata} and the initial time \code{0} for each sequence.  New versions of the data have \code{NA} (\code{xdata}) or prior values with appropriate weight (\code{ydata}).  Missing times are filled in \code{xdata, ydata, edata}, including a time \code{0} which serves as a prior mean for \code{ydata} for time code{1}.  The group and time indices in columns \code{groupCol} and \code{timeCol} of \code{xdata} reference the time for a given time series.  Missing values in the columns \code{groupVars} of \code{xdata} are filled automatically filled in.  This assumes that values for these variables are fixed for the group.  If \code{FILLMEANS}, the missing  values in \code{ydata} are filled with means for the group and given a low weight specified in \code{missingEffort}.
       |                                                                                                                                                                                                                                                                                                                                                                                                              ^
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fun.class.regime.bi.Rd: pam, fanny
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GLD.lm.Rd: fun.RMFMKL.ml.m, fun.RMFMKL.ml, fun.RMFMKL.lm,
    fun.RPRS.ml.m, fun.RPRS.ml, fun.RPRS.lm
  GLD.lm.full.Rd: fun.RMFMKL.ml.m, fun.RMFMKL.ml, fun.RMFMKL.lm,
    fun.RPRS.ml.m, fun.RPRS.ml, fun.RPRS.lm
  GLD.lm.full.surv.Rd: fun.RMFMKL.ml.m, fun.RMFMKL.ml, fun.RPRS.ml.m,
    fun.RPRS.ml
  GLD.lm.surv.Rd: fun.RMFMKL.ml.m, fun.RMFMKL.ml, fun.RPRS.ml.m,
    fun.RPRS.ml
  qqgld.default.Rd: qqplot.gld, qqplot.gld.bi
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) NEWS.Rd:16: Lost braces; missing escapes or markup?
    16 |         \item Now \code{AICc == Inf} when {n <= p + 1}.
       |                                           ^
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
checkRd: (-1) glmc.control.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) glmc.control.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) summarylr.Rd:34: Lost braces
    34 | \item{method}{NULL or character vector of length 0, 1 or 2; may be code{"LRT"} or \code{"Rao"} or \code{c("LRT", "Rao")} to compute specified P-values.
       |                                                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  glmglrt.Rd: p_value.default
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) glmmSimData.Rd:4: Lost braces; missing escapes or markup?
     4 | \description{Section 4.1.2 of the refence below descries a simulation study with data generated from a probit mixed model with six fixed effects parameters and a bivariate random effects vector having a 2 by 2 symmetric positive definite covariance matrix. The function simulates a data set from this model with 2500 groups and the number of observation in each group being a random draw from {20,21,...,30}.}
       |                                                                                                                                                                                                                                                                                                                                                                                                          ^
'library' or 'require' calls not declared from:
  ‘MASS’ ‘nlme’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RRglmer.Rd: glmer, lmerControl, glmerControl, lme4
  residuals.RRglmerMod.Rd: residuals.glmResp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  glmmRefit.Rd: glmmTMB
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘glmnet/libs/glmnet.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) ccancer.Rd:16: Lost braces
    16 |                          a factor with levels either \\code{F} (female) or code{M} (male)}
       |                                                            ^
checkRd: (-1) ccancer.Rd:16: Lost braces
    16 |                          a factor with levels either \\code{F} (female) or code{M} (male)}
       |                                                                                ^
checkRd: (-1) galapagos.Rd:4: Lost braces
     4 | \title{{Gal\'{a}pagos} Island species data}
       |              ^
checkRd: (-1) galapagos.Rd:6: Lost braces
     6 |   The number of species on the {Gal\'{a}pagos} Islands
       |                                ^
checkRd: (-1) galapagos.Rd:6: Lost braces
     6 |   The number of species on the {Gal\'{a}pagos} Islands
       |                                      ^
checkRd: (-1) galapagos.Rd:40: Lost braces
    40 |    {Gal\'{a}pagos} (the endemics). 
       |    ^
checkRd: (-1) galapagos.Rd:40: Lost braces
    40 |    {Gal\'{a}pagos} (the endemics). 
       |          ^
checkRd: (-1) galapagos.Rd:44: Lost braces
    44 |   Species number and endemism: The {Gal\'{a}pagos} Archipelago revisited.
       |                                          ^
checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) consensus.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) getfit.Rd:14: Lost braces
    14 |   \item{object}{A fitted model object, of class \code{glm}, \code{lm} or code{glm.nb}}
       |                                                                              ^
checkRd: (-1) getfit.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-methods.Rd:14: Lost braces
    14 | code{glmulti} finds what are the \code{n} best models (the confidence set of models) among all possible models (the candidate set, as specified by the user).
       |     ^
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
possible bashism in configure.ac line 44 (test -a/-o):
  if test [ -n "$PKG_CPPFLAGS" -a -n "$PKG_LIBS" ] ; then
  possible bashism in configure.ac line 47 (test -a/-o):
      if test [ -n "$PKG_CPPFLAGS" -o -n "$PKG_LIBS" ] ; then
  possible bashism in configure.ac line 87 (test -a/-o):
      if test [ -n "$GLPK_INCLUDE" -a -n "$GLPK_LIB" ] ; then
  possible bashism in configure.ac line 113 (test -a/-o):
              if test [ -d "/usr/include" -o -d "/usr/local/include" ] ; then
  possible bashism in configure.ac line 119 (test -a/-o):
              if test [ -d "/usr/local/lib" -o -d "/usr/local/lib64" -o -d "/usr/lib" -o -d "/usr/lib64"] ; then
  possible bashism in configure.ac line 148 (test -a/-o):
              if test [ -d "$prefix/lib" -o -d "$prefix/lib64" ] ; then
  possible bashism in configure.ac line 160 (test -a/-o):
  dnl #            if test [ -d "$prefix/include" -a -d "$prefix/lib" ] ; then
checkRd: (-1) getRiiGLPK.Rd:35: Lost braces; missing escapes or markup?
    35 |   Returns the current scale factor $r_{ii}$ for row \code{i} of the specified
       |                                       ^
checkRd: (-1) getSjjGLPK.Rd:35: Lost braces; missing escapes or markup?
    35 |   Returns the current scale factor $s_{jj}$ for column \code{j} of the
       |                                       ^
checkRd: (-1) setRiiGLPK.Rd:28: Lost braces; missing escapes or markup?
    28 |     Scale factor $r_{ii}$.
       |                     ^
checkRd: (-1) setSjjGLPK.Rd:28: Lost braces; missing escapes or markup?
    28 |     Scale factor $s_{jj}$.
       |                     ^
checkRd: (-1) rtheta.Rd:50-76: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gmChangePassword.Rd: shiny
  gmConnectServer.Rd: dbConnect, RMySQL
  gmSQL.Rd: dbSendQuery
  gmSQLValues.Rd: dbEscapeStrings
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Maf.data.frame.Rd:65: Lost braces
    65 | the lag distance to take. \%For other options see code{getEmpVariogramSlice}.}
       |                                                       ^
checkRd: (-1) NGSAustralia.Rd:114: Lost braces; missing escapes or markup?
   114 | \item{MRB}{obtained from simplifying the major crustal boundaries of {Korsch2015a, Korsch2015b}}
       |                                                                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Maf.data.frame.Rd: cdt, princomp.acomp
  coloredBiplot.genDiag.Rd: coloredBiplot
  gsi.EVario2D.Rd: variogram
  gsi.EVario3D.Rd: variogram
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  descGetMissing.Rd: txtInt
  describeFactors.Rd: txtInt
  describeMean.Rd: txtInt
  describeMedian.Rd: txtInt
  describeProp.Rd: txtInt
  mergeDesc.Rd: htmlTable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) ATEgel.Rd:24: Lost braces
    24 | \item{g}{A formula as \code{y~z}, where code{y} is the response and
       |                                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bwWilhelm.Rd: kernHAC, bwAndrews
  estfun.Rd: kernHAC, vcovHAC, sandwich
  gel.Rd: kernHAC, bwAndrews, bwNeweyWest
  gmm.Rd: kernHAC
  smoothG.Rd: weightsAndrews
  sysGmm.Rd: kernHAC, bwAndrews, bwNeweyWest
  vcov.Rd: kernHAC
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ndset.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:
    ‘1-pitch-normalize-value.R’
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FNN.Rd: layer_dropout
  rPrior.Rd: rCopula
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gofArchmChisq.Rd: gofTstat
  gofArchmGamma.Rd: gofTstat
  gofArchmSnB.Rd: gofTstat
  gofArchmSnC.Rd: gofTstat
  gofCvM.Rd: gofTstat
  gofKS.Rd: gofTstat
  gofRosenblattChisq.Rd: gofTstat
  gofRosenblattGamma.Rd: gofTstat
  gofRosenblattSnB.Rd: gofTstat
  gofRosenblattSnC.Rd: gofTstat
  plot.gofCOP.Rd: pirateplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  glmMLE.Rd: glm2
  testGLMGamma.Rd: glm2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) BVDWSTOXX.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:16: Escaped LaTeX specials: \& \&
checkRd: (-1) BVDWSTOXX.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:37: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gar_auth.Rd: Token-class
  gar_auto_auth.Rd: Token-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  makeDockerClusterPSOCK.Rd: as.cluster
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  request_make.Rd: httr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) gl_nlp.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gl_auth.Rd: gar_attach_auto_auth
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cell-specification.Rd: cellranger
  request_make.Rd: httr
  sheets_id.Rd: googledrive
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘gt_make_grid.Rd’
checkRd: (-1) google_find_place.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) google_find_place.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) google_find_place.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) google_map.Rd:54: Lost braces; missing escapes or markup?
    54 | of `{sf}` objects).}
       |     ^
checkRd: (-1) compute_lower_bound_1tree.Rd:31: Lost braces; missing escapes or markup?
    31 | instance from vertex 1.  Internally, it creates the graph Kn-{v1}
       |                                                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  apply_incidence_map.Rd: as_edgelist
  compute_cut_weight.Rd: as_edgelist
  compute_lower_bound_1tree.Rd: mst, igraph
  dfs_tree.Rd: bfs, dfs
  dijk.Rd: shortest_paths, igraph
  generate_fundamental_cycles.Rd: as_edgelist
  gor.Rd: igraph
  is_cover.Rd: as_edgelist
  shave_cycle.Rd: as_edgelist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘collections.R’ ‘packages.R’ ‘published.R’ ‘related.R’ ‘utils.R’
Malformed Description field: should contain one or more complete sentences.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  00.GPArotateDF.Rd: NormalizingWeight
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  trait.posterior.Rd: pcubature
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) solve_game.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) solve_game.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) solve_game.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) solve_game.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) solve_game.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘balanced.Rd’ ‘geks.Rd’ ‘grouped.Rd’ ‘splice.R’
Specified C++11: please drop specification unless essential
checkRd: (-1) Auxil.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Auxil.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Auxil.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Auxil.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Predict.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Predict.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Predict.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘service-cohere.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:
    ‘predict.R’ ‘utils.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LR_GradientConjugate_gpumatrix.Rd: Matrix-class
  gpu.matrix-class.Rd: Matrix-class
  gpu.matrix.Rd: Matrix-class
  matrix-product.Rd: %&%
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Malformed Title field: should not end in a period.
checkRd: (-1) grade-package.Rd:51-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:58-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:72-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:79-81: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  grafzahl.Rd: corpus, docvars
  predict.grafzahl.Rd: corpus
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' call not declared from: ‘Rgraphviz’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  grand.Rd: igraph
  grand.table.Rd: igraph
  grand.text.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Granger.inference.difference.Rd:65: Lost braces; missing escapes or markup?
    65 |         least one root larger than one) on bootstrapped \verb{x} and {y}.
       |                                                                      ^
checkRd: (-1) Granger.inference.difference.Rd:68: Lost braces; missing escapes or markup?
    68 |         least one root larger than one) on bootstrapped \verb{x} and {z}.
       |                                                                      ^
checkRd: (-1) Granger.inference.difference.Rd:71: Lost braces; missing escapes or markup?
    71 |         least one root larger than one) on bootstrapped \verb{x}, \verb{y} and {z}.
       |                                                                                ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘amino_acid_pairs.R’
checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) crdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) descApp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) layoutApp.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) rbdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) ttApp.Rd:43: Escaped LaTeX specials: \&
Unknown package ‘edmcr’ in Rd xrefs
Specified C++11: please drop specification unless essential
Unknown package ‘rtweet’ in Rd xrefs
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gmmpairs.Rd: ggplot2
  plot-DcLbmFit-missing-method.Rd: ggplot2
  plot-DcLbmPath-missing-method.Rd: ggplot2
  plot-DcSbmFit-missing-method.Rd: ggplot2
  plot-DiagGmmFit-missing-method.Rd: ggplot2
  plot-GmmFit-missing-method.Rd: ggplot2
  plot-IclPath-missing-method.Rd: ggplot2
  plot-LcaFit-missing-method.Rd: ggplot2
  plot-MoMFit-missing-method.Rd: ggplot2
  plot-MultSbmFit-missing-method.Rd: ggplot2
  plot-SbmFit-missing-method.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) MinimiseEPL.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MinimiseEPL.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MinimiseEPL.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MinimiseEPL.Rd:20: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  caDescribeOpts.Rd: describeMean, describeFactors
  prGetStatistics.Rd: describeMean, describeFactors
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) GREMLINS.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GREMLINS.Rd:23: Lost braces in \itemize; meant \describe ?
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
checkRd: (-1) setgreportOption.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:24: Lost braces
    24 | \item{code{figpos}:}{LaTeX figure environment position; default is \code{"htb!"}}
       |           ^
checkRd: (-1) setgreportOption.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setgreportOption.Rd:29: Lost braces in \itemize; meant \describe ?
Malformed Description field: should contain one or more complete sentences.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  agopenTrue.Rd: agopen
  graphWidth.Rd: Ragraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘otgrid.R’ ‘otgridtransport.R’ ‘pivot_measure.R’ ‘transport1d.R’
    ‘transport_cost.R’ ‘transport_costmat.R’ ‘transport_df.R’
    ‘without_zeros.R’
checkRd: (-1) NEWS.Rd:669: Lost braces; missing escapes or markup?
   669 |     parameters are rounded so they belong to one of {0, 0.5, 1}. (Simon)
       |                                                     ^
checkRd: (-1) gradients.Rd:96-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gradients.Rd:100-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gradients.Rd:104-107: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  readCoordsJS.Rd: fromJSON
  readMappingsJS.Rd: fromJSON
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.Rd:30: Lost braces
    30 | resp. code{'exponential'} or \code{'no_lag'} for \code{fit_easylinear}.}
       |           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cost.Rd: modCost
  fit_growthmodel.Rd: modFit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘p1_20up-vs-p2_25up_in_str1.txt’ ‘p1_20up-vs-p2_25up_in_str2.txt’
  ‘p2_25up-vs-p1_20up_in_str1.txt’ ‘p2_25up-vs-p1_20up_in_str2.txt’
  ‘s0_20up.txt’ ‘s0_30up.txt’ ‘s0_f2up.txt’ ‘strs.vec_01mx.txt’
  ‘strs.vec_02mx.txt’ ‘strs.vec_03mx.txt’ ‘strs.vec_04mx.txt’
  ‘strs.vec_05mx.txt’ ‘strs.vec_06mx.txt’ ‘strs.vec_30up.txt’
  ‘strs.vec_50up.txt’ ‘strs.vec_f2up.txt’ ‘uni_p1_20up-p2_25up.txt’
checkRd: (-1) matches.Rd:33: Lost braces; missing escapes or markup?
    33 | be set to an index value of \code{length+1}.  If {indexes=FALSE}, they will
       |                                                  ^
File ‘grr/libs/grr.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) runGRM.Rd:24: Lost braces
    24 |    from \code{\link{mirt}} or code{\linkS4class{lavaan}} from from
       |                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ESplot.Rd: scale_color_viridis_d, ggplot
  FSplot.Rd: ggplot
  ICCplot.Rd: scale_color_viridis_d, ggplot
  genLavSyn.Rd: lavaan
  infoPlot.Rd: scale_color_viridis_d, ggplot
  runGRM.Rd: lavaan, SingleGroupClass-class, mirt, lavaan-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) GRS.Powerfunc.Rd:22: Lost braces
    22 | {Power: }{Matrix of power values plotted}
       |          ^
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘FMD mag discontinuities_disc.png’ ‘FMD mag
  discontinuities_disc1.res’ ‘FMD mag discontinuities_disc2.res’
  ‘IDYLLWILD_bvmed.png’ ‘IDYLLWILD_fig.png’ ‘Schuster's
  diagram_schu.png’ ‘hour.res’
checkRd: (-1) qdb.p.correct.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{refpts}{a numeric vector used as a reference point to determine the correct side of the \code{qdb} for classifying \code{x}. The \code{length(refpts)} should be equal to {ncol(x)}. Default to \code{colMeans(x)}. }
       |                                                                                                                                                                                 ^
checkRd: (-1) crossval.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘expected_time.R’ ‘gs_info_ahr.R’ ‘gs_update_ahr.Rd’ ‘to_integer.Rd’
checkRd: (-1) lisiecki2005.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lisiecki2005.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lisiecki2005.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:29: Lost braces in \itemize; meant \describe ?
File ‘gsl/libs/gsl.so’:
  Found non-API calls to R: ‘EXTPTR_PTR’, ‘EXTPTR_TAG’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
checkRd: (-1) artset1987.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gte.Rd:98: Lost braces; missing escapes or markup?
    98 | \code{left} and {right} for illustrative purpose), one would need a third variable (\code{status}) taking the value 0 
       |                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gte.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 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_ieqtls.R’ ‘calculate_isqtls.R’ ‘download.R’
    ‘get_annotation.R’ ‘get_downloads_page_data.R’ ‘get_file_list.R’
    ‘get_gene_expression.R’ ‘get_genomic_features.R’ ‘get_image.R’
    ‘get_sample_biobank_data.R’ ‘get_service_info.R’
    ‘get_significant_single_tissue_eqtls_by_location.R’
    ‘get_single_nucleus_gex.R’ ‘get_tissue_site_detail.R’ ‘gtex_query.R’
    ‘handle_http_errors.R’ ‘utils.R’ ‘validate_args.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:
    ‘adjust_speed.R’ ‘adjust_speed.Rd’ ‘gps_as_sflinestring.Rd’
    ‘gps_as_sfpoints.Rd’ ‘gtfs2gps.Rd’ ‘write_gtfs.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘gfrance85.Rd’
checkRd: (-1) PLSSVD.Rd:24: Lost braces; missing escapes or markup?
    24 | The number of low-dimension (k < {N, M, L}, Default: .minDim(X, Y))
       |                                  ^
checkRd: (-1) guidedPLS.Rd:33: Lost braces; missing escapes or markup?
    33 | The number of low-dimension (k < {N, M, L, O}, Default: .minDim(X1, X2, Y1, Y2))
       |                                  ^
checkRd: (-1) sPLSDA.Rd:24: Lost braces; missing escapes or markup?
    24 | The number of low-dimension (k < {N, M, L}, Default: .minDim(X, Y))
       |                                  ^
checkRd: (-1) guild_merge.Rd:38: Lost braces; missing escapes or markup?
    38 |     \item{\code{summary_name}}{Name used for the run summary. Use '${run_id}' in the name to include the run ID.}
       |                                                                     ^
checkRd: (-1) guild_merge_cli.Rd:88: Lost braces; missing escapes or markup?
    88 | \item{summary_name}{Name used for the run summary. Use '${run_id}' in the name to include the run ID.}
       |                                                          ^
Found the following files/directories:
  ‘RRprof.out’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  adonis3.Rd: vegdist, permustats
  dmanova.Rd: vegdist, nearPD
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GUTS-package.Rd: Rcpp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) esSim.Rd:81: Lost braces; missing escapes or markup?
    81 | \eqn{83} SNPs are in cluster {-}, \eqn{714} SNPs are in cluster \eqn{0},
       |                              ^
checkRd: (-1) esSimDiffPriors.Rd:91: Lost braces; missing escapes or markup?
    91 | \eqn{64} SNPs are in cluster {-}, \eqn{708} SNPs are in cluster \eqn{0},
       |                              ^
checkRd: (-1) gWidgets2tcltk-undocumented.Rd:285: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gWidgets2tcltk-undocumented.Rd:286-293: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gWidgets2tcltk-undocumented.Rd:378: Lost braces
   378 | \item{visible}{logical. If code{TRUE} window is drawn when
       |                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gWidgets2tcltk-undocumented.Rd: gbutton, gprogressbar
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 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’
Found the following files/directories:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  habCluster-package.Rd: raster, Rcpp, igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Error(s) in re-building vignettes:
  ...
--- re-building ‘hacksig.Rmd’ using rmarkdown

Quitting from hacksig.Rmd:215-225 [unnamed-chunk-19]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `msigdbr()`:
! Unknown subcollection.
---
Backtrace:
    ▆
 1. ├─... %>% deframe()
 2. ├─tibble::deframe(.)
 3. ├─dplyr::mutate(., genes = map(genes, compose(as_vector, unname)))
 4. ├─tidyr::nest(., genes = c(gene_symbol))
 5. ├─dplyr::distinct(., gs_name, gene_symbol)
 6. └─msigdbr::msigdbr(species = "Homo sapiens", subcategory = "KEGG")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'hacksig.Rmd' failed with diagnostics:
Unknown subcollection.
--- failed re-building ‘hacksig.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_kinetics.Rd: bind_rows
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  diversities_table.Rd: pander, pandoc.table
  individual_pathotypes.Rd: pander
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  format_long_hazards.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.ga.breed’ ‘.ga.fitness’ ‘.ga.init’ ‘.ga.mutate’ ‘.ga.step’
  ‘.ga.weight’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Parsimnet-class.Rd: network, networx
  as.DNAbin-methods.Rd: DNAbin
  as.dna-methods.Rd: DNAbin, phyDat
  as.network-methods.Rd: network
  as.networx-methods.Rd: networx, as.splits
  as.phyDat-methods.Rd: phyDat
  parsimnet-methods.Rd: network
  pielegend-methods.Rd: floating.pie, plot.network.default
  pieplot-methods.Rd: network.layout, floating.pie, network.vertex,
    plot.network.default
  plot-methods.Rd: plot.network.default
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘hdis_sax.R’ ‘hmo_sax.R’ ‘hmo_xsax.R’
'library' or 'require' call not declared from: ‘rbenchmark’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  att.Rd: estimatr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++14: please drop specification unless essential
checkRd: (-1) deff.sigma.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:35: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dcbs.alg.Rd: foreach
  sbs.alg.Rd: foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) phenowheat.Rd:18: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) phenowheat.Rd:19: Lost braces in \enumerate; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cure_estimate.Rd: survfit
  nonzerocure_test.Rd: survfit
  sufficient_fu_test.Rd: survfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) lasso.proj.Rd:62: Lost braces; missing escapes or markup?
    62 |     indicated using an index vector with entries in {1,...,p} or a list thereof.}
       |                                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lasso.cv.Rd: cv.glmnet
  lasso.firstq.Rd: glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘lvma_utils.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mediate_hdmm.Rd: mediate
  mediate_hima.Rd: hdi
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package required but not available: ‘ggjoy’

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:
    ‘the_XXX.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:
    ‘plt-gartner-magic-chart.R’ ‘utils-save-to-excel.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-random-walk.R’ ‘ts-vva-plot.R’
Malformed Title field: should not end in a period.
checkRd: (-1) colByValue.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.}
       |                       ^
checkRd: (-1) heatmaply.Rd:282: Lost braces
   282 | row and column dendrograms. The default uses stats{reorder.dendrogram}}
       |                                                   ^
checkRd: (-1) heatmapr.Rd:93: Lost braces
    93 | \item{reorderfun}{function(d, w) of dendrogram and weights for reordering the row and column dendrograms. The default uses stats{reorder.dendrogram}}
       |                                                                                                                                 ^
checkRd: (-1) is.plotly.Rd:16: Lost braces
    16 | Helpful for the plot_method in link{heatmaply}.
       |                                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RColorBrewer_colors.Rd: brewer.pal, viridis
  heatmaply.Rd: scale_color_gradient
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 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.heckmange.R’
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘AddHealth.Rd’ ‘oral.Rd’
'library' or 'require' calls not declared from:
  ‘KernSmooth’ ‘aplpack’ ‘foreign’
checkRd: (-1) marker_h2.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:96-97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:98-99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:41-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:46-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:49-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:52-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:55-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:61-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:66-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) phermite.Rd:38: Lost braces; missing escapes or markup?
    38 |   {b} and \code{m} to be lower (or greater) than \code{q}.
       |   ^
checkRd: (-1) hero.Rd:67-68: Lost braces
    67 | then \code{\link[pbapply]{pblapply}} is used. If code{package ==
       |                                                      ^
checkRd: (-1) hero.Rd:69: Lost braces
    69 | code{package == "Rmpi"}, then \code{\link[Rmpi]{mpi.applyLB}} is used.}
       |     ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘autoplot.R’ ‘clarke_wright.R’ ‘cvrplib.R’ ‘heumilkr_solution.R’
checkRd: (-1) predictPair.Rd:20: Lost braces; missing escapes or markup?
    20 | A number in the set {-1, 0, 1}, where 1 means row1 is predicted to
       |                     ^
checkRd: (-1) predictPairInternal.Rd:18: Lost braces; missing escapes or markup?
    18 | A number in the set {-1, 0, 1}, where 1 means row1 is predicted to
       |                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.hglasso.Rd: layout.kamada.kawai, plot.igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ftp_ls.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_threshold.R’ ‘compute_chromosomes_length.R’
    ‘create_hidecan_plot.R’ ‘gwaspoly_helper_functions.R’
    ‘input_data_constructors.R’
checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^
checkRd: (-1) hierNet.Rd:28: Lost braces; missing escapes or markup?
    28 |     terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |               ^
checkRd: (-1) hierNet.logistic.Rd:30: Lost braces; missing escapes or markup?
    30 |     terms, th_{jj}X_j^2, in the model.  Default TRUE.}  
       |               ^
checkRd: (-1) hierNet.logistic.Rd:63: Lost braces
    63 | \seealso{\link{predict.hierNet.logistic},link{hierNet.logistic.path}}
       |                                              ^
checkRd: (-1) hierNet.logistic.path.Rd:39: Lost braces; missing escapes or markup?
    39 |   terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |             ^
checkRd: (-1) hierNet.path.Rd:38: Lost braces; missing escapes or markup?
    38 |   terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |             ^
Specified C++11: please drop specification unless essential
File ‘highs/libs/highs.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘highslib/lib/libhighs.a’
  Found ‘abort’, possibly from ‘abort’ (C)
    Object: ‘highslib/lib/libhighs.a’
  Found ‘exit’, possibly from ‘exit’ (C)
    Object: ‘highslib/lib/libhighs.a’
  Found ‘printf’, possibly from ‘printf’ (C)
    Object: ‘highslib/lib/libhighs.a’
  Found ‘putchar’, possibly from ‘putchar’ (C)
    Object: ‘highslib/lib/libhighs.a’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘highslib/lib/libhighs.a’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘highslib/lib/libhighs.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘maps.R’ ‘utils.R’
File ‘hipread/libs/hipread.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hlm_resid.lmerMod.Rd: ranef
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) hlt.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hlt.Rd:77-78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hlt.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hlt.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hlt.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hlt.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hltsim.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
Fdebug: multiple local function definitions for ‘deb’ with different
  formal arguments
html_describe_con: multiple local function definitions for ‘g’ with
  different formal arguments
checkRd: (-1) nafracCalc.Rd:45: Lost braces
    45 |   as if code{y} were not of class \code{"multipleHmmDataSets"}.
       |             ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) sampleMcmc.Rd:93: Lost braces; missing escapes or markup?
    93 |   disable some of them, by adding a \code{$UPDATER_NAME=FALSE} pair to the {updater} argument. Another usage of
       |                                                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotBeta.Rd: image.plot
  plotGamma.Rd: image.plot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘theme_hmsid.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hms.Rd: vec_cast
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) HOasso.Rd:43: Lost braces; missing escapes or markup?
    43 | Arguments \code{x} and {y} are \code{character} objects and can assume values   \code{"sout"}, \code{"dout"}, \code{"lout"}, \code{"sin"}, \code{"din"}, \code{"lin"} representing the out-strength, out-degree, out-log-strength, in-strength, in-degree, and in-log-strength respectively.
       |                        ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘daily_temp.R’ ‘extra_viz.R’ ‘instrumental_temp.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:
    ‘rstar_glm.Rd’ ‘run_sim_rstar_glm.Rd’ ‘sim_rstar_glm.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  holland-package.Rd: MplusAutomation
  sim_score_data.Rd: rmvnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  poly2form.Rd: legendre.polynomials
  psiandrew.Rd: rlm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) hd.ord.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hd.ord.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hot.deck.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) HPLB.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:38: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  scale_x_percent.Rd: guides
  theme_ipsum.Rd: ggplot2
  theme_ipsum_es.Rd: ggplot2
  theme_ipsum_gs.Rd: ggplot2
  theme_ipsum_inter.Rd: ggplot2
  theme_ipsum_ps.Rd: ggplot2
  theme_ipsum_pub.Rd: ggplot2
  theme_ipsum_rc.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  critical.value.Rd: davies
  size.Rd: davies
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' calls not declared from:
  ‘Ecdat’ ‘LowRankQP’ ‘VGAM’ ‘e1071’ ‘fda’ ‘fda.usc’ ‘mlbench’ ‘nlme’
  ‘quantreg’ ‘refund’ ‘rgl’ ‘rstan’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  HSDiC_ADMM.Rd: solve.QP
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
File ‘htmltools/libs/htmltools.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
'::' or ':::' import not declared from: ‘rstudioapi’
Specified C++11: please drop specification unless essential
checkRd: (-1) CalcROC.Rd:47: Lost braces
    47 | The accuracy of the classifier is the mean value of dQuote{(optSn, optSp)} for two-class problem and the mean value of \dQuote{(optSn, optSp,optS3)} for three-class problem.
       |                                                           ^
checkRd: (-1) simgl.Rd:50: Lost braces; missing escapes or markup?
    50 | Uses the {updog} R package for simulating read counts and generating
       |          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hwep-package.Rd: future
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ws_download.Rd:31: Lost braces; missing escapes or markup?
    31 | (while using the {hwsdr} package for HWSD v2.0).
       |                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hybridModel.Rd: GillespieSSA
  simHM.Rd: GillespieSSA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 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_divergence.R’ ‘add_levelpaths.R’ ‘add_pfafstetter.R’
    ‘add_streamorder-level.R’ ‘add_toids.R’ ‘disambiguate.R’
    ‘format_index_ids.Rd’ ‘get_hydro_location.R’
    ‘index_points_to_lines.R’ ‘make_attribute_topology.R’
    ‘make_index_ids.R’ ‘make_node_topology.R’
    ‘navigate_connected_paths.R’ ‘navigation_network.R’ ‘sort_network.R’
    ‘to_flownetwork.R’ ‘utils.R’
checkRd: (-1) extractPeriod.Rd:57: Lost braces
    57 | NOTE: all the dates in the datalist should follow the format in ?as.Date{base}.
       |                                                                         ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘psubs.Rd’ ‘pwa.Rd’ ‘tennis.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hyper.fit.Rd: LaplaceApproximation, LaplacesDemon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  map-sel-poly.Rd: levelplot
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:
    ‘hypothesis-api.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:
    ‘equations.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calc_areas.Rd: area, values
  generateHypsoTables.Rd: crop, mask, classify
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) IATData.Rd:24: Lost braces; missing escapes or markup?
    24 | Dan Martin {dpmartin42@gmail.com}
       |            ^
checkRd: (-1) setServerLogLevel.Rd:20: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:23: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) betaS1lr.Rd:28: Lost braces; missing escapes or markup?
    28 |  \item{Rm1U}{matrix R^{-1}U (see reference).}
       |                       ^
checkRd: (-1) lrsmoother.Rd:32: Lost braces; missing escapes or markup?
    32 |   R^{-1}U (see reference) and \link{smoothCon} for the definition of smoothobject}
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  forward.Rd: gam
  ibr.Rd: gam, smoothCon
  ibr.fit.Rd: gam, smoothCon
  lrsmoother.Rd: smoothCon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AnnotateDBSVCF.Rd: BSgenome
  AnnotateSBSVCF.Rd: BSgenome
  GeneExpressionData.Rd: data.table
  ICAMS.Rd: BSgenome
  MutectVCFFilesToCatalog.Rd: BSgenome
  MutectVCFFilesToCatalogAndPlotToPdf.Rd: BSgenome
  MutectVCFFilesToZipFile.Rd: BSgenome
  NormalizeGenomeArg.Rd: BSgenome
  PlotTransBiasGeneExp.Rd: data.table
  PlotTransBiasGeneExpToPdf.Rd: data.table
  StrelkaSBSVCFFilesToCatalog.Rd: BSgenome
  StrelkaSBSVCFFilesToCatalogAndPlotToPdf.Rd: BSgenome
  StrelkaSBSVCFFilesToZipFile.Rd: BSgenome
  VCFsToCatalogs.Rd: BSgenome
  VCFsToCatalogsAndPlotToPdf.Rd: BSgenome
  VCFsToDBSCatalogs.Rd: BSgenome
  VCFsToSBSCatalogs.Rd: BSgenome
  VCFsToZipFile.Rd: BSgenome
  revc.Rd: reverseComplement
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  crt.minimax.control.Rd: nl.opts
  sens.control.Rd: nl.opts
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘icd_lookup.R’
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  run.umap.Rd: umap_transform
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 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’
checkRd: (-1) Bpa.Rd:39-40: Lost braces
    39 | stocks. \doi{10.17895/ices.pub.3036}{\emph{ICES Advice
       |                                     ^
checkRd: (-1) Fpa.Rd:42-43: Lost braces
    42 | stocks. \doi{10.17895/ices.pub.3036}{\emph{ICES Advice
       |                                     ^
checkRd: (-1) icesRound.Rd:64-65: Lost braces
    64 | \doi{10.17895/ices.pub.3038}{\emph{ICES Advice Technical
       |                             ^
checkRd: (-1) mohn.Rd:71-72: Lost braces
    71 | \doi{10.17895/ices.pub.5997}{\emph{ICES Scientific Reports
       |                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  taf.colors.Rd: TAF-package
  taf.skeleton.sa.org.Rd: TAF-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  INCAnumclu.Rd: pam, diana, fanny
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) ic.ranks.Rd:46: Lost braces; missing escapes or markup?
    46 | \item{n_adjust}{an integer-valued entry for advanced control over the lower- or upper-bound algorithms. When the "adjustL" parameter is TRUE, the new value of n_adjust is chosen automatically as the best adjustment on the lower affine bound of the chi-square quantiles according to the data. If adjustU is TRUE, then n_adjust contains the point at which the upper affine bound is tangent on the chi-square quantiles. Possible values {1,...,n-1}. If both adjustL and adjustU variables are left FALSE, then the default choice is that the lower affine bound passes between the chi-square quantiles at 1 and n-1 degrees of freedom, and the upper affine bound is tangent on n-1.}
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ICSClust.Rd: ICS-S3
  component_plot.Rd: ICS-S3
  normal_crit.Rd: jarque.test, anscombe.test, bonett.test,
    agostino.test
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ics.distances.Rd: ics2
  icsOut-class.Rd: plot.ics
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) data.Rd:7: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data.Rd:9: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  covSIR.Rd: ics
  ggplot.ictest.Rd: ggpairs
  ggplot.ladle.Rd: ggpairs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  filter_log_style.Rd: crayon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' calls not declared from:
  ‘MASS’ ‘flowStats’ ‘hyperSpec’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gev.d.fit.Rd: gev.fit
  gev.d.params.Rd: gev.fit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘calibrate_LLR.R’ ‘concordance.R’ ‘contentmask.R’ ‘create_corpus.R’
    ‘delta.R’ ‘density_plot.R’ ‘impostors.R’ ‘lambdaG.R’ ‘lambdaG.Rd’
    ‘lambdaG_visualize.R’ ‘lambdaG_visualize.Rd’ ‘most_similar.Rd’
    ‘ngram_tracing.R’ ‘performance.R’ ‘posterior.R’ ‘tokenize_sents.R’
    ‘utils.R’ ‘vectorize.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:
    ‘idmc_transform_daily.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  isurvdiff.Rd: Surv
  isurvdiff.smax.Rd: Surv
  isurvfit.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  madstat.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following assignments to the global environment:
File ‘IgorR/R/ReadIgorBinary.R’:
  assign(WaveName, rval, envir = .GlobalEnv)
File ‘igraph/libs/igraph.so’:
  Found non-API call to R: ‘Rf_allocSExp’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Malformed Description field: should contain one or more complete sentences.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ig_to_igr.R’ ‘st_igr_as_sf.R’ ‘st_irishgridrefs.R’
checkRd: (-1) simHawkes1a.Rd:35: Lost braces; missing escapes or markup?
    35 | distribution; 'd${dis}' gives the density function \eqn{g(\cdot)}.}
       |                  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) lab.qcs.Rd:24: Lost braces
    24 | It develops an object of \code{lab.qcs}-code{link{class}} to perform statistical quality control.
       |                                             ^
checkRd: (-1) lab.qcs.Rd:24: Lost braces
    24 | It develops an object of \code{lab.qcs}-code{link{class}} to perform statistical quality control.
       |                                                  ^
checkRd: (-1) define_target_function.Rd:41: Lost braces; missing escapes or markup?
    41 | be done either as a single vector of values (e.g. `function(x) { ... }`), or individual inputs for each parameter
       |                                                                ^
checkRd: (-1) define_target_function.Rd:42: Lost braces; missing escapes or markup?
    42 | (e.g. `function(x1, x2) { ... }`). If a single vector is used, all parameters will be passed to the target function as
       |                         ^
checkRd: (-1) image_contour_detector.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_contour_detector.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_contour_detector.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitSpline.Rd:109: Lost braces
   109 |        \code{response} and it will have the same order of code{x} as \code{data}. 
       |                                                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  anomPlot.Rd: ggplot
  corrPlot.Rd: ggplot
  imagetimesPlot.Rd: ggplot
  longiPlot.Rd: ggplot, labeller
  probeDF.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) image_line_segment_detector.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_line_segment_detector.Rd:66-72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_line_segment_detector.Rd:73-76: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) imagesToKerasInput.Rd:23: Lost braces
    23 | \item{grayscale}{logical. Defines color channels of images: 1 if code{TRUE}, 3 if \code{FALSE}.}
       |                                                                      ^
Specified C++11: please drop specification unless essential
checkRd: (-1) oversample.Rd:23-24: Lost braces
    23 | minority examples and majority ones, that is, the quotient {size of
       |                                                            ^
checkRd: (-1) oversample.Rd:24: Lost braces; missing escapes or markup?
    24 | minority class}/{size of majority class}. There are methods, such as
       |                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  imgur_login.Rd: oauth2.0_token
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coding.Rd: data.table, copy_to
  dbAnnotate.Rd: data.table, copy_to
  geneUsage.Rd: data.table, copy_to
  getKmers.Rd: data.table, copy_to
  immunr_hclust.Rd: fviz_nbclust, hcut, dbscan
  immunr_pca.Rd: isoMDS, Rtsne
  inc_overlap.Rd: data.table, copy_to
  pubRep.Rd: data.table, copy_to
  repAlignLineage.Rd: data.table
  repClonality.Rd: data.table, copy_to
  repDiversity.Rd: data.table, copy_to
  repExplore.Rd: data.table, copy_to
  repGermline.Rd: data.table
  repOverlap.Rd: data.table, copy_to
  repSample.Rd: data.table, copy_to
  select_barcodes.Rd: data.table, copy_to
  seqCluster.Rd: data.table
  seqDist.Rd: data.table
  spectratype.Rd: data.table, copy_to
  top.Rd: data.table, copy_to
  trackClonotypes.Rd: data.table, copy_to
  vis.immunr_gene_usage.Rd: chordDiagram
  vis.immunr_hclust.Rd: fviz_dend
  vis.immunr_kmeans.Rd: fviz_cluster
  vis.immunr_ov_matrix.Rd: chordDiagram
  vis.immunr_public_statistics.Rd: upset
  vis_box.Rd: melt
  vis_circos.Rd: chordDiagram
  vis_hist.Rd: melt
  vis_textlogo.Rd: geom_logo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) stringCSSRule.Rd:22: Lost braces
    22 | using the {{placeholder}} convention.
       |           ^
checkRd: (-1) stringTemplate.Rd:23: Lost braces
    23 | placeholders are marked using the {{placeholder}} convention.
       |                                   ^
checkRd: (-1) stringTemplate.Rd:12: Lost braces
    12 | {{placeholder}} format.}
       | ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  flexPage.Rd: htmlDependency, tagList, shinyUI
  flexPanel.Rd: HTML, htmlDependency, tagList
  gridPage.Rd: htmlDependency, tagList, shinyUI
  gridPanel.Rd: HTML, htmlDependency, tagList
  stringCSSRule.Rd: htmlTemplate
  stringTemplate.Rd: htmlTemplate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) imptree_params.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imptree_params.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imptree_params.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.imptree.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 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’
checkRd: (-1) kmpp.Rd:27: Lost braces
    27 |   \item{call}{a string containing the matched function call that generates this sQuote{inaparc} object.}
       |                                                                                       ^
'::' or ':::' imports not declared from:
  ‘GGally’ ‘NbClust’ ‘cluster’ ‘factoextra’ ‘vegclust’
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  if_case.Rd: magrittr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  add.blocks.Rd: igraph
  curveball.Rd: igraph
  incidence.from.adjacency.Rd: igraph
  incidence.from.distribution.Rd: igraph
  incidence.from.probability.Rd: igraph
  incidence.from.vector.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) make_likelihood_matrix.Rd:16: Lost braces; missing escapes or markup?
    16 | This function creates a matrix such that P[t, s] = P(C = t | I = s) = theta_{t-s} for s <= t and 0 otherwise.
       |                                                                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  incRplot.Rd: ggplot2
  incRt.Rd: getSunlightTimes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) IndexComp.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IndexComp.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly
File ‘indexthis/libs/indexthis.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:
  cooks.distance.Rd: ols, lad, ridge
  leverages.Rd: ols, ridge
  logLik.displacement.Rd: ols, lad, ridge
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) process_stats.Rd:11: Lost braces; missing escapes or markup?
    11 | the {janitor} package}
       |     ^
checkRd: (-1) theme_industRial.Rd:40: Lost braces; missing escapes or markup?
    40 | adapted from the package {cowplot} by Claus O.Wilke and reflects the principles
       |                          ^
checkRd: (-1) theme_industRial.Rd:45: Lost braces; missing escapes or markup?
    45 | It basically combines the half open theme with a grid background from {cowplot}
       |                                                                       ^
checkRd: (-1) vaccinesim.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vaccinesim.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vaccinesim.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vaccinesim.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vaccinesim.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vaccinesim.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) voters.Rd:18: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  score_calc.Rd: grad
  score_matrix.Rd: grad
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Deltachi.Rd: lavaan, sem
  Likedist.Rd: lavaan, sem
  fitinfluence.Rd: lavaan, sem
  genCookDist.Rd: lavaan, sem
  parinfluence.Rd: lavaan, sem
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘c.txt’ ‘rho.txt’ ‘sta.txt’ ‘topo.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:
    ‘gg_injprev_polar.R’ ‘gg_injriskmatrix.R’ ‘helpers.R’ ‘injprev.R’
    ‘injsummary.R’ ‘prepare_data.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:
    ‘plot_functions.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  manipulate.Rd: ape
  purge.Rd: kmer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  csmf.diag.Rd: heidel.diag, gelman.diag
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
checkRd: (-1) ask.user.yn.question.Rd:44: Lost braces; missing escapes or markup?
    44 | menu in the {utils} package, yesno in the {devtools} package.
       |             ^
checkRd: (-1) ask.user.yn.question.Rd:44: Lost braces; missing escapes or markup?
    44 | menu in the {utils} package, yesno in the {devtools} package.
       |                                           ^
checkRd: (-1) install.FFmpeg.Rd:25: Lost braces; missing escapes or markup?
    25 | This function is useful for saveVideo() in the {animation} package.
       |                                                ^
checkRd: (-1) install.SWFTools.Rd:27: Lost braces; missing escapes or markup?
    27 | This function is useful for saveSWF() in the {animation} package.
       |                                              ^
checkRd: (-1) os.shutdown.Rd:25: Lost braces; missing escapes or markup?
    25 | This function is a modified version of Yihui's shutdown function from the {fun} package.
       |                                                                           ^
Malformed Title field: should not end in a period.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘autoplot.restricted.Rd’ ‘autoplot.riskfactor.Rd’ ‘rating_factors.Rd’
'library' or 'require' call not declared from: ‘rworldmap’
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘Error_Estimation_Response_1.tiff’ ‘Error_Estimation_Response_2.tiff’
  ‘Error_Estimation_Response_3.tiff’
Specified C++11: please drop specification unless essential
checkRd: (-1) remit.Rd:32: Lost braces
    32 | A data set to replicate the findings of Escrib\`{a}-Folch,
       |                                                 ^
checkRd: (-1) remit.Rd:38: Lost braces
    38 | Escrib\`{a}-Folch, A., Meseguer, C. and Wright, J. (2018), Remittances and Protest in Dictatorships. American Journal of Political Science, 62: 889-904. \doi{10.1111/ajps.12382}
       |         ^
checkRd: (-1) interval-internal.Rd:40: Lost braces
    40 | \item{dqfunc}{function, density of the results of the quantile function, e.g., function(x){dnorm(qnorm(x))} (used for 'general' scores, 
       |                                                                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  inTextSummaryTable-stats.Rd: roundHalfUpTextFormat
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) decompose_volume.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decompose_volume.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decompose_volume.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decompose_volume.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fit_volume.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fit_volume.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fit_volume.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fit_volume.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forecast_volume.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_plots.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_plots.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_plots.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) intRvals-package.Rd:60: Lost braces
    60 | B\'{e}dard, J. & Gauthier, G. 1986. Assessment of faecal output in geese. Journal of Applied Ecology, 23, 77-90.
       |    ^
checkRd: (-1) partition.Rd:64: Lost braces
    64 | Bates, D., M\"{a}chler, M., Bolker, B.M. & Walker, S.C. (2015). Fitting linear mixed-effects models using lme4. Journal of Statistical Software, 67, 1-48.
       |               ^
Specified C++11: please drop specification unless essential
checkRd: (-1) cox_cure_net.Rd:132: Lost braces
   132 | \code{surv_lambda} (or code{cure_lambda}) that produces all-zero
       |                            ^
checkRd: (-1) Inventorymodel-package.Rd:34: Lost braces
    34 | M.G. Fiestras-Janeiro, I. García-Jurado, A. Meca, M.A. Mosquera (2015). Cooperation on capacitated inventory situations with fixed holding costs. emph{European Journal of Operational Research}, \bold{241}(3), 719--726.
       |                                                                                                                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NormalizedLaplacian.Rd: Matrix-class
  PerturbedLaplacian.Rd: Matrix-class
  RegularizedLaplacian.Rd: Matrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  iNZightSummary.Rd: survey
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘aggregate.R’ ‘append_rows.R’ ‘class_intervals.R’ ‘extract_dt_comp.R’
    ‘helpers.R’ ‘join_data.R’ ‘mutate.R’ ‘read_text.R’ ‘separate_var.R’
    ‘sort_vars.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  survey_IQR.Rd: srvyr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘decomposition.R’ ‘feat.R’ ‘forecastplot.R’ ‘iNZightTS.R’ ‘rawplot.R’
    ‘seasonplot.R’
checkRd: (-1) f.influence.Rd:25: Lost braces; missing escapes or markup?
    25 | where F is the field of influence, k is order of influence, l_{ij} is the ith row and jth column element of the Leontief Inverse and -s indicates the sth element has been removed.
       |                                                               ^
checkRd: (-1) aiPux.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dls2007.Rd:19: Lost braces
    19 | impact. emph{Journal of Applied Psychology}, 92(5), 1380.
       |             ^
checkRd: (-1) paretoXX.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXX.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXX.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXY.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXY.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXY.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_iota.Rd: ggplot2
  plot_iota2_alluvial.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘DATAPTR’, ‘NAMED’, ‘R_GetConnection’,
    ‘R_ReadConnection’, ‘R_WriteConnection’, ‘SETLENGTH’, ‘SET_NAMED’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Missing dependency on R >= 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_lhat_glm.Rd’ ‘ipd.R’ ‘logistic_get_stats.Rd’ ‘ols_get_stats.Rd’
    ‘postpi_analytic_ols.Rd’ ‘postpi_boot_logistic.Rd’
    ‘postpi_boot_ols.Rd’ ‘ppi_logistic.Rd’ ‘ppi_mean.Rd’ ‘ppi_ols.R’
    ‘ppi_ols.Rd’ ‘ppi_plusplus_logistic.Rd’
    ‘ppi_plusplus_logistic_est.Rd’ ‘ppi_plusplus_mean.Rd’
    ‘ppi_plusplus_mean_est.Rd’ ‘ppi_plusplus_ols.Rd’
    ‘ppi_plusplus_ols_est.Rd’ ‘ppi_plusplus_quantile.Rd’
    ‘ppi_plusplus_quantile_est.Rd’ ‘ppi_quantile.Rd’ ‘pspa_logistic.Rd’
    ‘pspa_mean.Rd’ ‘pspa_ols.Rd’ ‘pspa_poisson.Rd’ ‘pspa_quantile.Rd’
    ‘simdat.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  curvIPEC.Rd: hessian, jacobian, rms.curv
  skewIPEC.Rd: ginv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) check_convergence.Rd:47: Lost braces
    47 | \code{conv_plot}: code{ipm} invisibly.
       |                       ^
checkRd: (-1) init_ipm.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:63-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:70-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init_ipm.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make_ipm.Rd:276: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) make_ipm.Rd:277-281: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) make_ipm.Rd:282-286: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) make_ipm.Rd:287-291: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) make_ipm.Rd:292-293: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DNAbin2index.Rd: DNAbin
  EmptyCells.Rd: DNAbin
  code.simple.gaps.Rd: DNAbin
  collapseUnsupportedEdges.Rd: phylo
  combMyTree.Rd: phylo
  del.miss.Rd: DNAbin
  deleteGaps.Rd: DNAbin
  fixNodes.Rd: phylo, read.nexus
  forceEqualTipHeights.Rd: is.ultrametric, chronos
  index2DNAbin.Rd: DNAbin
  ips-package.Rd: ladderize, rotate
  ips.16S.Rd: DNAbin
  ips.28S.Rd: DNAbin
  ips.cox1.Rd: DNAbin
  mafft.Rd: phylo
  mafft.merge.Rd: DNAbin, AAbin, phylo
  mrbayes.Rd: DNAbin
  multistate.Rd: ace
  neighboringPairs.Rd: mst
  ntip.Rd: phylo
  pathd8.Rd: phylo
  phylo2mafft.Rd: phylo
  phylo2mst.Rd: phylo
  pis.Rd: DNAbin
  raxml.Rd: DNAbin, phylo
  raxml.partitions.Rd: DNAbin, cbind.DNAbin
  rbeauti.Rd: DNAbin
  read.Rd: cbind.DNAbin
  sister.Rd: phylo
  splitIntoClades.Rd: phylo
  terminalSisters.Rd: phylo
  tipHeights.Rd: phylo, branching.times
  traitRate.Rd: phylo, DNAbin, read.tree
  write.fas.Rd: DNAbin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ipwpoint.Rd: multinom, polr
  ipwtm.Rd: coxph, multinom, polr, geeglm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
File ‘IRISSeismic/libs/IRISSeismic.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
    Object: ‘libmseed/libmseed.a’
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
    Object: ‘libmseed/libmseed.a’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘libmseed/libmseed.a’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘libmseed/libmseed.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) partial_eigen.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) partial_eigen.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:41-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:47-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
Missing dependency on R >= 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.pvalues.R’ ‘helper.R’ ‘hypothesis_templates.R’ ‘irtpwr.R’
    ‘mml.fit.R’ ‘setup.data.R’
checkRd: (-1) analyseISE.Rd:66: Lost braces; missing escapes or markup?
    66 |         False positive rate used for detection threshold (not output) to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                                                     ^
checkRd: (-1) analyseISE.Rd:69: Lost braces; missing escapes or markup?
    69 |         False negative rate used to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                ^
checkRd: (-1) describeISE.Rd:71: Lost braces; missing escapes or markup?
    71 |         False positive rate used for detection threshold (not output) to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                                                     ^
checkRd: (-1) describeISE.Rd:74: Lost braces; missing escapes or markup?
    74 |         False negative rate used to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘chain-simulation.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  islasso.Rd: cv.glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘iso8601todataframe.R’
Specified C++11: please drop specification unless essential
File ‘isoband/libs/isoband.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) CLM.Rd:30: Lost braces
    30 | item{tau0}{the mean circular Kendall Tau of the initial order with the data.}
       |     ^
checkRd: (-1) CLM.Rd:30: Lost braces
    30 | item{tau0}{the mean circular Kendall Tau of the initial order with the data.}
       |           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mrl.Rd: rho.circular
  plot.isocir.Rd: eqscplot, plot.circular
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘calibfit.R’ ‘isofind.R’ ‘prepsources.R’ ‘serialize.R’
Specified C++14: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bicycle_theft.R’ ‘car_fleet.R’ ‘crimes_against_life.R’
    ‘gun_seizure.R’ ‘gun_seizure_historical.R’ ‘monthly_stats.R’
    ‘monthly_stats_dictionary.R’ ‘population.R’ ‘spatial_info.R’
    ‘upp_data.R’ ‘yearly_stats.R’ ‘yearly_stats_dictionary.R’
checkRd: (-1) is_israd_database.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) is_israd_database.Rd:26: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘RMTplot.pdf’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  createFastIhtPrior.Rd: fitCyclopsModel
  createIhtPrior.Rd: fitCyclopsModel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘iRNGStream.R’ ‘r_to_py.iteror.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘itrax_munsell.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fvisgam.Rd: gradientLegend
  plot_diff2.Rd: gradientLegend
  plot_parametric.Rd: dotplot_error
  plot_pca_surface.Rd: gradientLegend
  plot_topo.Rd: gradientLegend
  pvisgam.Rd: gradientLegend
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cmcc_bioclim.Rd: sf, sfc
  detect_envi_change.Rd: st_as_stars, read_stars, explain, geom_smooth
  dim_reduce.Rd: sf, sfc
  future_cmcc_bioclim.Rd: sf, sfc
  future_worldclim2.Rd: sf, sfc
  independent_response.Rd: st_as_stars, read_stars
  isotree_po.Rd: isolation.forest, sf
  mainland_africa.Rd: sf, sfc
  marginal_response.Rd: st_as_stars, read_stars
  plot.EnvironmentalOutlier.Rd: geom_sf
  plot.ShapDependence.Rd: geom_smooth
  shap_dependence.Rd: st_as_stars, read_stars, explain
  shap_spatial_response.Rd: st_as_stars, read_stars, explain
  spatial_response.Rd: st_as_stars, read_stars, explain
  suspicious_env_outliers.Rd: outlier.tree, crs, sf
  variable_analysis.Rd: st_as_stars, read_stars, explain
  variable_contrib.Rd: explain
  worldclim2.Rd: sf, sfc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 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_conservation_status.R’ ‘get_vernacularname.R’
checkRd: (-1) sTsls.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{pi}{the matrix E[XZ']E[ZZ']^{-1}}
       |                                   ^
checkRd: (-1) sTslsSplines.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{pi}{matrix, corresponds to E[XZ']E[ZZ']^{-1}, the first stage
       |                                               ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ivo_flextable_theme.Rd’ ‘ivo_table.Rd’ ‘ivo_table_add_mask.Rd’
    ‘ivo_table_masked.Rd’ ‘ivo_tables.R’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) jaccard.test.Rd:41: Lost braces; missing escapes or markup?
    41 | The {bootstrap} method uses resampling with replacement binary vectors to compute a p-value (see optional arguments).
       |     ^
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’
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.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘jdenticon.R’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) data_timeinv.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{X5}{categorical covariate taking values from {1, 2, 3, 4, 5}; time-invariant}
       |                                                    ^
checkRd: (-1) data_timeinv.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{g}{true latent class identifier {1, 2, 3, 4}, which is determined by 
       |                                       ^
checkRd: (-1) data_timevar.Rd:15: Lost braces; missing escapes or markup?
    15 | \item{X5}{categorical covariate taking values from {1, 2, 3, 4, 5}; time-varying}
       |                                                    ^
checkRd: (-1) data_timevar.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{g}{true latent class identifier {1, 2, 3, 4}, which is determined by 
       |                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  jlctree.Rd: rpart.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) jointLPM.Rd:298: Lost braces; missing escapes or markup?
   298 | following transformation b_1 + b_2*I_1(Y(t)) + ... + b_{n+2}*I_{n+1}(Y(t)),
       |                                                        ^
checkRd: (-1) jointLPM.Rd:298: Lost braces; missing escapes or markup?
   298 | following transformation b_1 + b_2*I_1(Y(t)) + ... + b_{n+2}*I_{n+1}(Y(t)),
       |                                                                ^
checkRd: (-1) jointLPM.Rd:299: Lost braces; missing escapes or markup?
   299 | where I_1,...,I_{n+1} is the basis of quadratic I-splines. To constraint the
       |                 ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) jmdem.control.Rd:42: Lost braces; missing escapes or markup?
    42 |     The control argument of \code{jmdem} is by default passed to the control argument of {jmdem.fit}, which uses its elements as arguments to {jmdem.control}: the latter provides defaults and sanity checking.
       |                                                                                          ^
checkRd: (-1) jmdem.control.Rd:42: Lost braces; missing escapes or markup?
    42 |     The control argument of \code{jmdem} is by default passed to the control argument of {jmdem.fit}, which uses its elements as arguments to {jmdem.control}: the latter provides defaults and sanity checking.
       |                                                                                                                                               ^
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  jnt_cat.Rd: corStruct, corClasses
  jnt_cont.Rd: corStruct, corClasses
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘helpfunctions_melt.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SpATS.nogeno.Rd: SAP, PSANOVA, SpATS, controlSpATS
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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:
    ‘joyn-merge.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  queryBuilderInput.Rd: shiny
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) jrt.Rd:45-46: Lost braces
    45 | \item{Difference models (more or less constrained versions of the
       |      ^
checkRd: (-1) jrt.Rd:54-55: Lost braces
    54 |  \item{Divide-by-total models (more or less constrained versions of the
       |       ^
checkRd: (-1) jSDM_binomial_probit_long_format.Rd:45: Lost braces
    45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr 
       |                                             ^
checkRd: (-1) jSDM_binomial_probit_long_format.Rd:45: Lost braces; missing escapes or markup?
    45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr 
       |                                                ^
checkRd: (-1) jSDM_binomial_probit_long_format.Rd:45: Lost braces
    45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr 
       |                                                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  jmodelMult.Rd: lme, coxph, Surv
  jmodelTM.Rd: lme, coxph, Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘includeFlickr.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  includeAudio.Rd: knitr
  includeText.Rd: knitr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
Missing dependency on R >= 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_to_json.Rd’ ‘import_from_json.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘just.install.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kanjivec.Rd: dendextend
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘kantorovich_ompr.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:
    ‘kappa_inference.R’
checkRd: (-1) get.fit.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:57-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.sim.trajectories.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.sim.trajectories.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘GaussianMixtureCalls.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  contour.kdevinecop.Rd: contour.kdecopula
  kdevinecop.Rd: kdecopula
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) kdist.Rd:14: Lost braces; missing escapes or markup?
    14 | The {kdist} functions dk, pk, qk and rk, calculates the K-distribution
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MannKendall.Rd: tsboot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' calls not declared from:
  ‘MCMCglmm’ ‘car’ ‘coda’ ‘emmeans’ ‘lattice’ ‘outliers’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  KerasCallback.Rd: R6Class
  KerasConstraint.Rd: R6Class
  KerasLayer.Rd: R6Class
  KerasWrapper.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) kernelFactory.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{method}{Can be one of the following: POLynomial kernel function (\code{pol}), LINear kernel function (\code{lin}), Radial Basis kernel Function \code{rbf}), random choice (random={pol, lin, rbf}) (\code{random}), burn- in choice of best function (burn={pol, lin, rbf }) (\code{burn}). Use \code{random} or \code{burn} if you don't know in advance which kernel function is best.}
       |                                                                                                                                                                                          ^
checkRd: (-1) kernelFactory.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{method}{Can be one of the following: POLynomial kernel function (\code{pol}), LINear kernel function (\code{lin}), Radial Basis kernel Function \code{rbf}), random choice (random={pol, lin, rbf}) (\code{random}), burn- in choice of best function (burn={pol, lin, rbf }) (\code{burn}). Use \code{random} or \code{burn} if you don't know in advance which kernel function is best.}
       |                                                                                                                                                                                                                                                                   ^
Specified C++11: please drop specification unless essential
checkRd: (-1) compute_all_tests.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) subjOCCDIF.Rd:23: Lost braces
    23 | the scale on which to evaluate each subject. \code{stype = "ObsScore"} uses the subject's total score. \code{stype = "Theta"} uses the subject's rank on the \code{thetadist} scale. \code{stype = "ThetaML"} uses the maximum likelihood estimate for the subject on the \code{thetadist} scale. code{stype = "ScoreML"} uses the maximum likelihood estimate for the subject on the overall test score scale.
       |                                                                                                                                                                                                                                                                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  keyed-df-one-tbl.Rd: dplyr
  keyed-df-two-tbl.Rd: dplyr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) useKeys.Rd:13: Lost braces; missing escapes or markup?
    13 | This function adds the {keys} dependencies to your application
       |                        ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
checkRd: (-1) kfda.Rd:26: Lost braces
    26 |  \item{kpca.train}{An object of class "kpca". It has results of \code{kpca} function. (see{\code{\link[kernlab]{kpca}}} (in package \pkg{kernlab}))}
       |                                                                                           ^
checkRd: (-1) kfino_plot.Rd:52: Lost braces; missing escapes or markup?
    52 |        plus the OK values. Prediction corresponds to E[X_{t} | Y_{1...t}] 
       |                                                          ^
checkRd: (-1) kfino_plot.Rd:52: Lost braces; missing escapes or markup?
    52 |        plus the OK values. Prediction corresponds to E[X_{t} | Y_{1...t}] 
       |                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Kernel.Rd: R6Class
  MLP.Rd: R6Class
  RBF.Rd: R6Class
  Warp.Rd: R6Class
  ode.Rd: R6Class
  rkg3.Rd: R6Class
  rkhs.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) mount_appdata.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{x}{An object of class \code{KinPairData} or {KinPairSimulation}}
       |                                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ibdMatrix.Rd: Matrix
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:
    ‘balance.R’ ‘data.R’ ‘order.R’ ‘revise.R’ ‘utils.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cross_spectrum.Rd: pspectrum
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘kit/libs/kit.so’:
  Found non-API call to R: ‘Rf_isFrame’

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) klausuR.answ-class.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:18-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:110-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:114-116: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:117-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:119-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:121-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:124-126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:152-155: Lost braces in \itemize; meant \describe ?
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:
    ‘linkedLR.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kmBlockORPC.Rd: genRandomPar
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) plotkmc.Rd:21: Lost braces; missing escapes or markup?
    21 |     list of two functions,flist=list( f1=function( x ) { x } ,f2=function( x ) { x^2 } )  
       |                                                        ^
checkRd: (-1) plotkmc.Rd:21: Lost braces; missing escapes or markup?
    21 |     list of two functions,flist=list( f1=function( x ) { x } ,f2=function( x ) { x^2 } )  
       |                                                                                ^
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  knit_bootstrap_md.Rd: knit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) knockoff.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knockoff.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MapPolygon.Rd:20: Lost braces
    20 |   \item{shape}{If the estimators in the function link[KnowBR]{KnowBPolygon} were calculated using an external shape file, it is necessary to indicate the file in this argument. It is not necessary to select any polygon within the file, just to load the whole shape file.}
       |                                                              ^
checkRd: (-1) SurveyQ.Rd:26: Lost braces
    26 |   \item{shape}{If the estimators in the function link[KnowBR]{KnowBPolygon} were calculated using an external shape file, it is necessary to indicate the file in this argument. It is not necessary to select any polygon within the file, just to load the whole shape file.}
       |                                                              ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘Koboconnect.R’ ‘other.R’
'library' or 'require' calls not declared from:
  ‘RColorBrewer’ ‘lattice’
'data(package=)' call not declared from: ‘vegan’
Specified C++11: please drop specification unless essential
checkRd: (-1) kpmt.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compose.Rd:13: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) compose.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) EGIparallel.Rd:60: Lost braces; missing escapes or markup?
    60 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion.
       |                                    ^
checkRd: (-1) max_sur_parallel.Rd:29: Lost braces; missing escapes or markup?
    29 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion. 
       |                                    ^
checkRd: (-1) max_timse_parallel.Rd:30: Lost braces; missing escapes or markup?
    30 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion. 
       |                                    ^
checkRd: (-1) max_vorob_parallel.Rd:30: Lost braces; missing escapes or markup?
    30 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion.
       |                                    ^
checkRd: (-1) print_uncertainty_nd.Rd:72: Lost braces
    72 | Optional argument. When set to code{NULL} (default) the function performs the projections on plans spanned by each pair (i,j) of dimension. Otherwise, the argument is an array of size 2 corresponding to the dimensions spanning the (only) plan on which the projection is performed.
       |                                    ^
checkRd: (-1) Predict_kernel_Ridge_MM.Rd:45: Lost braces; missing escapes or markup?
    45 |   and alpha_train is the BLUP of alpha for the model, i.e. alpha_train=Cov(alpha,Y_train)*Var(Y_train)^{-1}*(Y_train - E[Y_train]) }
       |                                                                                                        ^
checkRd: (-1) ks_test_stat.Rd:14: Lost braces
    14 | are valid. See /code{LcKS} for accepted functions.}
       |                     ^
Found the following files/directories:
  ‘KSEA Bar Plot.tiff’ ‘KSEA Kinase Scores.csv’
  ‘KSEA.Merged.Heatmap.png’ ‘Kinase-Substrate Links.csv’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_imputations.Rd: imputeTS, forecast
  kssa.Rd: imputeTS, forecast
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) GenSyntheticLogistic.Rd:46: Lost braces; missing escapes or markup?
    46 | 3) Every coordinate yi of the outcome vector y exists in {-1, 1}^n is sampled 
       |                                                          ^
checkRd: (-1) L0Learn-package.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) L0Learn-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CreateDataSet.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateDataSet.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateDataSet.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindElement.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindElement.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindNbrClusters.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindNbrClusters.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindStructure.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindStructure.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) l1_spectralclustering.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) l1_spectralclustering.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) l1_spectralclustering.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) l1_spectralclustering.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) reconcile.Rd:26: Lost braces
    26 | refer to as the sQuote{comm} data.frame.  The other data.frame contains all the
       |                       ^
Unknown package ‘optpart’ in Rd xrefs
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘as_base_data_frame.R’ ‘as_base_data_frame2.R’
    ‘as_labeled_data_frame.R’ ‘irregular2.R’
checkRd: (-1) ln_quantile_value.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_stopwords.Rd: stopwords, data_stopwords_misc
  identify_language.Rd: cld2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lacm.Rd: gauss.quad
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  contagdiscstate.Rd: Hest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bounding_box.Rd: data.table
  voxelize.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 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_gaps_perc.Rd’ ‘get_cbh_metrics.Rd’ ‘get_cum_break.Rd’
    ‘get_depths.Rd’ ‘get_distance.Rd’ ‘get_effective_gap.Rd’
    ‘get_gaps_fbhs.Rd’ ‘get_layers_lad.Rd’ ‘get_real_depths.Rd’
    ‘get_real_fbh.Rd’
checkRd: (-1) conn.Rd:300: Lost braces
   300 | Soranno et al. (2017) \doi{10.1093/gigascience/gix101}{Gigascience 6:12}
       |                                                       ^
checkRd: (-1) lakes_limno.Rd:36: Lost braces
    36 | Soranno et al. (2017) \doi{10.1093/gigascience/gix101}{Gigascience 6:12}
       |                                                       ^
'library' or 'require' call not declared from: ‘strucchange’
'library' or 'require' call not declared from: ‘plyr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘NDVI2LAI.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  load.all.data.Rd: load.ts
  load.meta.Rd: load.ts
  metab.bayesian.Rd: ts.meta.depths
  metab.bookkeep.Rd: ts.meta.depths
  metab.kalman.Rd: ts.meta.depths
  metab.mle.Rd: ts.meta.depths
  metab.ols.Rd: ts.meta.depths
  o2.at.sat.Rd: water.density
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) lambda.r-package.Rd:71-74: Lost braces
    71 | x \%g\% y \%:=\% {
       |                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bootstrap.Rd: boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) GenerateData.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:41-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) landmix.estimator.Rd:59-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) landmix.estimator.Rd:67-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DOS.Rd:34: Lost braces; missing escapes or markup?
    34 |         Band-specific sensor $G_{rescale}$ (gain). Require either gain and offset or Grescale and Brescale to convert DN to radiance.
       |                                 ^
checkRd: (-1) DOS.Rd:37: Lost braces; missing escapes or markup?
    37 |         Band-specific sensor $B_{rescale}$ (bias). Require either gain and offset or Grescale and Brescale to convert DN to radiance.
       |                                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  xylowess.fnc.Rd: xyplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) LML.Rd:43: Lost braces
    43 |     is specified only with the \code{GD}, code{HME}, or \code{NSIS}
       |                                               ^
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
checkRd: (-1) MISS.Rd:106: Lost braces
   106 |   code{Fit$Imp}. In the presence of numerous missing values, say more
       |       ^
checkRd: (-1) Matrices.Rd:316: Lost braces
   316 |   Gauss-Hermite quadrature rules. A grid of order eqn{K} provides an
       |                                                      ^
checkRd: (-1) PMC.Rd:214: Lost braces
   214 |   item{nu}{This is the degrees of freedom parameter \eqn{\nu}{nu} for
       |       ^
checkRd: (-1) PMC.Rd:214-215: Lost braces
   214 |   item{nu}{This is the degrees of freedom parameter \eqn{\nu}{nu} for
       |           ^
checkRd: (-1) caterpillar.plot.Rd:15: Lost braces
    15 |     code{demonoid.hpc}, \code{iterquad}, \code{laplace}, \code{pmc},
       |         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  draw.lar.Rd: treemap
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  latentcor.Rd: nearPD
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ESEM.Rd: lavaan
  add_population_error.Rd: bifactor
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Intercept-ergmTerm-49126971.Rd: edges-ergmTerm, ergm, ergmTerm
  bilinear-ergmTerm-3e739bd7.Rd: ergm, ergmTerm
  ergmm.Rd: ergmTerm, ergm-package, network
  ergmm.prior.Rd: ergmTerm
  euclidean-ergmTerm-6ab46c25.Rd: ergm, ergmTerm
  euclidean2-ergmTerm-939e9c32.Rd: ergm, ergmTerm
  latentcov-ergmTerm-fba43306.Rd: ergm, ergmTerm
  latentnet-package.Rd: ergmTerm
  loopcov-ergmTerm-bbc2e00a.Rd: ergm, ergmTerm
  loopfactor-ergmTerm-19d02eff.Rd: ergm, ergmTerm
  loops-ergmTerm-968722e8.Rd: ergm, ergmTerm
  receivercov-ergmTerm-ea158ece.Rd: nodeicov-ergmTerm,
    nodeifactor-ergmTerm, nodecov-ergmTerm, nodefactor-ergmTerm, ergm,
    ergmTerm
  rreceiver-ergmTerm-abdcadad.Rd: ergm, ergmTerm
  rsender-ergmTerm-b342610b.Rd: ergm, ergmTerm
  rsociality-ergmTerm-7ae668b9.Rd: ergm, ergmTerm
  sendercov-ergmTerm-a7b5c66c.Rd: nodeocov-ergmTerm,
    nodeofactor-ergmTerm, nodecov-ergmTerm, nodefactor-ergmTerm, ergm,
    ergmTerm
  socialitycov-ergmTerm-339101cf.Rd: nodecov-ergmTerm,
    nodefactor-ergmTerm, ergm, ergmTerm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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:
    ‘main.R’ ‘operators.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  latrend.Rd: Verbose
  latrendBatch.Rd: Verbose
  latrendBoot.Rd: Verbose
  latrendCV.Rd: Verbose
  latrendRep.Rd: Verbose
  update.lcModel.Rd: Verbose
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  latte-optim.Rd: mp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.layer.Rd: panel.axis
  c.trellis.Rd: xyplot, print.trellis, update.trellis, trellis.object
  combineLimits.Rd: Lattice, xyplot
  custom.theme.Rd: simpleTheme, trellis.par.get, trellis.device
  dendrogramGrob.Rd: levelplot
  doubleYScale.Rd: simpleKey
  ecdfplot.Rd: panel.qqmath, panel.xyplot, qqmath
  ggplot2like.theme.Rd: simpleTheme, axis.default, trellis.par.set,
    lattice.options
  horizonplot.Rd: xyplot.ts, levelplot, xyplot, update.trellis,
    print.trellis, Lattice
  layer.Rd: trellis.currentLayout, trellis.par.set, panel.superpose,
    update.trellis
  mapplot.Rd: xyplot, Lattice
  marginal.plot.Rd: xyplot, panel.densityplot, panel.dotplot
  panel.2dsmoother.Rd: levelplot, panel.levelplot
  panel.3dmisc.Rd: cloud, panel.cloud
  panel.ellipse.Rd: panel.xyplot
  panel.key.Rd: simpleKey, draw.key, xyplot
  panel.lmlineq.Rd: panel.abline, panel.lmline, panel.text
  panel.qqmath.tails.Rd: qqmath, panel.qqmath, panel.xyplot
  panel.scaleArrow.Rd: panel.arrows, panel.text, panel.abline
  panel.segplot.Rd: levelplot, panel.segments, panel.arrows
  panel.smoother.Rd: panel.loess
  panel.tskernel.Rd: panel.lines, xyplot.ts
  panel.voronoi.Rd: levelplot, panel.levelplot, panel.xyplot
  panel.xblocks.Rd: xyplot.ts, panel.rect
  panel.xyarea.Rd: panel.polygon, panel.superpose, panel.qqmath,
    panel.xyplot
  panel.xyimage.Rd: xyplot, panel.xyplot, panel.abline
  resizePanels.Rd: Lattice, xyplot
  rootogram.Rd: xyplot
  scale.components.Rd: xscale.components.default
  segplot.Rd: levelplot, update.trellis, print.trellis, Lattice, xyplot
  theEconomist.theme.Rd: simpleTheme, panel.xyplot, xyplot
  tileplot.Rd: levelplot, xyplot
  useOuterStrips.Rd: xyplot, Lattice
  xyplot.stl.Rd: xyplot.ts, update.trellis, print.trellis, xyplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘00methods.R’ ‘creg_datalist.R’ ‘creg_input.R’ ‘creg_partable.R’
    ‘creg_startvals.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:
    ‘contr.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘lay.Rd’
Specified C++11: please drop specification unless essential
Found the following calls to attach():
File ‘lazyData/R/requireData.R’:
  attach(NULL, pos = pos, name = searchDataName)
See section ‘Good practice’ in ‘?attach’.
File ‘lazyeval/libs/lazyeval.so’:
  Found non-API calls to R: ‘PRENV’, ‘R_PromiseExpr’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
File ‘lazy/libs/lazy.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:
  fitLCA.Rd: poLCA
Please provide package anchors for all Rd \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.lcc.Rd: anova.lme, nlme
  coef.lcc.Rd: nlme
  getVarCov.lcc.Rd: nlme
  lcc.Rd: nlme
  logLik.lcc.Rd: nlme
  print.anova.lcc.Rd: anova.lme, nlme
  ranef.lcc.Rd: nlme
  residuals.lcc.Rd: nlme
  vcov.lcc.Rd: nlme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gw.zi.Rd: zeroinfl
  gw.zi.bw.Rd: zeroinfl
  gw.zi.cv.Rd: zeroinfl
  gw.zi.light.Rd: zeroinfl
  gw.zi.mc.test.Rd: zeroinfl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Plot_Biplot.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) TS_diagnostics_plot.Rd:19: Lost braces
    19 | \item{interactive}{\code{logical} input, should be code{TRUE} unless
       |                                                        ^
checkRd: (-1) plot.TS_fit.Rd:29: Lost braces
    29 | \item{interactive}{\code{logical} input, should be code{TRUE} unless
       |                                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FindTopicsNumber.Rd: LDAcontrol-class
  Griffiths2004.Rd: LDAcontrol-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'::' or ':::' import not declared from: ‘tm’
'data(package=)' call not declared from: ‘tm’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  layer.Rd: R6Class
  leabRa.Rd: R6Class
  network.Rd: R6Class
  unit.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘addCOG.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addFeatures.Rd: addCircleMarkers, addPolylines, addPolygons
  addRasterRGB.Rd: plotRGB, addRasterImage
  addStarsImage.Rd: addRasterImage
  garnishMap.Rd: addLayersControl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘legendSymbols.Rd’
checkRd: (-1) dynamicMapLayerOptions.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{layerDefs}{A string representing a query to run against the service before the image is rendered. This can be a string like "3:STATE_NAME="Kansas"" or an object mapping different queries to specific layers {3:"STATE_NAME="Kansas"", 2:"POP2007>25000"}.}
       |                                                                                                                                                                                                                     ^
checkRd: (-1) featureLayerOptions.Rd:35: Lost braces; missing escapes or markup?
    35 | Can be an object like {start:"startTime", end:"endTime"} or a string like "created".}
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addEsriFeatureLayer.Rd: addTiles, labelOptions, popupOptions
  addEsriHeatmapFeatureLayer.Rd: addTiles
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addRasterImage.Rd: projectRaster
  gadmCHE.Rd: getData
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘addCityShape.Rd’ ‘addProvinceShape.Rd’ ‘areaCalculator.R’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^
'library' or 'require' calls not declared from:
  ‘coda’ ‘lattice’ ‘survival’
checkRd: (-1) clusterDistance.Rd:28-29: Lost braces
    28 | \code{approach} indicates the algorithm used to get the value. \code{distance} indicates the distance used to get the value. Possible values: {\code{'MAX'},
       |                                                                                                                                               ^
checkRd: (-1) clusterDistance.details.Rd:28-29: Lost braces
    28 | \code{approach} indicates the algorithm used to get the value. \code{distance} indicates the distance used to get the value. Possible values: {\code{'MAX'},
       |                                                                                                                                               ^
checkRd: (-1) clusterDistanceByApproach.Rd:24-25: Lost braces
    24 | \code{approach} indicates the algorithm used to get the value. Possible values: {\code{'MAX'},
       |                                                                                 ^
checkRd: (-1) clusterDistanceByApproach.details.Rd:24-25: Lost braces
    24 | \code{approach} indicates the algorithm used to get the value. Possible values: {\code{'MAX'},
       |                                                                                 ^
checkRd: (-1) S2mu.Rd:18: Lost braces; missing escapes or markup?
    18 | \code{S2mu} computes a estimation of the variance, given a sample {x} with known population mean (denoted by \code{mu}).
       |                                                                   ^
checkRd: (-1) sample.quantile.Rd:20: Lost braces; missing escapes or markup?
    20 | \code{sample.quantile} computes a estimation of different quantiles, given a sample {x}, using order statistics.
       |                                                                                     ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘grab_crosswalk.R’ ‘lehdr.R’
File ‘leidenAlg/libs/leidenAlg.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Objects: ‘libleidenalg.a’, ‘librigraph.a’
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
    Object: ‘librigraph.a’
  Found ‘abort’, possibly from ‘abort’ (C)
    Object: ‘librigraph.a’
  Found ‘putchar’, possibly from ‘putchar’ (C)
    Object: ‘librigraph.a’
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘libleidenalg.a’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘librigraph.a’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘librigraph.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘addCappedL1.Rd’ ‘addElasticNet.Rd’ ‘addLasso.Rd’ ‘addLsp.Rd’
    ‘addMcp.Rd’ ‘addScad.Rd’ ‘fit.Rd’
    ‘getTuningParameterConfiguration.Rd’ ‘mixedPenalty.Rd’
    ‘regularizationHelper.R’ ‘stabilitySelection.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lessSEM.Rd: Stat
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lets.presab.Rd: terra, sf
  lets.presab.grid.Rd: terra, sf
  lets.shFilter.Rd: terra, sf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘letter_value.R’ ‘print_lv.R’
checkRd: (-1) hash_sentiment_slangsd.Rd:28-37: Lost braces
    28 | article{DBLP:journals/corr/Wu-etal16,
       |        ^
checkRd: (-1) hash_sentiment_slangsd.Rd:29: Lost braces; missing escapes or markup?
    29 |   author    = {Liang Wu and Fred Morstatter and Huan Liu},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:30-31: Lost braces
    30 |   title     = {SlangSD: Building and Using a Sentiment Dictionary of Slang 
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:32: Lost braces; missing escapes or markup?
    32 |   journal   = {CoRR},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:33: Lost braces; missing escapes or markup?
    33 |   volume    = {abs/1608.05129},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:34: Lost braces; missing escapes or markup?
    34 |   year      = {2016},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:35: Lost braces; missing escapes or markup?
    35 |   url       = {http://arxiv.org/abs/1608.05129},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:36: Lost braces; missing escapes or markup?
    36 |   timestamp = {Wed, 17 Aug 2016 23:32:57 GMT}
       |               ^
checkRd: (-1) sw_python.Rd:32: Lost braces; missing escapes or markup?
    32 | * Neither the name of the {organization} nor the names of its
       |                           ^
checkRd: (-1) flowunit.Rd:30: Lost braces; missing escapes or markup?
    30 | Usually flow units are of dimension $L^3 T^{-1}$. Currently a length $l$ can be on of \code{c("metre", "cm", "centimetre" "litre")}, whereas time $T$ can be one in \code{c("days", "hours", "mins", "secs")}, possibly abbreviated. The numerator of the fraction (everything before the literal \code{"/"}) is interpreted as the length (superscripts like \code{"^3"} are discarded), the denominator as time. E.g. valid units would be \code{"cm^3/s"}, \code{"m^3/day"} or \code{"litre/sec"}.
       |                                            ^
checkRd: (-1) seasindex.Rd:30: Lost braces
    30 | Laaha, G. and Bl{\"o}schl, G. (2006), Seasonality indices for regionalizing
       |                 ^
checkRd: (-1) seasindex.Rd:34: Lost braces
    34 | Mitteilungen, Inst. f{\"u}r Wasserbau u. Ingenieurhydrologie,
       |                      ^
checkRd: (-1) seasratio.Rd:31: Lost braces
    31 | Laaha, G. and Bl{\"o}schl, G. (2006), Seasonality indices for regionalizing low flows. Hydrol. Process., 20
       |                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  apply.seasonal.Rd: apply.daily, apply.monthly, apply.yearly
  as.xts.lfobj.Rd: as.xts
  cdf_ev.Rd: lmom
  fill_na.Rd: na.approx
  plot.deficit.Rd: plot.xts, dygraph
  rfa.Rd: regfit, lmom-package
  rfaplot.Rd: lmrd, lmom-package
  sbplot.Rd: barchart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  density.stppp.Rd: density.ppp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) prior_to_num.Rd:13: Lost braces; missing escapes or markup?
    13 |   {'uniform', 'normal', 'student-t', 'gamma', 'inv-gamma', 'log-normal'}
       |   ^
File ‘LibOPF/libs/LibOPF.so’:
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘include/libOPF.a’
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
    Object: ‘include/libOPF.a’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘include/libOPF.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) isingdata.Rd:14: Lost braces; missing escapes or markup?
    14 |     \item{X}{a 5000-by-100 matrix, each entry is in {-1,1}.}
       |                                                     ^
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
File ‘lidR/libs/lidR.so’:
  Found non-API call to R: ‘Rf_GetOption’

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:
  InsuranceContract.ParameterDefaults.Rd: mortalityTable
  makeContractGridDimname.Rd: mortalityTable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Person.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hmd.DA.Rd: MclustDA, Mclust
  hmd.DA.mx.Rd: MclustDA, Mclust
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) lx_list_lights.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:27: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Lightning.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) likelihood_calculation.Rd:24: Lost braces
    24 | For eqn{i = 1\dots N} independent observations in a vector \var{X}, with individual observations \eqn{x_i}{xi}, and a set of parameter values \eqn{\theta}:
       |        ^
checkRd: (-1) simulated_annealing_algorithm.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:27: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.likert.Rd: theme
  plot.likert.gap.Rd: theme
  print.xlikert.Rd: print.xtable
  xtable.likert.Rd: xtable, print.xtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' calls not declared from:
  ‘data.table’ ‘magrittr’ ‘purrr’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  morphs.Rd: tourr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘lineup-shiny.Rd’ ‘taggle-shiny.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘map.feature.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getLinkCommunities.Rd: igraph
  getOCG.clusters.Rd: igraph
  linkcomm-package.Rd: igraph, RColorBrewer
  meta.communities.Rd: igraph
  newLinkCommsAt.Rd: igraph
  plotLinkCommGraph.Rd: igraph, igraph.plotting
  plotOCGraph.Rd: igraph, igraph.plotting
  read.OCG.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘auto.R’
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fxInteractive.Rd: gam, lme
  fxInteractive.glm.Rd: gam, print.xtable, xtable
  fxInteractive.lm.Rd: print.xtable, xtable
  fxInteractive.lme.Rd: lme, predict.lme, print.xtable, xtable
  wrapRpSlider.Rd: rp.slider
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  VARselect.Rd: lm.ridge
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ld_build_html_site.Rd:41: Lost braces
    41 | directory specified by `rmd_dir`. Note that this is an {{rmarkdown}}
       |                                                        ^
checkRd: (-1) ld_create_doc.Rd:29: Lost braces
    29 | directory specified by `rmd_dir`. Note that this is an {{rmarkdown}}
       |                                                        ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘list_bind.R’
checkRd: (-1) lit.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lit.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lit.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lit_plink.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lit_plink.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lit_plink.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gamut_plink.Rd: genio
  lit_plink.Rd: genio
  marginal_plink.Rd: genio
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) is_natural_number.Rd:17: Lost braces; missing escapes or markup?
    17 | Test for natural numbers according to ISO 80000-2, that is the set  {0, 1, 2, ...}
       |                                                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  list_duplicates.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) vcov.liu.Rd:20: Lost braces
    20 | A list of matrix of estimated covariances in the linear Liu regression model for scalar or vector biasing parameter \code{d}{d} is produced. Each list element has row and column names corresponding to the parameter names given by the \code{coef(mod)}. List items are named correspond to values of biasing parameter \eqn{d}{d}.}
       |                                                                                                                             ^
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  xtable.lm.beta.Rd: xtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘lme4/libs/lme4.so’:
  Found non-API call to R: ‘CLOENV’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) relLik.Rd:16: Lost braces
    16 | \item{AIC(x), BIC(x) }{The \code{AIC} or ]code{BIC} value of the first model object.}
       |                                               ^
checkRd: (-1) relLik.Rd:17: Lost braces
    17 | \item{AIC(y), BIC(y) }{The \code{AIC} or ]code{BIC} value of the second model object.}
       |                                               ^
checkRd: (-1) bootstrap_pvals.Rd:78: Lost braces; missing escapes or markup?
    78 | $(n_{extreme} + 1) / (B + 1)$.
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  approx.Z.Rd: nlme
  smSplineEx1.Rd: lme
  smspline.Rd: predict.lme, nlme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fithd.Rd: nlme, lme, gls, gnls
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cauchypoly.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) normpoly.Rd:38: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) normpoly.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) lmomPi-Package.Rd:9: Lost braces
     9 | {\code{\link{cdf}}}{: generic distribution function;  }  
       |                    ^
checkRd: (-1) lmomPi-Package.Rd:10: Lost braces
    10 | {\code{\link{qua}}}{: generic quantile function;  } 
       |                    ^
checkRd: (-1) lmomPi-Package.Rd:11: Lost braces
    11 | {\code{\link{pel}}}{: fitting of probability distribution function through L-moments. }
       |                    ^
checkRd: (-1) lmomPi-Package.Rd:27: Lost braces; missing escapes or markup?
    27 | The function  \code{\link{spi.cdf}()} is compared against \code{SPEI::spi()} in SPEI package (\url{https://cran.r-project.org/package=SPEI}). The differences in SPI extimation have order of magnitude averagely about 10^{-8},  due to  the different fitting methods implemented in the two packages. 
       |                                                                                                                                                                                                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cdf.Rd: cdfexp, cdfgam, cdfgev, cdfglo, cdfgpa, cdfgno, cdfgum,
    cdfkap, cdfln3, cdfnor, cdfpe3, cdfwak, cdfwei
  pel.Rd: pel..., samlmu, pelexp, pelgam, pelgev, pelglo, pelgpa,
    pelgno, pelgum, pelkap, pelln3, pelnor, pelpe3, pelwak, pelwei
  qua.Rd: quaexp, quagam, quagev, quaglo, quagpa, quagno, quagum,
    quakap, qualn3, quanor, quape3, quawak, quawei
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) vcov.Rd:20: Lost braces
    20 | A list of matrix of estimated covariances in the linear ridge regression model for scalar or vector biasing parameter \code{K}{K} is produced. Each list element has row and column names corresponding to the parameter names given by the \code{coef(mod)}. List items are named correspond to values of biasing parameter \eqn{K}{K}.}
       |                                                                                                                               ^
Specified C++11: please drop specification unless essential
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘mod_carga_datos.R’ ‘mod_correlacion_utils.R’ ‘mod_dispersion.R’
    ‘mod_distribuciones.R’ ‘mod_distribuciones_fct.R’
    ‘mod_distribuciones_utils.R’ ‘mod_normal_utils.R’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Author
    Maintainer
Specified C++11: please drop specification unless essential
File ‘lobstr/libs/lobstr.so’:
  Found non-API calls to R: ‘BODY’, ‘CLOENV’, ‘ENCLOS’, ‘EXTPTR_PROT’,
    ‘EXTPTR_TAG’, ‘FORMALS’, ‘FRAME’, ‘HASHTAB’, ‘NAMED’, ‘OBJECT’,
    ‘PRCODE’, ‘PRENV’, ‘PRVALUE’, ‘R_lsInternal’, ‘Rf_findVarInFrame3’,
    ‘TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) mte_tilde_at.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mte_tilde_at.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mte_tilde_at.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mte_tilde_at.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mte_tilde_at.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘locate.R’
checkRd: (-1) Rvarlacf.Rd:104: Lost braces
   104 |         eqn{(2s+1)^{-2}} (this was the default in versions prior to
       |            ^
checkRd: (-1) Rvarlacf.Rd:104: Lost braces; missing escapes or markup?
   104 |         eqn{(2s+1)^{-2}} (this was the default in versions prior to
       |                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EstBetaCov.Rd: PsiJ
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) FootballBrain.Rd:15: Lost braces; missing escapes or markup?
    15 |     { } \tab {or \code{FBConcuss}=football player with concussion history} \cr
       |     ^
checkRd: (-1) HappyPlanetIndex.Rd:14: Lost braces; missing escapes or markup?
    14 |     { } \tab {\code{5}=South Asia, \code{6}=East Asia, \code{7}=former Communist countries}\cr
       |     ^
checkRd: (-1) RockandRoll2012.Rd:17: Lost braces; missing escapes or markup?
    17 |     { } \tab {\code{Lifetime Achievement}, \code{Sideman}} \cr
       |     ^
checkRd: (-1) RockandRoll2015.Rd:17: Lost braces; missing escapes or markup?
    17 |     { } \tab {\code{Lifetime Achievement}, \code{Sideman}} \cr
       |     ^
checkRd: (-1) StudentSurvey.Rd:12: Lost braces; missing escapes or markup?
    12 |     \item{\code{Sex}}{code {F}=female or \code{M}=male}
       |                            ^
checkRd: (-1) SynchronizedMovement.Rd:16: Lost braces; missing escapes or markup?
    16 |     { } \tab {for High/Low Synchronization + High/Low Exertion}\cr
       |     ^
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PRDenEstC.Rd: bkde, dpik
  locpol.Rd: locpoly
  locpolSmoothers.Rd: locpoly
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bittermelon.R’ ‘lofi.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘emayili_emailer.R’ ‘login_server.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  logistf-package.Rd: mice
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) logdensity.Rd:33: Lost braces; missing escapes or markup?
    33 | The function \code{logdensity} computes kernel density estimates (KDE) of strictly positive distributions by performing the KDE in the log domain and then transforming the result back again. The syntax and function structure is largely borrowed from the function \code{density} in package {stats}.
       |                                                                                                                                                                                                                                                                                                  ^
checkRd: (-1) logdensity_fft.Rd:33: Lost braces; missing escapes or markup?
    33 | The function \code{logdensity_fft} computes kernel density estimates (KDE) of strictly positive distributions by performing the KDE via fast fourier transform utilizing the \code{fft} function. The syntax and function structure is largely borrowed from the function \code{density} in package {stats}.
       |                                                                                                                                                                                                                                                                                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  HMSkew-nonlin.Rd: gnm
  RCTrans-nonlin.Rd: gnm
  YRCSkew-nonlin.Rd: gnm
  anoas.Rd: gnm
  assoc.Rd: gnm
  hmskew.Rd: gnm
  hmskewL.Rd: gnm
  rc.Rd: gnm
  rcL.Rd: gnm
  rcL.trans.Rd: gnm
  svyassocmod.Rd: gnm
  unidiff.Rd: gnm, checkEstimable, qvcalc
  yrcskew.Rd: gnm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘logger.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  inlineLologPlugin.Rd: cppFunction, sourceCpp
  plot.Rcpp_DirectedNet.Rd: plot.network
  plot.Rcpp_UndirectedNet.Rd: plot.network
  plot.lologGmm.Rd: geom_histogram
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  partition.X.Rd: partitions
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) SAheart.Rd:96: Lost braces
    96 |   J.E. Rossouw, J.P.D. Plessis, A.J.S. Benad\'{e}, P.C.J. Jordaan, 
       |                                               ^
checkRd: (-1) SAheart.Rd:97: Lost braces
    97 |   J.P. Kotz\'{e}, P.L. Jooste, and J.J. Ferreira (1983)
       |              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  g_getLocations.Rd: l_getLocations
  g_getPlots.Rd: l_getPlots
  geom_imageGlyph-deprecated.Rd: geom_image_glyph, geom_polygon_glyph
  geom_pointrangeGlyph-deprecated.Rd: geom_pointrange
  geom_serialAxesGlyph-deprecated.Rd: geom_serialaxes_glyph
  geom_textGlyph-deprecated.Rd: geom_text
  ggSerialAxes-deprecated.Rd: coord_serialaxes
  interactivity.Rd: l_info_states
  l_ggplot.Rd: ggplot
  linking.Rd: l_getLinkedStates, l_setLinkedStates, l_configure
  scaleBox.Rd: l_scale3D
  selection.Rd: l_userOptions
  zoom.Rd: l_scaleto_plot, l_scaleto_layer, l_scaleto_world,
    l_scaleto_active, l_scaleto_selected
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) l_binCut.Rd:30: Lost braces
    30 | when 'code{labels = FALSE}, the default \code{active} is  \code{-1}; and when \code{labels} is a vector of length equal
       |           ^
checkRd: (-1) loon.shiny.Rd:93-102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loon.shiny.Rd:95-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loon.shiny.Rd:97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loon.shiny.Rd:98-100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loon.shiny.Rd:103-108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loon.shiny.Rd:105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loon.shiny.Rd:106: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  loon.shiny.Rd: ggplot2loon, grid.arrange, shinyApp, runApp
  shiny.loon-deprecated.Rd: ggplot2loon, grid.arrange, shinyApp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  l_tour.Rd: grand_tour, dependence_tour, frozen_tour, guided_tour,
    planned_tour
  tour_pairs.Rd: l_pairs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lpacf.Epan.Rd: plot.lacf
  lpacf.Rd: plot.lacf
  summary.lpacf.Rd: print.lacf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  surv.colors.Rd: Surv
  surv.scale.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AvBasis.wst2D.Rd: wst2D, wst2D.object
  imwr.imwd.rd: imwd.object, filter.select, imwr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) plot.int.lsbclust.Rd:112: Lost braces
   112 | \code{"rows"} and code{"columns"}.}
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cfsim.Rd: cl_agreement
  cfsim.T3Clusf.Rd: cl_agreement
  cfsim.akmeans.Rd: cl_agreement
  cfsim.lsbclust.Rd: cl_agreement
  int.lsbclust.Rd: cl_agreement
  lsbclust.Rd: cl_agreement
  plot.T3Clusf.Rd: theme
  plot.bicomp.Rd: grid.arrange, scale_fill_gradient2, theme
  plot.col.kmeans.Rd: theme
  plot.int.lsbclust.Rd: grid.arrange, geom_segment, theme
  plot.lsbclust.Rd: theme
  plot.ovl.kmeans.Rd: theme
  plot.row.kmeans.Rd: theme
  plot.step.lsbclust.Rd: grid.arrange, theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lsprobust.plot.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 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_plot_labels.Rd’ ‘datasim_helpers.R’ ‘datasim_make.Rd’
    ‘model_eval.R’ ‘model_eval.Rd’ ‘model_plot.R’ ‘model_skeleton.Rd’
    ‘model_values.R’ ‘model_values.Rd’ ‘mosaic_cull_for_do.Rd’ ‘ntiles.R’
    ‘ntiles.Rd’ ‘point_plot.R’ ‘point_plot.Rd’ ‘print.R’
    ‘random_terms.Rd’ ‘regression_summaries.Rd’ ‘sims.R’
    ‘statistical_annotations.Rd’ ‘trials.R’ ‘trials.Rd’ ‘zero_one.Rd’
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) spectral.density.Rd:55: 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:
    ‘smr_custom.R’ ‘smr_major.R’ ‘smr_minor.R’
checkRd: (-1) k.Rd:27: Lost braces
    27 |  code{\link{ACSPlan-class}}, 
       |      ^
Specified C++11: please drop specification unless essential
File ‘luajr/libs/luajr.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
    Object: ‘luajit/src/libluajit.a’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘luajit/src/libluajit.a’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘luajit/src/libluajit.a’
File ‘luajr/libs/luajr.so’:
  Found non-API call to R: ‘DATAPTR’

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.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  luca.Rd: coxph, clogit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Upload_to_db.Rd:43: Lost braces
    43 | lucas]{Connect_to_db}
       |       ^
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  evaluate.Rd: nn_module
  fit.luz_module_generator.Rd: nn_module
  luz_load_model_weights.Rd: torch_load
  predict.luz_module_fitted.Rd: nn_module
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) LVGP_fit.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_predict.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_predict.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) math_example.Rd:21: Lost braces
    21 | Data are sampled from the modified math function based on the first example in the paper listed in code{references}.
       |                                                                                                        ^
Specified C++11: please drop specification unless essential
checkRd: (-1) StEM_pcirt.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{response}{N by J matrix containing {0,1,...,M-1} responses, where N is the number of respondents and J is the number of items.}
       |                                          ^
checkRd: (-1) geom_lv.Rd:101: Lost braces; missing escapes or markup?
   101 | determines whether the width of the box for letter value LV(i) should be proportional to i (linear), proportional to $2^{-i}$ (height), or  whether
       |                                                                                                                         ^
checkRd: (-1) geom_lv.Rd:102: Lost braces; missing escapes or markup?
   102 | the area of the box should be proportional to $2^{-i}$ (area).}
       |                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_lv.Rd: stat_quantile
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘classify.R’ ‘extract.R’ ‘score.R’
checkRd: (-1) xytb-class.Rd:26: Lost braces; missing escapes or markup?
    26 | v: \tab speed (m.s^{-1})\cr
       |                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  xytb-class.Rd: distVincentyEllipsoid
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  factor_poly.Rd: mp
  gb.Rd: mp, mpolyList
  ideal.Rd: mp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) examinee-class.Rd:61: Lost braces; missing escapes or markup?
    61 | \item{\code{routing_based_on}}{a vector containing the routing was based on \code{estimated_theta_by_phase} or {estimated_theta_by_test} at each module position.}
       |                                                                                                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  createModule.Rd: loadConstraints, loadItemPool, loadItemAttrib,
    loadStAttrib
  examinee-class.Rd: item_pool-class
  excludeAdministeredItems.Rd: constraints-class
  maat.Rd: config_Shadow-class
  module-class.Rd: constraints-class
  output_maat-class.Rd: config_Shadow-class
  simTheta.Rd: mvrnorm
  updateAssessmentLevelTheta.Rd: config_Shadow-class
  updateGrade.Rd: item_pool-class
  updateItemData.Rd: output_Shadow_all-class, item_pool-class
  updateThetaUsingCombined.Rd: config_Shadow-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mediate_iv.Rd: el.test, BBoptim, spg
  mediate_zi.Rd: survreg, Surv, mgcv, s, summary.mediate, plot.mediate
  mediate_zi_vcoef.Rd: summary.mediate, plot.mediate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) mada-data.Rd:45: Lost braces
    45 | Kriston, L., H{\"o}elzel, L., Weiser, A., Berner, M., & Haerter, M. (2008).\dQuote{ Meta-analysis: Are 3
       |               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SummaryPts.Rd: rmvnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  magerr.Rd: draw.ellipse
  magproj.Rd: mapproject, deg2hms, deg2dms
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘magrittr/libs/magrittr.so’:
  Found non-API calls to R: ‘Rf_allocSExp’, ‘Rf_findVarInFrame3’,
    ‘SET_ENCLOS’, ‘SET_PRCODE’, ‘SET_PRENV’, ‘SET_PRVALUE’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  reportCovariates.Rd: wtd.var
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) RepLOptim.Rd:21: Lost braces; missing escapes or markup?
    21 |         \item{gr}{A function to return the gradient for the \dQuote{nlminb}, \dQuote{BFGS}, \dQuote{CG} and {L-BFGS-B} methods.  If it is \sQuote{NULL}, a finite-difference approximation will be used. For the \dQuote{SANN} method it specifies a function to generate a new candidate point.  If it is \sQuote{NULL} a default Gaussian Markov kernel is used.}
       |                                                                                                             ^
checkRd: (-1) Robda-methods.Rd:69: Lost braces
    69 | \seealso{\code{\link{lda}}, \code{\link{qda}}, \code{\link{snda}}, \code{\linkS4class{IData}}, \code{\linkS4class{RobEstControl}},code{\link{ConfMat}} }
       |                                                                                                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RobEstControl-class.Rd: CovControlMcd-class, CovControl-class
  fasttle-methods.Rd: rrcov.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) makeProject.Rd:34: Lost braces
    34 | email{noahsilverman@ucla.edu}
       |      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as_tbl_graph.malan_pedigreelist.Rd: tbl_graph
  get_nodes_edges.Rd: as_tbl_graph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MALDIrppa-package.Rd: MALDIquant
  addMetadata.Rd: AbstractMassObject-class
  alignPeaks.Rd: MassPeaks, MALDIquant, referencePeaks, binPeaks,
    warpMassPeaks
  countPeaks.Rd: MassPeaks
  detectOutliers.Rd: MassSpectrum, covMcd
  importSpectra.Rd: MassSpectrum
  peakPatterns.Rd: intensityMatrix, MassPeaks
  rawToPeaks.Rd: MassPeaks
  rawToSpectra.Rd: MassSpectrum
  redResolution.Rd: MassSpectrum-class
  screenSpectra.Rd: MassSpectrum, Qn
  snrPeaks.Rd: MassPeaks, detectPeaks
  spectra.Rd: MassSpectrum
  summaryPeaks.Rd: MassPeaks
  summarySpectra.Rd: MassSpectrum
  transfIntensity.Rd: MassSpectrum-class, transformIntensity
  wavSmoothing.Rd: MassSpectrum
  writeIntensity.Rd: intensityMatrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘llm-extract.R’ ‘llm-use.R’ ‘llm_custom.Rd’ ‘m-backend-prompt.R’
    ‘m-backend-submit.R’ ‘m-defaults.R’ ‘utils.R’
checkRd: (-1) create_terminal_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                              ^
checkRd: (-1) create_terminal_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                                                   ^
checkRd: (-1) full_repo_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                              ^
checkRd: (-1) full_repo_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                                                   ^
checkRd: (-1) manet.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MangroveTree.Rd:37: Lost braces
    37 |       An object of class \\code{\link[Mangrove]{MangrovePed}}
       |                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  manhattanly.Rd: plotly
  volcanoly.Rd: plotly
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mp_interpolate.Rd: na.approx
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) manipulateWidget.Rd:113-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manipulateWidget.Rd:118-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manipulateWidget.Rd:121-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manipulateWidget.Rd:124-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EEGwide.Rd:30-33: Lost braces
    30 |   if(requireNamespace("ggplot2")){ 
       |                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GetGeneList.Rd: rentrez
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:
    ‘model_averaging.Rd’
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fixes
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  selectFeatures.Rd: geos_binary_pred
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  modgam.Rd: gam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘leg_comp.Rd’ ‘leg_draw.Rd’
Missing dependency on R >= 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_gsw_time_series.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mapStats.Rd: spplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clip.rpart.Rd: rpart, prune.rpart
  draw.clust.Rd: pltree
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mapView.Rd: levelplot, addControl, addLegend, addRasterImage,
    addCircles, addPolygons, addPolylines, addMapPane,
    highlightOptions, st_sf, brick, satellite, st_sfc, st_bbox,
    SpatialPixelsDataFrame, SpatialGridDataFrame,
    SpatialPointsDataFrame, SpatialPoints, SpatialPolygonsDataFrame,
    SpatialPolygons, SpatialLinesDataFrame, SpatialLines
  mapviewColors.Rd: level.colors
  mapviewOptions.Rd: addRasterImage, addLegend, addMapPane,
    rasterOptions
  mapviewOutput.Rd: shinyWidgetOutput
  viewExtent.Rd: popupTable, addControl, addRectangles
  viewRGB.Rd: plotRGB
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) locate_shift.Rd:29: Lost braces
    29 | \code{\link{quickfit}}, code{\link{locator}}
       |                             ^
checkRd: (-1) marcher-package.Rd:14: Lost braces; missing escapes or markup?
    14 | 1. \code{\link{estimate_shift}} {Estimate a range shift process.}
       |                                 ^
checkRd: (-1) marcher-package.Rd:16: Lost braces; missing escapes or markup?
    16 | 2. \code{\link{simulate_shift}} {Simulate a range shift process.}
       |                                 ^
checkRd: (-1) marcher-package.Rd:18: Lost braces; missing escapes or markup?
    18 | 3. \code{\link{plot.shiftfit}} {Visualize a range shift process.}
       |                                ^
checkRd: (-1) marcher-package.Rd:20: Lost braces; missing escapes or markup?
    20 | 4. \code{\link{test_rangeshift}} {Test whether a range shift occurred.}
       |                                  ^
checkRd: (-1) marcher-package.Rd:22: Lost braces; missing escapes or markup?
    22 | 5. \code{\link{test_return}} {Test whether a migration was a return migration.}
       |                              ^
checkRd: (-1) marcher-package.Rd:24: Lost braces; missing escapes or markup?
    24 | 6. \code{\link{test_stopover}} {Test whether a stopover occurred during a migration.}
       |                                ^
checkRd: (-1) quickfit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickfit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘data_analysis_descriptive.R’ ‘functions.R’ ‘main.R’
    ‘merge_quality_articles.R’
checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rsm.Rd: survreg.fit
  rsm.surv.Rd: survreg.fit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) marima.Rd:28: Lost braces; missing escapes or markup?
    28 | ( if(is.ts(DATA)) { DATA <- as.matrix(data.frame(DATA)) } and a message
       |                   ^
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) markdownInput.Rd:17: Lost braces
    17 | \item{inputId}{The code{input} slot that will be used to access the value.}
       |                        ^
checkRd: (-1) markdownInput.Rd:35: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) markdownInput.Rd:36: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) markdownInput.Rd:81-82: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) markdownInput.Rd:84-86: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) markdownInput.Rd:89-90: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) moduleMarkdownInput.Rd:64-65: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) moduleMarkdownInput.Rd:67-69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) moduleMarkdownInput.Rd:72-73: Lost braces in \enumerate; meant \describe ?
Specified C++11: please drop specification unless essential
'library' or 'require' calls not declared from:
  ‘MCMCpack’ ‘matlab’ ‘microbenchmark’
checkRd: (-1) Markovchart.Rd:154: Lost braces
   154 | If either \code{h} or \code{k} have length greater than 1, then the \code{G-value} (weighted average of average cost and cost standard deviation) is calculated for all given values without optimisation. The value of the function in this case is a data frame of class code{Markov_grid} with \code{length(h)*length(k)} number of rows and three columns for \code{h}, \code{k} and the \code{G-value}.
       |                                                                                                                                                                                                                                                                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  autoplot.bathy.Rd: coord_map
  get.area.Rd: areaPolygon
  plotArea.Rd: areaPolygon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) marqLevAlg-package.Rd:14: Lost braces; missing escapes or markup?
    14 | (GH^{-1}G).
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MARSSFisherI.Rd: fdHess, nlme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) focalCompare.Rd:14: Lost braces
    14 | \item{fun}{The function fun should take multiple numbers, and return a single number. For example mean, modal, min or max. It should also accept a na.rm argument (or ignore it, e.g. as one of the 'dots' arguments. For example, length will fail, but function(x, ...){na.omit(length(x))} works. (Specifications from `raster::focal`)}
       |                                                                                                                                                                                                                                                                          ^
checkRd: (-1) hr_levels.Rd:9-12: Lost braces
     9 | kernelBiweight <- function(x, mean = 0, sd = 1) {
       |                                                 ^
checkRd: (-1) hr_levels.Rd:33-36: Lost braces
    33 | kernelCosine <- function(x, mean = 0, sd = 1) {
       |                                               ^
checkRd: (-1) hr_levels.Rd:41-44: Lost braces
    41 | kernelEpanechnikov <- function(x, mean = 0, sd = 1) {
       |                                                     ^
checkRd: (-1) hr_levels.Rd:58-61: Lost braces
    58 | kernelOptCosine <- function(x, mean = 0, sd = 1) {
       |                                                  ^
checkRd: (-1) hr_levels.Rd:65-68: Lost braces
    65 | kernelRectangular <- function(x, mean = 0, sd = 1) {
       |                                                    ^
checkRd: (-1) hr_levels.Rd:72-75: Lost braces
    72 | kernelSquaredCosine <- function(x, mean = 0, sd = 1) {
       |                                                      ^
checkRd: (-1) hr_levels.Rd:79-82: Lost braces
    79 | kernelTriangular <- function(x, mean = 0, sd = 1) {
       |                                                   ^
checkRd: (-1) hr_levels.Rd:86-89: Lost braces
    86 | kernelTricube <- function(x, mean = 0, sd = 1) {
       |                                                ^
checkRd: (-1) hr_levels.Rd:93-96: Lost braces
    93 | kernelTriweight <- function(x, mean = 0, sd = 1) {
       |                                                  ^
checkRd: (-1) hr_levels.Rd:100-103: Lost braces
   100 | kernelUniform <- function(x, mean = 0, sd = 1) {
       |                                                ^
checkRd: (-1) CF2004.Rd:8: Lost braces; missing escapes or markup?
     8 |   \item{X2}{an optional second variable with same length as \code{X}, should the equation be multiple (see Details) {in mm}}
       |                                                                                                                     ^
checkRd: (-1) Rand.index.Rd:22: Lost braces; missing escapes or markup?
    22 | The two vectors \code{x} and \code{y} must have equal length. Given a set \eqn{S} and two partitions \eqn{X} and \eqn{Y} of \eqn{S}, the Rand index is the proportion of pairs of elements in \eqn{S} (out of all pairs) that are either concordant in both \eqn{X} and \eqn{Y} (i.e., they belong to the same member of \eqn{X} and to the same member of \eqn{Y}) or discordant (i.e., not concordant) in both \eqn{X} and {Y}.  
       |                                                                                                                                                                                                                                                                                                                                                                                                                              ^
checkRd: (-1) predict.matchFeat.Rd:21: Lost braces
    21 | The function \code{predict.matchFeat} finds the best matching for new feature vectors relative to an existing set of cluster/class centers. If code{object} results from a call to \code{\link{match.gaussmix}}, the same function is used for prediction (with fixed mean vectors and covariance matrices). In other cases, the function \code{\link{match.template}} is used for prediction. 
       |                                                                                                                                                    ^
Specified C++11: please drop specification unless essential
checkRd: (-1) Match.Rd:90: Lost braces; missing escapes or markup?
    90 | expression in braces. For example, the condition "{[ab]*}" is equivalent
       |                                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kNearNeighbors.Rd: knn.dist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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:
    ‘latexMatrix.R’
checkRd: (-1) MatrixCorrelation.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatrixCorrelation.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RV.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RV.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RV.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RV.Rd:67-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:64-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allCorrelations.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) r1.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) r1.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) r1.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) r1.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) r1.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Matrix_eQTL_main.Rd:31: Lost braces; missing escapes or markup?
    31 |     {genepos} in the call of \code{Matrix_eQTL_main} function.
       |     ^
checkRd: (-1) Matrix_eQTL_main.Rd:35: Lost braces; missing escapes or markup?
    35 |     the data frames \code{snpspos} and {genepos}.
       |                                        ^
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘column_group_by_drop_default.Rd’ ‘context.Rd’ ‘filter_column.Rd’
    ‘filter_row.Rd’ ‘join.Rd’ ‘row_group_by_drop_default.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘Unary.R’ ‘Utilities.R’ ‘named_triplet.R’ ‘reallocate.R’
    ‘rename_to_piece_byname.Rd’ ‘select_rows_cols_byname.Rd’
    ‘to_named_triplet.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘df_to_msg.Rd’ ‘matsindf_apply.R’ ‘utilities.R’
Found the following files/directories:
  ‘utilities.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  predict.mave.Rd: mars
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) MaxentVariableSelection-package.Rd:46: Lost braces; missing escapes or markup?
    46 | \tab Tyberghein L, Verbruggen H, Pauly K, Troupin C, Mineur F and {De Clerck}, O (2012)\cr
       |                                                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  carw.Rd: raster
  maxlike-package.Rd: raster
  maxlike.Rd: raster-package, raster
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  activePar.Rd: nObs
  nObs.Rd: nParam
  nParam.Rd: nObs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘map_5.png’ ‘maze_5.html’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  upsilon.Rd: lavaan, boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) findDescendingTrans.Rd:29: Lost braces
    29 |    Foster, S.D., Hosack, G.R., J. Monk, Lawrence, E., Barrett, N.S., Williams, A. and Przeslawski, P. (2020) Spatially-Balanced Designs for Transect-Based Surveys. Methods in Ecology and Evolution. emph{11}: 95--105
       |                                                                                                                                                                                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mcaSmoother.Rd: lmrob
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) SIGMAS.Rd:17: Lost braces; missing escapes or markup?
    17 | Sigmahat =  (Y^{T} Y)/n;
       |                ^
checkRd: (-1) SIGMAS.Rd:18: Lost braces; missing escapes or markup?
    18 | Sigmahat_fit = (Y^{T}  P_fx  Y)/n;
       |                   ^
checkRd: (-1) matpower.Rd:17: Lost braces; missing escapes or markup?
    17 | The function computes M^{power} for a symmetric matrix M. }
       |                         ^
checkRd: (-1) satisfaction.Rd:28: Lost braces
    28 | Della Valle E (2010) Della Valle E 2010 Analisi Multidimensionale dei Dati: la Qualit\'{a} del Lavoro nelle Cooperative Sociali. 
       |                                                                                        ^
checkRd: (-1) satisfaction.Rd:29: Lost braces
    29 | Unpublished thesis, Seconda Universit\'{a}  degli Studi di Napoli, Capua Italy.
       |                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AuditorFitter.Rd: data.table
  CVLearnerAuditorFitter.Rd: data.table
  LearnerAuditorFitter.Rd: data.table
  MCBoost.Rd: data.table
  SubgroupAuditorFitter.Rd: data.table
  SubpopAuditorFitter.Rd: data.table
  mlr_pipeops_mcboost.Rd: R6Class, data.table, PipeOp, Learner
  ppl_mcboost.Rd: Graph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
checkRd: (-1) MCbound.precalc1.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  method_plot.Rd: hdi
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  caterplot.Rd: denstrip
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) ess.Rd:14: Lost braces
    14 | \code{g} should take a vector input only. Ifcode{g} is \code{NULL}, \code{g} is set to be identity, which is estimation
       |                                                 ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘left_join_codebook.Rd’ ‘setup_dir.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:
    ‘summary.mcpmod_simulation.R’
Found the following significant warnings:
  modiSBML.c:492:37: warning: ‘%s’ directive output may be truncated writing up to 5118 bytes into a region of size between 1 and 5119 [-Wformat-truncation=]
  modiSBML.c:578:37: warning: ‘%s’ directive output may be truncated writing up to 5118 bytes into a region of size between 1 and 5119 [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/MCSimMod.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’
checkRd: (-1) eigp.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:41: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial version.
checkRd: (-1) mcvis.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mcvis.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mcvis.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CDF_3dPlot.Rd: lattice
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  linkage.Rd: agnes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) get_mdgc.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_mdgc.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_mdgc.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_mdgc.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ramachandran.Rd: hist2d
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) mdp_example_forest.Rd:36: Lost braces; missing escapes or markup?
    36 | Let {1, ... S} be the states of the forest. the Sth state being the oldest.
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.pcmap3d.Rd: rgl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  findOptimalSmacofSym.rd: data.Normalization, dist.GDM, smacofSym
  optSmacofSymInterval.rd: data.Normalization, interval_normalization,
    dist.Symbolic, smacofSym
  optSmacofSym_mMDS.rd: data.Normalization, dist.GDM, smacofSym
  optSmacofSym_nMDS.rd: data.Normalization, dist.GDM, smacofSym
  rotation2dAnimation.rd: ani.options, im.convert, saveGIF, saveHTML,
    saveLatex, saveSWF
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  betaturn.Rd: microtable, trans_beta
  taxaturn.Rd: microtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) bhm.mcmc.Rd:37: Lost braces; missing escapes or markup?
    37 |   where \eqn{N_{ij}} denotes the number of times that the error profile \eqn{i} is cited on a report from hospital {j} and \eqn{y_{ij}} is the corresponding number of times that profile \eqn{i} in hospital \eqn{j} was reported with harm.
       |                                                                                                                    ^
checkRd: (-1) strings-internal.Rd:14: Lost braces
    14 | code{stringPlaceExact}: find location of string, using exact match
       |     ^
checkRd: (-1) strings-internal.Rd:17: Lost braces
    17 | code{stringPlaceFuzzy}: find location of string, using partial match
       |     ^
checkRd: (-1) strings-internal.Rd:19: Lost braces
    19 | code{stringPlace}: find location of string, generic
       |     ^
checkRd: (-1) strings-internal.Rd:21: Lost braces
    21 | code{checkFuzzy}: check for "close" string matches
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  neLht-methods.Rd: coef.glht
  neLht.Rd: coef.glht
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mediate.Rd: survreg, Surv, mgcv, s
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  generate_comorbidity_df.Rd: ddply
  melt_icd9list.Rd: ddply
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) MED.Rd:25: Lost braces
    25 | The vector of treatment assignments of length \eqn{n}. Must be coded as \eqn{\{0,1} {{0,1}}.
       |                                                                                     ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘mx_syntax.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Xtab.Rd: sparseMatrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Mega2gdsfmt.Rd: gdsfmt
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘Data_Correlation.txt’ ‘correlation_FDR_table.txt’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  melt_delim.Rd: tibble
  melt_delim_chunked.Rd: tibble
  melt_fwf.Rd: tibble
  melt_table.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘meltr/libs/meltr.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) mgLandscape.Rd:79: Lost braces
    79 | A code{$summary} table giving the results of the variation partitioning.  The following table
       |       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mgLandscape.Rd: raster
  mgMap.Rd: ade4
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘memo/libs/memo.so’:
  Found non-API calls to R: ‘BODY’, ‘CLOENV’, ‘FORMALS’, ‘PRCODE’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  memmodel.Rd: boot.ci, boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bread.glmerMod.Rd: glmerMod-class
  bread.lmerMod.Rd: lmerMod-class
  estfun.glmerMod.Rd: glmerMod-class
  estfun.lmerMod.Rd: lmerMod-class
  llcont.glmerMod.Rd: glmerMod-class
  llcont.lmerMod.Rd: lmerMod-class
  vcov.glmerMod.Rd: glmerMod-class
  vcov.lmerMod.Rd: lmerMod-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  VarCorr.merModList.Rd: merMod-class
  modelFixedEff.Rd: tidy
  plotFEsim.Rd: merMod
  plotREsim.Rd: merMod
  ranef.merModList.Rd: merMod-class
  thetaExtract.Rd: merMod
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  QIC.Rd: ginv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) CVLasoelacox.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:70-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:74-76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:77-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:82-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FEmrt.Rd: rpart, rpart.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘spec_builder.R’ ‘xml_builders.R’
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) datagenerator.Rd:17: Lost braces; missing escapes or markup?
    17 | Returns data frame with \code{n*K} rows (if \code{n} is a scalar), or \code{sum(n)} rows (if \code{n} is a \code{K}-element vector). The data frame contains columns "y", "x1", \dots, "x_{p-1}" and "group" if \code{family="gaussian"}, \code{"binomial"} or \code{"poisson"}; or contains columns "time", "status", "x1", \dots, "x_{p-1}" and "group" if \code{family="cox"}.
       |                                                                                                                                                                                           ^
checkRd: (-1) datagenerator.Rd:17: Lost braces; missing escapes or markup?
    17 | Returns data frame with \code{n*K} rows (if \code{n} is a scalar), or \code{sum(n)} rows (if \code{n} is a \code{K}-element vector). The data frame contains columns "y", "x1", \dots, "x_{p-1}" and "group" if \code{family="gaussian"}, \code{"binomial"} or \code{"poisson"}; or contains columns "time", "status", "x1", \dots, "x_{p-1}" and "group" if \code{family="cox"}.
       |                                                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) asympVar_LinReg.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gamma_EB.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gamma_EB.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gamma_EB.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rland.graph.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘metalite_table1_to_rtf.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:
    ‘MetaNLP.R’ ‘delete_functions.R’ ‘useful_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:
    ‘metaRangePriorityQueue.Rd’ ‘metaRangeProcess.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  forest.metarep.Rd: forest.meta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  doiplot.Rd: metabias, funnel.meta
  forest.orbbound.Rd: forest.meta
  funnel.limitmeta.Rd: funnel.meta
  lfkindex.Rd: metabias, funnel.meta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘build.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  KODAMA.chem.sim.Rd: KODAMA.matrix, KODAMA.visualization
  chemical.dissimilarity.Rd: fp.sim.matrix, get.fingerprint
  clusters.detection.Rd: KODAMA.matrix, KODAMA.visualization
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getRaster.Rd: Extent, extent, getZ
  meteo-package.Rd: raster, zoo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'library' or 'require' call not declared from: ‘xts’
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘aemet_helpers.R’ ‘meteocat_helpers.R’ ‘meteoclimatic_helpers.R’
    ‘meteogalicia_helpers.R’ ‘ria_helpers.R’ ‘utils.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fit.lasso.Rd: glmnet, cv.glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
'library' or 'require' call not declared from: ‘tibble’
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  splineFunction1D.Rd: gam
  splineFunction2D.Rd: gam
  univExpansion.Rd: funData-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.mfp.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  predict.mfp.Rd: predict.coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) summarize_stats_CSV.Rd:81: Lost braces; missing escapes or markup?
    81 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       | ^
checkRd: (-1) summarize_stats_CSV.Rd:81: Lost braces; missing escapes or markup?
    81 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       |                                      ^
checkRd: (-1) summarize_stats_CSV_decoupled.Rd:84: Lost braces; missing escapes or markup?
    84 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       | ^
checkRd: (-1) summarize_stats_CSV_decoupled.Rd:84: Lost braces; missing escapes or markup?
    84 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       |                                      ^
checkRd: (-1) calcQuantiles.Rd:52: Lost braces; missing escapes or markup?
    52 | {M/F}\emph{Mean}(patchNum).csv and {M/F}\emph{Quantile}(quantNum)_(patchNum).csv.
       | ^
checkRd: (-1) calcQuantiles.Rd:52: Lost braces; missing escapes or markup?
    52 | {M/F}\emph{Mean}(patchNum).csv and {M/F}\emph{Quantile}(quantNum)_(patchNum).csv.
       |                                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Network.Rd: R6Class
  Patch.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘read_mgi_biotype_conflict_rpt.R’
Specified C++14: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  flexCItest.Rd: gaussCItest, disCItest
  getSuff.Rd: gaussCItest, disCItest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  translogCheckCurvature.Rd: semidefiniteness, quasiconvexity,
    quasiconcavity
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  find.defaultMethod.Rd: mice
  mice.impute.2l.2stage.bin.Rd: mice
  mice.impute.2l.2stage.heckman.Rd: mice
  mice.impute.2l.2stage.norm.Rd: mice
  mice.impute.2l.2stage.pois.Rd: mice
  mice.impute.2l.glm.bin.Rd: mice
  mice.impute.2l.glm.norm.Rd: mice
  mice.impute.2l.glm.pois.Rd: mice
  mice.impute.2l.jomo.Rd: mice, jomo1ran
  mice.par.Rd: mids-class, mice
  micemd-package.Rd: mice
  overimpute.Rd: mice
  plot.mira.Rd: mice, mids-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:
    ‘micer.R’
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  small.16S.Rd: microcontax
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getDomain.Rd: readFasta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package unavailable to check Rd xrefs: ‘microcontax.data’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘api.R’ ‘handlers-static.R’ ‘static-assets.Rd’
Missing dependency on R >= 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_dependencies.R’ ‘micromodal.R’ ‘micromodal.Rd’
    ‘use_micromodal.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  latex.AEdotplot.Rd: flextable
  msWord.Rd: flextable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) readFastq.Rd:62: Lost braces
    62 | code{\link{readFasta}}.
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  findOrfs.Rd: tibble
  gff2fasta.Rd: tibble
  lorfs.Rd: tibble
  msalign.Rd: tibble
  readFasta.Rd: tibble
  readFastq.Rd: tibble
  readGFF.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:
    ‘cylinder-bundle-compartment.R’ ‘cylinder-bundle-geometry.R’
    ‘samplers.R’ ‘utils.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mifa.Rd: mice
  mifa_ci_boot.Rd: mice
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.estMigConnectivity.Rd: plotCI
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:
    ‘flexImputeModel.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:
    ‘model_tests.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:
    ‘detect_segments.R’ ‘find_best_split.R’ ‘identify_migrations.R’
    ‘utils.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AIPW.Rd: mice
  MeanScore.Rd: mice
  miAIPW.Rd: mice
  miSIPW.Rd: mice
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) miive.Rd:120-239: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:241-264: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:266-277: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:279-286: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:288-293: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:295-311: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:313-337: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:339-352: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:353-370: Lost braces in \itemize; meant \describe ?
checkRd: (-1) miive.Rd:426: Lost braces
   426 | \link{MIIVsem}{miivs}
       |               ^
checkRd: (-1) miivs.Rd:33-160: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_grouped_data_partition.Rd:60: Lost braces; missing escapes or markup?
    60 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
checkRd: (-1) create_grouped_data_partition.Rd:62: Lost braces; missing escapes or markup?
    62 | Kelly Sovacool, {sovacool@umich.edu}
       |                 ^
checkRd: (-1) create_grouped_k_multifolds.Rd:30: Lost braces; missing escapes or markup?
    30 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
checkRd: (-1) get_partition_indices.Rd:58: Lost braces; missing escapes or markup?
    58 | Kelly Sovacool, {sovacool@umich.edu}
       |                 ^
checkRd: (-1) set_hparams_glmnet.Rd:16: Lost braces; missing escapes or markup?
    16 | Zena Lapp, {zenalapp@umich.edu}
       |            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  formatting.Rd: print.tbl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) milr.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milr.Rd:46-47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milr.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milr.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milr.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milr.Rd:51-52: 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:
    ‘convert_antibiotics.R’
checkRd: (-1) acs2016.Rd:14: Lost braces
    14 |   \item{BROADBND}{Cellular data plan for a smartphone or other mobile device}{1 yes 2 no}
       |                                                                              ^
checkRd: (-1) acs2016.Rd:21: Lost braces
    21 |   \item{MHP}{Mobile home costs}{$, yearly}
       |                                ^
Specified C++11: please drop specification unless essential
Missing dependency on R >= 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.R’ ‘formula.R’ ‘toy_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:
    ‘s3methods.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  miniButtonBlock.Rd: shiny
  miniTabstripPanel.Rd: shiny
  miniTitleBar.Rd: shiny
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘minqa/libs/minqa.so’:
  Found non-API call to R: ‘CLOENV’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Missing dependency on R >= 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_nest.Rd’ ‘nest_cv.R’ ‘top_perc.R’ ‘top_perc.Rd’
    ‘w2l_split.Rd’
checkRd: (-1) gof.estimates.Rd:59-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gof.estimates.Rd:63-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gof.estimates.Rd:67-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:63-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:67-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:71-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:89-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:92-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdata.frame.Rd:132: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) rdata.frame.Rd:133-134: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) rdata.frame.Rd:135-137: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) rdata.frame.Rd:138-139: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) rdata.frame.Rd:144: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) rdata.frame.Rd:145-147: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) rdata.frame.Rd:148-150: Lost braces in \enumerate; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  02missing_data.frame.Rd: bayesglm
  get_parameters.Rd: polr
  mi2stata.Rd: write.dta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) sim.data.Rd:11: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:12: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:13: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:15: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:16: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:17: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:18: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:20: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:23: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:25: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:26: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:27: Lost braces in \enumerate; meant \describe ?
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mirtsvd.Rd: rotations
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: ‘maps’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  misclassGLM.Rd: ucminf
  misclassMlogit.Rd: ucminf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  textable.Rd: xtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) sumKeepAttr.Rd:19: Lost braces
    19 |       (only relevant if code{x} has only one element).}
       |                             ^
Specified C++14: please drop specification unless essential
File ‘misha/libs/misha.so’:
  Found non-API call to R: ‘Rf_GetOption’

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:
  missForest.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:
  pic.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:
  MIFAMD.Rd: with.mids, pool, summary.mira
  MIMCA.Rd: with.mids, pool, summary.mira
  MIPCA.Rd: with.mids, pool, summary.mira
  prelim.Rd: with.mids, pool, summary.mira
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cv.missoNet.Rd: glasso
  missoNet.Rd: glasso
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MonteCarlo.Rd: foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) PV.Rd:14: Lost braces
    14 | plausible value in turn; with code{rewrite=FALSE} a new data set is
       |                                   ^
Specified C++11: please drop specification unless essential
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
Error(s) in re-building vignettes:
  ...
--- re-building ‘a-mixKernelInstallation.Rmd’ using rmarkdown
--- finished re-building ‘a-mixKernelInstallation.Rmd’

--- re-building ‘mixKernelUsersGuide.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/mixKernel.Rcheck/vign_test/mixKernel/vignettes/mixKernelUsersGuide_files/figure-html/cim_kernel-1.png
800x1000 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 43589 bytes
Input file size = 43727 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 40078
  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 = 40078

Output IDAT size = 40078 bytes (3511 bytes decrease)
Output file size = 40156 bytes (3571 bytes = 8.17% decrease)


Quitting from mixKernelUsersGuide.Rmd:144-160 [plotIndiv_PCA]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'mixKernelUsersGuide.Rmd' failed with diagnostics:
Continuous values supplied to discrete scale.
ℹ Example values: 3, 17, 17, 17, and 3
--- failed re-building ‘mixKernelUsersGuide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) mixmeta-package.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) mixmeta.ml.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ml.igls.Rd:62: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kdeem.Rd: ucminf
  mixregPvary.Rd: regmixEM
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mix.hist.Rd: histogram
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:
    ‘contexts.R’ ‘ctx_tree.R’ ‘glm_fit.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:
    ‘mlb_player_tiers.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_lines.Rd: geom_hline, geom_vline
  scale_axes_mlb.Rd: theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Texture.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) mldrGUI.Rd:22-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mldrGUI.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mldrGUI.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mldrGUI.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mldrGUI.Rd:32-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gp.list.Rd:16: Escaped LaTeX specials: \#
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mlergm.Rd: ergm.terms
  mlnet.Rd: network, ggnet2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) MLGL.Rd:43: Lost braces; missing escapes or markup?
    43 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
checkRd: (-1) cv.MLGL.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
checkRd: (-1) overlapgglasso.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
checkRd: (-1) stability.MLGL.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{y}{vector of size n. If loss = "logit", elements of y must be in {-1,1}}
       |                                                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MLGL.Rd: gglasso
  cv.MLGL.Rd: cv.gglasso, predict.cv.gglasso
  overlapgglasso.Rd: gglasso
  stability.MLGL.Rd: gglasso
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) mlim.Rd:58: Lost braces
    58 |              Note that code{"XGB"} is only available in Mac OS and Linux. moreover,
       |                            ^
checkRd: (-1) refBasedCts.Rd:44: Lost braces
    44 | using reference based imputation as proposed by \doi{10.1080/10543406.2013.834911}{Carpenter et al (2013)}. This approach
       |                                                                                   ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘actions.R’ ‘analyze.Rd’ ‘as.data.frame.mp_power.Rd’
    ‘as.list.mp_parameters.Rd’ ‘base.R’ ‘center.Rd’ ‘correlations.R’
    ‘effect_size.R’ ‘generate.Rd’ ‘list.R’ ‘mechanisms.R’ ‘mechanisms.Rd’
    ‘model.R’ ‘parameters.R’ ‘parameters.Rd’ ‘power_analysis.Rd’
    ‘print.mp_power.Rd’ ‘simulation.R’ ‘subset.mp_model.Rd’
    ‘summary.mp_power.Rd’ ‘to_formula.Rd’ ‘utils.R’ ‘variables.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mlogit.Rd: Formula
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:
    ‘example.simfun.R’ ‘fit.surrogate.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as_duckdb_backend.Rd: DataBackendDataTable, as_data_backend,
    DataBackend, Task
  as_sqlite_backend.Rd: DataBackendDataTable, as_data_backend,
    DataBackend, Task
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) groupdiff_tau.Rd:23: Lost braces
    23 | \code{groupdiff_tau()} computes \eqn{min(x/y, y/x)}, i.e. the smallest symmetric ratio between \eqn{x} and eqn{y}
       |                                                                                                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MeasureFairness.Rd: mlr_measures_classif.ce,
    mlr_measures_classif.fpr, mlr_measures, Task
  MeasureFairnessComposite.Rd: Task
  MeasureFairnessConstraint.Rd: Task
  MeasureSubgroup.Rd: mlr_measures_classif.fpr
  compas.Rd: TaskClassif
  compute_metrics.Rd: Task
  fairness_accuracy_tradeoff.Rd: PredictionClassif, BenchmarkResult,
    ResampleResult, Task, Measure, TaskClassif
  fairness_compare_metrics.Rd: PredictionClassif, BenchmarkResult,
    ResampleResult, Measure, TaskClassif, Task
  fairness_prediction_density.Rd: PredictionClassif, ResampleResult,
    BenchmarkResult, Task, TaskClassif
  fairness_tensor.Rd: data.table, PredictionClassif, ResampleResult,
    TaskClassif, Task
  groupdiff_tau.Rd: Task
  groupwise_metrics.Rd: Task
  mlr_learners_classif.fairfgrrm.Rd: Learner, mlr_learners, lrn
  mlr_learners_classif.fairzlrm.Rd: Learner, mlr_learners, lrn
  mlr_learners_fairness.Rd: Task
  mlr_learners_regr.fairfrrm.Rd: Learner, mlr_learners, lrn
  mlr_learners_regr.fairnclm.Rd: Learner, mlr_learners, lrn
  mlr_learners_regr.fairzlm.Rd: Learner, mlr_learners, lrn
  mlr_measures_fairness.Rd: Task
  mlr_pipeops_equalized_odds.Rd: R6Class, PipeOpTaskPreproc, PipeOp
  mlr_pipeops_explicit_pta.Rd: R6Class, PipeOpTaskPreproc, PipeOp
  mlr_pipeops_reweighing.Rd: R6Class, PipeOpTaskPreproc, PipeOp
  report_fairness.Rd: Task
  task_summary.Rd: Task
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  read_arff.Rd: data.table, 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:
  TaskClassifST.Rd: TaskClassif, DataBackend, DataBackendDataTable,
    convert_task
  TaskRegrST.Rd: TaskRegr, DataBackend, DataBackendDataTable,
    convert_task
  as_data_backend.Rd: DataBackend
  as_task_classif_st.Rd: DataBackend, TaskRegr, convert_task
  as_task_regr_st.Rd: DataBackend, TaskClassif, convert_task
  predict_spatial.Rd: Learner
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:
  ‘future’ ‘mlr3tuning’
checkRd: (-1) MBOMultiObjResult.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOMultiObjResult.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOMultiObjResult.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOMultiObjResult.Rd:11-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOMultiObjResult.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOSingleObjResult.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOSingleObjResult.Rd:9-11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOSingleObjResult.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOSingleObjResult.Rd:13-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOSingleObjResult.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MBOSingleObjResult.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) error_handling.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) error_handling.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) error_handling.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) error_handling.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) error_handling.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) error_handling.Rd:18-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) error_handling.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mbo_parallel.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mbo_parallel.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setMBOControlMultiObj.Rd:119-120: Lost braces
   119 | Notes in Computer Science, ISBN 978-3-642-37139-4, pp. 756{770,
       |                                                           ^
checkRd: (-1) trafos.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) trafos.Rd:29: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  TuneMultiCritControl.Rd: OptPath
  batchmark.Rd: data.table
  getClassWeightParam.Rd: LearnerParam
  getLearnerParamSet.Rd: ParamSet
  getParamSet.Rd: ParamSet
  makeBaseWrapper.Rd: ParamSet
  makeExtractFDAFeatMethod.Rd: ParamSet
  makeModelMultiplexerParamSet.Rd: ParamSet
  makeTuneControlMBO.Rd: OptPath
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) simpopmlx.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{fim}{the Fisher Information Matrix estimated by Monolix. fim={"sa", "lin"} (default="sa")}
       |                                                                    ^
Specified C++11: please drop specification unless essential
File ‘mmap/libs/mmap.so’:
  Found non-API calls to R: ‘Rf_allocSExp’, ‘SET_ENCLOS’, ‘SET_FRAME’,
    ‘SET_HASHTAB’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
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:
    ‘mmcif_data.Rd’ ‘mmcif_fit.Rd’ ‘mmcif_logLik.Rd’ ‘mmcif_pd_cond.Rd’
    ‘mmcif_pd_univariate.Rd’ ‘mmcif_sandwich.Rd’ ‘mmcif_start_values.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mmcif_fit.Rd: auglag
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) MMD_attr.Rd:62: Lost braces; missing escapes or markup?
    62 | \item Probability of attribution of each unknown individual to each source $p_{u,s}$
       |                                                                               ^
checkRd: (-1) mmeln.Rd:69: Lost braces; missing escapes or markup?
    69 |   \item{obj$M}{Number of total observations sum_{i=1}^N(pi)}
       |                                                 ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘BF_for_everyone.R’ ‘rc_game_mgmt.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:
    ‘iht_interpreter.Rd’ ‘lr_pow.Rd’ ‘pj_pow.Rd’ ‘replext_helpers.R’
    ‘replext_helpers_pgsql.R’ ‘rm_interpreter.Rd’
checkRd: (-1) average.fit.models.Rd:6: Lost braces; missing escapes or markup?
     6 | These function takes the output of pgls.iter and uses its list of objects { model fits, optimzations (e.g.AICc)} and performs a weighted average on the ctoefficients estimated in the former by weighting by the latter. The parameters can also optionally be converted to binary by specifying "binary=FALSE" or just running the alias wraper function for assessing evidence of variable importance (Burnham & Anderson 2000).
       |                                                                           ^
Specified C++14: please drop specification unless essential
checkRd: (-1) k2d.Rd:26: Lost braces
    26 | d_ND(x,y) = sqrt{ k(x,x) - 2k(x,y) + k(y,y)}.
       |                 ^
checkRd: (-1) k2d.Rd:34: Lost braces
    34 | d_n(x,y) = 1 - k(x,y)/sqrt{ k(x,x)k(y,y)},
       |                           ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘interop-car.R’ ‘mmrm_tidiers.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mnl_fd2_ova.Rd: multinom, nnet
  mnl_fd_ova.Rd: multinom, nnet
  mnl_pred_ova.Rd: multinom, nnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) mom.mtruncnorm.Rd:35: Lost braces
    35 |   \item{cum}{a logical value; if  code{TRUE}  (default value), cumulants 
       |                                       ^
checkRd: (-1) mom.mtruncnorm.Rd:43: Lost braces; missing escapes or markup?
    43 | The maximal value of {d} is \code{20}. If this threshold is exceeded, \code{NA}s
       |                      ^
checkRd: (-1) mt.Rd:110: Lost braces
   110 |   and code{tvpack}, downloaded in 2005 and again in 2007 from his webpage, 
       |           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nlmeModel.Rd: nlme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) creating.phenotypic.transform.Rd:20: Lost braces
    20 | trafo <- function(x){ return(x^2)}
       |                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mock.Rd: with_mock
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) lientz.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lientz.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lientz.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) modelDown.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) modelDown.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) modelDown.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) modelDown.Rd:31: 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:
    ‘combine.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  stack_coeff.Rd: tibble
  stack_metrics.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:
  model_grid.Rd: train
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) model.importance.plot.Rd:139: Lost braces
   139 | For binary CF models, if{importance.type = 2}, function uses AUC-based variables importances as described by Janitza et al. (2012). Here, the area under the curve instead of the accuracy is used to calculate the importance of each variable. This AUC-based variable importance measure is more robust towards class imbalance. 
       |                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  model.mapmake.Rd: writeFormats, writeRaster, compareRaster
Please provide package anchors for all Rd \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_arguments.Rd: testthat
  check_glance_outputs.Rd: glance
  check_single_augment_output.Rd: augment
  check_tibble.Rd: tidy, augment, glance
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:
    ‘pop_sd.Rd’ ‘tidy_summary.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lival.Rd: survey
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'::' or ':::' imports not declared from:
  ‘GGally’ ‘ade4’ ‘ggiraphExtra’ ‘lattice’
'library' or 'require' calls not declared from:
  ‘DescTools’ ‘FactoMineR’ ‘GGally’ ‘ISLR’ ‘Kendall’ ‘MASS’ ‘MBESS’
  ‘MVN’ ‘PCAmixdata’ ‘RColorBrewer’ ‘SuppDists’ ‘ade4’ ‘adegraphics’
  ‘broom’ ‘car’ ‘coin’ ‘combinat’ ‘corpcor’ ‘corrplot’ ‘devtools’
  ‘dplyr’ ‘factoextra’ ‘finalfit’ ‘ggcorrplot’ ‘ggdendro’
  ‘ggiraphExtra’ ‘ggpubr’ ‘glmnet’ ‘hnp’ ‘lattice’ ‘leaps’ ‘mice’
  ‘mvtnorm’ ‘naniar’ ‘ppcor’ ‘pspearman’ ‘pwr’ ‘questionr’ ‘rgl’ ‘rms’
  ‘vcd’ ‘vegan’ ‘yarrr’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  device_flow_auth.Rd: oauth_endpoint
  discover.Rd: oauth_endpoint
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gel4.Rd: vcovHAC
  gmm4.Rd: meatCL, vcovHAC
  momentModel.Rd: meatCL, vcovHAC
  momentStrength-methods.Rd: vcovHC, vcovHAC, meatCL
  sysMomentModel.Rd: meatCL, vcovHAC
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AIC.momentuHMM.Rd: quasiquotation
  AICweights.Rd: quasiquotation
  MIfitHMM.Rd: crwPostIS
  plotSat.Rd: CRS-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:
  LDA.Rd: lda
  img_plot.Rd: readJPEG
  ldk_contour.Rd: kde2d
  links_delaunay.Rd: delaunayn
  plot.LDA.Rd: kde2d
  plot.PCA.Rd: kde2d
  reLDA.Rd: predict.lda
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) circ_dist.Rd:21: Lost braces; missing escapes or markup?
    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                       ^
checkRd: (-1) circ_dist.Rd:21: Lost braces; missing escapes or markup?
    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                               ^
checkRd: (-1) circ_dist.Rd:21: Lost braces; missing escapes or markup?
    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                                                          ^
checkRd: (-1) legacy.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:40: 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:
    ‘define_extended_question.Rd’ ‘define_question.Rd’
    ‘define_questions_from_csv.Rd’ ‘define_questions_from_data_frame.Rd’
    ‘define_questions_from_excel.Rd’ ‘generate_xml.Rd’
    ‘generate_xml_file.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘Search.R’ ‘mood.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:
    ‘bigram.R’ ‘moranajp.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GetAleData.Rd: cforest, foreach, FeatureEffect, iml
  GetInteractionStrength.Rd: cforest, vip
  GetPartialData.Rd: cforest, partial, foreach, pdp
  fastcforest.Rd: ForestControl-class, cforest_control, ptrafo,
    cforest, RandomForest-class
  fastvarImp.Rd: varImp, cforest
  ggVarImp.Rd: varImp, varImpAUC
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:
    ‘stopwords.R’
checkRd: (-1) morphemepiece_cache_dir.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) morphemepiece_cache_dir.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) morphemepiece_cache_dir.Rd:22-24: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getOuterViewpoints.Rd: vcgSphere
  meshDist.Rd: shade3d, material3d
  render.Rd: shade3d, material3d
  warpmovie3d.Rd: shade3d
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calcPoly.Rd: surf.gls, expcov, surf.ls, trmat
  resample_grid.Rd: ahull, concaveman, inahull
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  make_df.Rd: bind_rows
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  chisq.Rd: after_stat
  freqpolygon.Rd: densityplot
  plotCumfreq.Rd: densityplot
  plotModel.Rd: xyplot
  themes.Rd: trellis.par.set, show.settings
  xpnorm.Rd: qqmath
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LearningHC.Rd: hc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.GrangerInteraction.Rd: plot.igraph
  plot.View.Rd: plot.zoo
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:
    ‘cast_vec.R’ ‘plot_response_rate.R’ ‘read_mpath.R’ ‘response_rate.R’
    ‘write_mpath.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:
    ‘alias_column_names.R’ ‘bin_data.Rd’ ‘coverage.R’ ‘database.R’
    ‘decrypt_gps.Rd’ ‘import.R’ ‘import_functions.R’ ‘linking.R’
    ‘location_functions.R’ ‘sensor_functions.R’
checkRd: (-1) thresh.est.Rd:16: Lost braces
    16 |   Calculates the stimulus level(s) for a probit model of a psychometric function for given levels of performance.  For a more general version, see \link[MASS]{dose.p} in pkg{MASS}.
       |                                                                                                                                                                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  panel.psyfun.Rd: lattice
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
checkRd: (-1) genotype_data.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) phenotype_data.Rd:15: Escaped LaTeX specials: \_
Missing dependency on R >= 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-contribution.R’ ‘compute-headcount-ratio-adjusted.R’
    ‘compute-headcount-ratio.R’ ‘compute-mpi.R’ ‘compute_mpi.Rd’
    ‘create-deprivation-matrix.R’ ‘define-deprivation.R’
    ‘define-mpi-specs.R’ ‘define_deprivation.Rd’ ‘define_mpi_specs.Rd’
    ‘helpers.R’ ‘save_mpi.R’ ‘write-as-excel.R’
checkRd: (-1) glmfence.Rd:21: Lost braces; missing escapes or markup?
    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
checkRd: (-1) lmfence.Rd:21: Lost braces; missing escapes or markup?
    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mplus.traceplot.Rd: plot.mcmc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) get.mpt.fia.Rd:60: Lost braces
    60 | \item{lnconst}{When inequality constraints are present, \code{lnconst} serves as an adjustment of code{lnInt}. It estimates the logarithm of the proportion of parameter space [0,1]^S that satisfies those inequality constraints, and the log integral term is given by \code{lnInt+lnconst}.
       |                                                                                                       ^
checkRd: (-1) prediction.plot.Rd:38: Lost braces
    38 | The labels on the x-axis. Default is \code{Tree 1} to code{Tree 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:
    ‘detfct.fit.opt.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  parallel_mrgsim_d.Rd: mrgsim_d, future_lapply
  parallel_mrgsim_ei.Rd: mrgsim_d, future_lapply
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) MultiManhattan.Rd:33: Lost braces; missing escapes or markup?
    33 |         \item{LogTimes}{Magnification of {-log10(P-value)}; the default is
       |                                          ^
checkRd: (-1) MultiManhattan.Rd:35: Lost braces; missing escapes or markup?
    35 |     \item{LODTimes}{Magnification of {LOD score}; the default is 1.2.}
       |                                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CompareMethodsNodeOrdering.Rd: pc, pc.stable, mmpc, mmhc, hc
  CompareMethodsVStructure.Rd: pc, pc.stable, mmpc, mmhc, hc
  CutModules.Rd: cut2
  EdgeOrientation.Rd: graph-class
  MRPC.Rd: pc, ci.test, gaussCItest, graph-class
  MRPCclass.Rd: pcAlgo-class, skeleton, pc, graph-class
  ModiSkeleton.Rd: skeleton, pc, ci.test, graph-class
  PlotDendrogram.Rd: plotDendroAndColors
  PlotGraphWithModules.Rd: ggnet2
  data_with_outliers.Rd: pc, pc.stable, mmpc, mmhc, hc
  data_without_outliers.Rd: pc, pc.stable, mmpc, mmhc, hc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) data_binary.Rd:10: Lost braces; missing escapes or markup?
    10 |            log E(Y_{t+1} | A_t = 0, I_t = 1) = alpha_0 + alpha_1 * time / total_T
       |                    ^
checkRd: (-1) msa-package.Rd:17: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa-package.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa-package.Rd:21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa.Rd:65: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa.Rd:67: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa.Rd:69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary.msa.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) n.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) n.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) n.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  chart_labels_text.Rd: fp_text
  ph_with.ms_chart.Rd: read_pptx
  set_theme.Rd: fp_text, fp_border
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) SignalProcessing.Rd:42: Lost braces; missing escapes or markup?
    42 |   \item{calibrateIntensity_method}{a \code{character} indicating the intensities calibration method used (\code{"TIC"} method by default).  This calibration method can be remplaced by \code{"PQN"} or {"median"}.See \code{calibrateIntensity-methods} of the \code{MALDIquant} R package for details.}
       |                                                                                                                                                                                                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ADtest.Rd: kSamples-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:
  ms_list_voices.Rd: GET
  ms_synthesize.Rd: POST
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:
    ‘BAM2OM.R’ ‘SSinternal.R’ ‘spatial_targ_opt.R’
'data(package=)' call not declared from: ‘MASS’
Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  P__disp.Rd: glm.nb
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) multivar_joint_shannon_entropy.Rd:20: Lost braces
    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
checkRd: (-1) total_correlation.Rd:20: Lost braces
    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  TSMCP.Rd: grpreg
Please provide package anchors for all Rd \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.MTest.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:
  cor.util.Rd: xyplot
  data.visualisation.Rd: xyplot
  grpplot.Rd: xyplot
  mdsplot.Rd: xyplot
  panel.elli.Rd: xyplot, panel.ellipse
  panel.smooth.line.Rd: xyplot
  pcaplot.Rd: xyplot
  plot.pcalda.Rd: xyplot
  plot.plsc.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:
  ring_detect.Rd: ringBorders, measuRing
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:
    ‘mtscr_score.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Compute_Cn1n2.Rd: Rcpp
  plot-MuChPoint.Rd: capushe
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) coef.mdf.Rd:17: Lost braces; missing escapes or markup?
    17 |   \item{type}{: Argument that controls the type of parameters to be returned. If \code{type="persons"} (default), a vector with the person parameters is returned. When \code{type="items"} then a vector with the item ranks obtained by the MUDFOLD item selection algorithm is returned. If {type="all"} then a list with both person and item coefficients is returned to the user.
       |                                                                                                                                                                                                                                                                                                ^
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PolyOrdinalLogBiplot.Rd: fa, principal
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) MultEq-package.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MultEq-package.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MultEq-package.Rd:30: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) dbivCMP.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{bivprob}{Bivariate probabilities, {p00, p01, p10, p11}.}
       |                                         ^
checkRd: (-1) PPCA.Rd:35: Lost braces
    35 | Returns an object of class 'pcaRes.'  See documentation in the package code{\link[pcaMethods:pcaMethods]{ pcaMethods}}
       |                                                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Loadings.Rd: pca, lda
  PPCA.Rd: pca
  completeData.Rd: pca
  ldaPlot.Rd: lda
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:
    ‘mlgraph.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gmeanrel.Rd: lme
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:
    ‘predict.R’ ‘sensitivity.R’ ‘treatment_profile.R’
checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Chenprob.Rd: coxph
  GAMprob.Rd: coxph, gam
  GLMprob.Rd: coxph
  KMprob.Rd: coxph
  multipleNCC-package.Rd: coxph
  pGAM.Rd: gam
  wpl.Rd: coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) nullestimation.Rd:17: Lost braces; missing escapes or markup?
    17 |           \code{U}        \tab The common latent space vectors. U in R^{n x d}\cr
       |                                                                        ^
checkRd: (-1) biomasse.Rd:30: Lost braces
    30 | Makowski, D., Jeuffroy, M.-H., Gu\'{e}rif, M., 2004 Bayesian methods for
       |                                    ^
checkRd: (-1) climat.Rd:20: Lost braces
    20 | Makowski, D., Jeuffroy, M.-H., Gu\'{e}rif, M., 2004 Bayesian methods for
       |                                    ^
checkRd: (-1) simulmodel.Rd:15: Lost braces
    15 |   \item{\dots}{... }{possible fixed parameters of the R-function}
       |                     ^
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:
    ‘grid-pipeline.R’ ‘inspect-decisions.R’ ‘multiverse-tables.R’
    ‘show-pipelines.R’ ‘utils.R’ ‘visualize-pipeline.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  condense.Rd: unnest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ComponentesPrincipais.Misto.Rd: PCAmix
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:
    ‘concat_pre_processors.Rd’
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘accessors.R’ ‘export_json.R’ ‘extract.R’
checkRd: (-1) metricUnfolding.Rd:69-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:71-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:73-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:75-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:80-86: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  msTrans_abs.Rd: doQmapQUANT, qmap
  tscale.Rd: lubridate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) cv.glm1path.Rd:74: Lost braces
    74 | \code{\link{glm1path}}, \\code{\link{glm1}}, \code{\link{glm}}, \code{\link{family}}
       |                               ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘DFA.R’ ‘mvDFA.R’ ‘simulate_Lorenz_noise.R’
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mvhist.Rd: mvmesh, SolidRectangle, mvhist, V2Hrep
  mvhistMisc.Rd: V2Hrep
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:
    ‘influence.mlm.Rd’ ‘mlm.influence.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  influencePlot.mlm.Rd: showLabels
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mardia.Rd: mvn
  mhz.Rd: mvn
  msk.Rd: mvn
  msw.Rd: mvn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) MVNtestchar-package.Rd:16-17: Lost braces; missing escapes or markup?
    16 | {Provides a test of multivariate normality of a sample which does not require estimation of the nuisance parameters, the mean      vector and covariance matrix.  Rather, a sequence of transformations removes these nuisance parameters, resulting in a set of    sample matrices that are positive definite.  If, and only if the original data is multivariate normal, these matrices are       uniformly distributed on the space of positive definite matrices in the unit hyper-rectangle.  The package performs a goodness    of fit test of this hypothesis. In addition to the test, functions in the package give visualizations of the  support region    of positive definite matrices for p equals 2.
       | ^
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
checkRd: (-1) dmvss.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dmvss.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dmvss.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dmvss.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dmvss.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
'library' or 'require' call not declared from: ‘mvtnorm’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  phyltree_paths.Rd: ape
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  matchedwake.Rd: cem, att, glm.nb
  slideWakeMatch.Rd: cem, att, glm.nb
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:
    ‘get_individual_algebra_results.R’
checkRd: (-1) mzipmed_data.Rd:22: Lost braces; missing escapes or markup?
    22 | @source {Simulated to serve as an example}
       |         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cendiff.Rd: survdiff
  cenfit.Rd: survfit
  cenmle-class.Rd: survreg
  cenmle-gaussian-class.Rd: survreg
  cenmle-lognormal-class.Rd: survreg
  cenreg-class.Rd: survreg
  cenreg-gaussian-class.Rd: survreg
  cenreg-lognormal-class.Rd: survreg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) M36NT2PM.dat.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) M36NT2PM.dat.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DSIVdata.Rd:15-23: Lost braces
    15 | for(i in 1:50){
       |               ^
checkRd: (-1) DSIVdata.Rd:17-21: Lost braces
    17 |   for(j in 1:50){
       |                 ^
checkRd: (-1) DSIVdata.Rd:31-39: Lost braces
    31 | for(i in 1:20){
       |               ^
checkRd: (-1) DSIVdata.Rd:33-37: Lost braces
    33 |   for(j in 1:20){
       |                 ^
checkRd: (-1) DSLIVEdata.Rd:10-18: Lost braces
    10 | for(i in 1:200){
       |                ^
checkRd: (-1) DSLIVEdata.Rd:12-16: Lost braces
    12 |   for(j in 1:200){
       |                  ^
checkRd: (-1) DSLIVEdata.Rd:26-34: Lost braces
    26 | for(i in 1:20){
       |               ^
checkRd: (-1) DSLIVEdata.Rd:28-32: Lost braces
    28 |   for(j in 1:20){
       |                 ^
checkRd: (-1) DSLIVEdata.Rd:50-54: Lost braces
    50 | for(kk in 1:length(p)){
       |                       ^
checkRd: (-1) drop_name_crossref.Rd:49: Lost braces; missing escapes or markup?
    49 | Takes one or several dois and extracts information from Crossref, then processes them into visual citations with \code{\link{drop_name}}. Requires {rcrossref} > v1.1, see README for further details.
       |                                                                                                                                                    ^
'::' or ':::' import not declared from: ‘Matrix’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘impute_below.Rd’ ‘impute_factor.Rd’ ‘impute_fixed.Rd’
    ‘impute_mean.Rd’ ‘impute_median.Rd’ ‘impute_mode.Rd’ ‘impute_zero.Rd’
    ‘replace_na_with.Rd’
File ‘nanoparquet/libs/nanoparquet.so’:
  Found non-API call to R: ‘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.
checkRd: (-1) fod.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fod.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fod.Rd:14: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
File ‘naryn/libs/naryn.so’:
  Found non-API call to R: ‘Rf_GetOption’

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:
  abcfgwc.Rd: cdist
  fgwc.Rd: cdist
  fgwcuv.Rd: cdist
  fpafgwc.Rd: cdist
  gsafgwc.Rd: cdist
  hhofgwc.Rd: cdist
  ifafgwc.Rd: cdist
  psofgwc.Rd: cdist
  tlbofgwc.Rd: cdist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  install.Rd: pak
  selfupdate.Rd: pak
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  WeightedNNBasedLinesetMatching.Rd: dotprops, neuron
  nat.nblast-package.Rd: neuronlist, neuronlistfh
  nblast.Rd: nat-package, plyr
  nblast_allbyall.Rd: neuronlist
  neuron_pairs.Rd: neuronlist
  plot3d.hclust.Rd: slice, colour_clusters
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 (2018-01-22)
    Version  (2017-08-22)
    Version
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.mesh3d.Rd: rgl
  boundingbox.Rd: mesh3d
  cmtk.reformatx.Rd: RunCmdForNewerInput, makelock
  find.neuron.Rd: select3d
  find.soma.Rd: select3d
  nat-package.Rd: igraph, select3d, rgl
  ndigest.Rd: digest
  neuron.Rd: dfs
  ngraph.Rd: igraph
  nopen3d.Rd: open3d
  nview3d.Rd: view3d
  pan3d.Rd: rgl.setMouseCallbacks
  seglist.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:
  fit_xform.Rd: xform, xyzmatrix, computeTransform
  fit_xform_brain.Rd: computeTransform
  guess_templatebrain.Rd: im3d
  local_reg_dir_for_url.Rd: user_data_dir
  xform_brain.Rd: cmtk.reformatx, xform, xformpoints, xformimage
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:
    ‘activate.Rd’
checkRd: (-1) NbClust.Rd:50: Lost braces; missing escapes or markup?
    50 |       \item \bold{Average} : The distance \eqn{D_{ij}}{D_ij} between two clusters \eqn{C_{i}}{C_i} and \eqn{C_{j}}{C_j} is the mean of the distances between the pair of points {x} and {y}, where \eqn{x \in C_{i}, y \in C_{j}}{x in C_i, y in C_j}.
       |                                                                                                                                                                                 ^
checkRd: (-1) NbClust.Rd:50: Lost braces; missing escapes or markup?
    50 |       \item \bold{Average} : The distance \eqn{D_{ij}}{D_ij} between two clusters \eqn{C_{i}}{C_i} and \eqn{C_{j}}{C_j} is the mean of the distances between the pair of points {x} and {y}, where \eqn{x \in C_{i}, y \in C_{j}}{x in C_i, y in C_j}.
       |                                                                                                                                                                                         ^
checkRd: (-1) nbconvert.Rd:49: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) nbconvert.Rd:50: Lost braces in \enumerate; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) ncpen.Rd:108: Lost braces; missing escapes or markup?
   108 |   \item{gamma}{extra shrinkage parameter for \code{classo} and {sridge} only.}
       |                                                                ^
checkRd: (-1) ncpen.reg.Rd:109: Lost braces; missing escapes or markup?
   109 |   \item{gamma}{extra shrinkage parameter for \code{classo} and {sridge} only.}
       |                                                                ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘assign_fold.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ndi-package.Rd: tidycensus, psych, sf, Matrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) norm_tests.Rd:69: Lost braces
    69 | Anderson-Darling test." See url{https://github.com/Lakens/perfect-t-test} for
       |                                ^
checkRd: (-1) t_neat.Rd:243: Lost braces
   243 | Anderson-Darling test." See url{https://github.com/Lakens/perfect-t-test} for
       |                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  aggr_neat.Rd: data.table
  rbind_loop.Rd: data.table
  read_dir.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:
  fBracelets.Rd: nPerm
  fNecklaces.Rd: nPerm
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:
    ‘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:
    ‘acquire_neon_data.R’ ‘check_qf_flags.R’ ‘compute_monthly_mean.R’
    ‘compute_monthly_mean.Rd’ ‘compute_neon_flux.R’
    ‘compute_surface_flux.R’ ‘correct_env_data.R’ ‘depth_interpolate.R’
    ‘determine_position.R’ ‘env_fingerprint_plot.R’ ‘fit_function.R’
    ‘flux_fingerprint_plot.R’ ‘insert_mean.R’ ‘measurement_detect.R’
    ‘measurement_merge.R’ ‘swc_correct.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:
    ‘neon_cloud.R’
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘as.data.frame.predict.R’
checkRd: (-1) GSS.Rd:17: Lost braces
    17 | code{2016}.}
       |     ^
checkRd: (-1) partial_correlation.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) partial_correlation.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) partial_correlation.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) partial_correlation.Rd:29: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_netassoc_network.Rd: plot.igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  netEst.dir.Rd: glmnet
  netEst.undir.Rd: glmnet
  netgsa-package.Rd: glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.select.Rd: select
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bbox.Rd: extent, coordinates
  coordinates.Rd: extent
  extent.Rd: coordinates
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  analyze_ptn.Rd: igraph
  origin-methods.Rd: igraph
  origin_multiple.Rd: fastgreedy.community,
    leading.eigenvector.community
  plot_ptn.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:
  permutationTest.Rd: statmod
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) PVmodule.Rd:27: Lost braces; missing escapes or markup?
    27 | In the resulting netSEM model, time was used as a proxy for damp heat exposure stress (S) variable and $P_{max}$ (maximum power generated by the modules) was used as the performance level response ($R$) variable, several mechanistic variables ($M$) were obtained through chemical evaluation methods, including FTIR and TGA  on EVA encapsulant. 
       |                                                                                                           ^
checkRd: (-1) netSEMp1.Rd:55: Lost braces
    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
       |                                                                                                                     ^
checkRd: (-1) netSEMp1.Rd:55: Lost braces
    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
       |                                                                                                                                ^
checkRd: (-1) netSEMp1.Rd:55: Lost braces
    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
       |                                                                                                                                              ^
'library' or 'require' call not declared from: ‘MASS’
checkRd: (-1) spec_clust.Rd:33: Lost braces; missing escapes or markup?
    33 | A label vector of size n x 1 with elements in {1,2,...,K}
       |                                               ^
checkRd: (-1) rc.plot.ideogram.Rd:20: Lost braces; missing escapes or markup?
    20 |  \item{las}{numeric in {0,1,2,3}; the style of chromosome labels. 0, always parallel to the track [default]; 1, always horizontal; 2, always perpendicular to the track; 3, always vertical.}
       |                        ^
checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) nodeLogic.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:46: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘map.png’ ‘maze.html’
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  communicability_matrix.Rd: expm, dgeMatrix-class
  contagion.Rd: Matrix
  criticality.Rd: Matrix
  impact_susceptibility.Rd: Matrix, expm, dgeMatrix-class
  risk_matrix.Rd: Matrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  convert2igraph.Rd: igraph
  sim.chordal.Rd: psych
  sim.swn.Rd: psych
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) networktree.Rd:56: Lost braces; missing escapes or markup?
    56 | with a matrix response {y}. \code{x1} and \code{x2} are used as
       |                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  copyNIfTIHeader.Rd: dropImageDimension, nifti
  datatype.Rd: convert.datatype, convert.bitpix
  double_ortho.Rd: orthographic
  ensure_array.Rd: nifti
  fast_readnii.Rd: readNifti, drop_img_dim
  img_list_to_ts.Rd: nifti
  img_ts_to_df.Rd: nifti
  img_ts_to_list.Rd: nifti
  img_ts_to_matrix.Rd: nifti
  ortho2.Rd: orthographic
  random_nifti.Rd: nifti
  readNIfTI2.Rd: readNIfTI, drop_img_dim
  remake_img.Rd: nifti
  replace_dropped_dimensions.Rd: nifti
  rescale_img.Rd: drop_img_dim
  tempimg.Rd: drop_img_dim
  writeNIfTI2.Rd: writeNIfTI, drop_img_dim
  write_nifti.Rd: writeNifti
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:
    ‘visualizations.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EXPGSC1.Rd: xts
  FEDFUNDS.Rd: xts
  GCEC1.Rd: xts
  GDPC1.Rd: xts
  GDPDEF.Rd: xts
  GPDIC1.Rd: xts
  GS10.Rd: xts
  IMPGSC1.Rd: xts
  PAYEMS.Rd: xts
  PCECC96.Rd: xts
  SP500.Rd: xts
  UNRATENSA.Rd: xts
  USREC.Rd: xts
  yth_filter.Rd: xts, zoo, yearmon, yearqtr, as.xts
  yth_glm.Rd: xts, zoo, yearmon, yearqtr, as.xts
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++14: please drop specification unless essential
'library' or 'require' call not declared from: ‘lattice’
checkRd: (-1) NHANES.Rd:278: Lost braces
   278 | \code{AgeFirstMarij}{Age participant first tried marijuana. Reported for participants aged 18 to 59 years.}
       |                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nhm.control.Rd: maxLik
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) bootstrap_param_est.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootstrap_param_est.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootstrap_param_est.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_data.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_data.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_data.Rd:44: 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:
    ‘create_comparison.R’ ‘create_comparisons.Rd’
    ‘extract_group_metrics.R’ ‘extract_group_metrics.Rd’
    ‘extract_layman.R’ ‘extract_layman.Rd’ ‘extract_mu.R’ ‘extract_mu.Rd’
    ‘extract_niche_size.R’ ‘extract_overlap.R’ ‘extract_sigma.R’
    ‘extract_similarities.R’ ‘extract_similarities.Rd’ ‘niche_ellipse.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotIncMatrix.Rd: scale_fill_distiller
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) postPredSPD.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) postPredSPD.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  compare.models.Rd: nimbleMCMC, runMCMC
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Malformed Description field: should contain one or more complete sentences.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nicqControl.Rd: bpcp, quantile.kmciLR
  nicqTest.Rd: bpcp, quantile.kmciLR
  powerNicqTest.Rd: uniroot.integer
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_model_params.R’ ‘level_from_quantiles.R’ ‘make_request.R’
    ‘nixtla_client_cross_validation.R’ ‘nixtla_client_detect_anomalies.R’
    ‘nixtla_client_forecast.R’ ‘nixtla_client_historic.R’
    ‘nixtla_client_plot.R’ ‘nixtla_validate_api_key.R’
    ‘validate_exogenous.R’
checkRd: (-1) mcrPlot.Rd:42-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mcrPlot.Rd:45-47: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  predict.pamrML.Rd: pamr.predict
  xtable.confusionMatrix.Rd: confusionMatrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Pwr.lme.Rd: anova.lme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘addBaseline1exp.Rd’ ‘addBaselineConst.Rd’ ‘addBaselineExp.Rd’
    ‘addBaselineLin.Rd’ ‘addCmtProp.Rd’ ‘addDepot.Rd’ ‘addDirectLin.Rd’
    ‘addEffectCmtLin.Rd’ ‘addEta.Rd’ ‘addIndirect.Rd’ ‘addIndirectLin.Rd’
    ‘addLogEstimates.Rd’ ‘addResErr.Rd’ ‘addTransit.Rd’
    ‘addWeibullAbs.Rd’ ‘convertEmax.Rd’ ‘convertEmaxHill.Rd’
    ‘convertKinR0.Rd’ ‘convertLogLin.Rd’ ‘convertMM.Rd’ ‘convertQuad.Rd’
    ‘fakeCc.Rd’ ‘pkTrans.Rd’ ‘removeDepot.Rd’ ‘removeLinesAndInis.Rd’
    ‘removeTransit.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  generate.data.Rd: rmvnorm, rmvt
  nlmm.Rd: varFunc, varFixed, varClasses, summary.varFunc,
    varWeights.varFunc, coef.varFunc
  nlmmControl.Rd: lme, lmeControl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) dot-make_long_data.Rd:44: Lost braces; missing escapes or markup?
    44 | training sample), psi (the value of this observations Psihat(P_{n,B_n}^0)),
       |                                                                ^
checkRd: (-1) dot-make_long_data_nested_cv.Rd:49: Lost braces; missing escapes or markup?
    49 | training sample), psi (the value of this observations Psihat(P_{n,B_n}^0)),
       |                                                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nlsLMList.formula.Rd: nlsList
  predict_nlme.Rd: predict.nlme, predict.lme, predict.gnls
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) anova.Rd:19: Lost braces
    19 |   Returns an object of class code{anova}.  These objects represent
       |                                  ^
checkRd: (-1) check_input_event_times.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_input_event_times.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_time_unit.Rd:12-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_time_unit.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_params_doc.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_params_doc.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_brts.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_brts.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_brts.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_brts.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_extinct.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_extinct.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_extinct.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_extinct.Rd:39-40: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nmarank.Rd: netmeta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++14: please drop specification unless essential
checkRd: (-1) ROCplots.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:108-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:111-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:114-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:118-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:121-124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:125: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AthenaConnection.Rd: DBIConnection-class
  Query.Rd: DBIConnection-class
  dbClearResult.Rd: DBIResult-class
  dbColumnInfo.Rd: DBIResult-class
  dbConnect-AthenaDriver-method.Rd: DBIDriver-class,
    DBIConnection-class
  dbDataType.Rd: DBIDriver-class, DBIConnection-class
  dbDisconnect.Rd: DBIConnection-class
  dbExistsTable.Rd: DBIConnection-class
  dbFetch.Rd: DBIResult-class
  dbGetInfo.Rd: DBIObject-class, DBIDriver-class, DBIConnection-class,
    DBIResult-class
  dbGetPartition.Rd: DBIConnection-class
  dbGetQuery.Rd: DBIConnection-class
  dbGetStatement.Rd: DBIResult-class
  dbGetTables.Rd: DBIConnection-class
  dbHasCompleted.Rd: DBIResult-class
  dbIsValid.Rd: DBIObject-class, DBIDriver-class, DBIConnection-class,
    DBIResult-class
  dbListFields.Rd: DBIConnection-class
  dbListTables.Rd: DBIConnection-class
  dbQuote.Rd: DBIConnection-class
  dbRemoveTable.Rd: DBIConnection-class
  dbShow.Rd: DBIConnection-class
  dbStatistics.Rd: dbSendQuery, DBIResult-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:
  phyplot.Rd: axisPhylo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) simulatePop.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imp_int_an.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imp_int_an.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ndmodel.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ndmodel.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ndmodel.Rd:18: 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:
    ‘libr_called.R’ ‘libr_unused.R’ ‘libr_used.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MvtF.Rd: hcubature, cubature
  MvtGlomx.Rd: hcubature, cubature
  MvtInvBeta.Rd: hcubature, cubature
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lp2.Rd: lp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) set.data.Rd:14: Lost braces; missing escapes or markup?
    14 |   \item{shape}{either \code{wide} or {long}. Default \code{wide}. See Details.}
       |                                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  set.data.Rd: mlogit.data
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) mle_parameters.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:42: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mle_parameters.Rd: multiroot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  autoplot.ts.Rd: geom_forecast, fortify
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Lcm.Rd:75: Lost braces
    75 |     \item{\code{GetTrace()}:}{retrieve all traced iterations. Returns a list with all the parameters set using the method SetTrace(). See description of snapshot{reference} method for a description of the parameters.  }
       |                                                                                                                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Lcm.Rd: C++Object-class
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: ‘coda’
Specified C++11: please drop specification unless essential
checkRd: (-1) plot.regression.circular.Rd:35: Lost braces
    35 |               code{plot.type="circle"} and \code{x} is the output of \code{\link{kern.reg.circ.lin}}) or to \code{\link{lines3d}} (if \code{plot.type="circle"})
       |                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ancova.circ.lin.Rd: circular
  bw.AA.Rd: circular, density.circular
  bw.CV.Rd: circular
  bw.boot.Rd: circular
  bw.circ.local.lik.Rd: circular
  bw.pi.Rd: circular
  bw.reg.circ.lin.Rd: circular
  bw.rt.Rd: circular
  circ.local.lik.Rd: circular
  circsizer.density.Rd: circular
  circsizer.regression.Rd: circular
  dcircmix.Rd: circular
  dpreg.circ.Rd: circular
  dwsn.Rd: circular
  kern.den.circ.Rd: circular, density.circular, plot.density.circular,
    lines.density.circular
  kern.dpreg.circ.Rd: circular
  kern.reg.circ.lin.Rd: circular
  lines.regression.circular.Rd: radial.plot, lines3d
  modalreg.circ.lin.Rd: circular
  noeffect.circ.lin.Rd: circular
  plot.regression.circular.Rd: radial.plot, lines3d
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) DiscHazRateAuxFunctions.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiscHazRateAuxFunctions.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiscHazRateAuxFunctions.Rd:48: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NPHMC-package.Rd: smcure
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nest_fill.Rd: tidyr_tidy_select
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
'::' or ':::' import not declared from: ‘crs’
'library' or 'require' call not declared from: ‘crs’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  aligned.test.Rd: rfit
  knn_cv.Rd: knn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) np.reg.test.Rd:148: Lost braces
   148 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
checkRd: (-1) nptest-package.Rd:73: Lost braces
    73 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
checkRd: (-1) NSAE.Rd:14: Lost braces; missing escapes or markup?
    14 | {Maintainer}: Saurav Guha \email{saurav.iasri@gmail.com}
       | ^
checkRd: (-1) NScluster-package.Rd:30-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NScluster-package.Rd:35-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NScluster-package.Rd:44-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NScluster-package.Rd:49-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mple.cppm.Rd:44-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mple.cppm.Rd:69-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mple.cppm.Rd:113-155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:36-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:90-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:123-148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:151-192: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:195-211: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nse.andrews.Rd: sandwich
  nse.boot.Rd: np
  nse.geyer.Rd: mcmc, mcmcse
  nse.hiruk.Rd: sandwich
  nse.nw.Rd: sandwich
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cnm.Rd: nnls
  cnmms.Rd: nnls
  cvps.Rd: nnls
  mlogit.Rd: nnls
  npnorm.Rd: nnls
  nppois.Rd: nnls
  plot.nspmix.Rd: nnls
  plotgrad.Rd: nnls
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_ntd.R’
checkRd: (-1) MSM.fit.Rd:21: Lost braces
    21 | \code{MSM.fit} returns an object of class code{MSM.lm} or \code{MSM.glm}, depending on the input model.
       |                                               ^
checkRd: (-1) SMC.Smooth.Rd:25: Lost braces; missing escapes or markup?
    25 | observation at current time step. It should return {xx} (the samples xt) and
       |                                                    ^
checkRd: (-1) SMC.Smooth.Rd:26: Lost braces; missing escapes or markup?
    26 | {logww} (their corresponding log weight).}
       | ^
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:
    ‘partition.Rd’
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.select.Rd: select
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) xyz2R.Rd:31: Lost braces
    31 |    \item Finally, code{T} is rotated an angle \code{z} about its NEWEST z-axis.
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  qqplot_maha.Rd: ad.test
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:
  ‘QRM’ ‘microbenchmark’ ‘mvtnorm’ ‘qrmtools’ ‘quadprog’ ‘rugarch’
  ‘sensitivity’ ‘zoo’
checkRd: (-1) OBMb.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ChangepointDetector.Rd:93: Lost braces; missing escapes or markup?
    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                               ^
checkRd: (-1) ChangepointDetector.Rd:93: Lost braces; missing escapes or markup?
    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                                         ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |        ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggplotmaply.Rd: ggplotly
  oceanmap.Rd: raster
  readbin.Rd: fields
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Chesapeake.Rd: Oxsat
  Sylt.Rd: image2D, ImageOcean, scatter2D, Oxsat
  TempTraject.Rd: image2D, ImageOcean, scatter2D, Oxsat
  WSnioz.Rd: image2D, ImageOcean, scatter2D, Oxsat
  moviepersp.Rd: persp3Drgl, jet.col
  movieslice.Rd: slice3Drgl, jet.col, slice3D
  quiver.Rd: jet.col, colkey, contour2D, image2D, arrows2D, arrows3D,
    Arrows
  tracers2D.Rd: colkey, contour2D, image2D, scatter2D
  tracers3D.Rd: points3Drgl, colkey, scatter3D
  vectorplot.Rd: jet.col, colkey, Arrows
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bootockc.Rd: bootFlexclust, stepFlexclust
  ockc.Rd: bootFlexclust, kcca
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  OCN_to_AEM.Rd: moran.randtest, aem
  aggregate_OCN.Rd: spam
  create_OCN.Rd: spam
  draw_elev2D_OCN.Rd: image.plot, imagePlot
  draw_elev3D_OCN.Rd: imagePlot
  draw_elev3Drgl_OCN.Rd: persp3d, rgl, rgl.snapshot, rgl.postscript,
    polygon3d
  draw_subcatchments_OCN.Rd: imagePlot
  draw_thematic_OCN.Rd: image.plot, imagePlot, sbar, north
  landscape_OCN.Rd: spam
  paths_OCN.Rd: spam
  plot.Rd: sbar, north
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) onlineCPD.Rd:35: Lost braces
    35 |  function(x, lambda){const_hazard(x, lambda=100)}
       |                     ^
checkRd: (-1) ocsApiUserProvisioningManager.Rd:87: Lost braces
    87 |  \item{code{addToGroup(userid, groupid)}}{
       |            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ocs4RLogger.Rd: R6Class
  ocsApiSharingManager.Rd: R6Class
  ocsApiUserProvisioningManager.Rd: R6Class
  ocsApiWebdavManager.Rd: R6Class
  ocsManager.Rd: R6Class
  ocsRequest.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:
    ‘duckdb_connection.R’ ‘get_database_functions.R’ ‘mysql_connection.R’
    ‘postgres_connection.R’ ‘snowflake_connection.R’
    ‘sqlite_connection.R’ ‘submit_query.R’ ‘vertica_connection.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:
    ‘octopus_api.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ODB-class.Rd: JDBCConnection-class, DBIConnection-class,
    DBIObject-class
  isClosed.Rd: dbConnect, dbDisconnect
  odb.tables.Rd: dbColumnInfo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getResult.Rd: deSolve
  setEvents.Rd: events
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) plot.ODEmorris.Rd:62-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ODEmorris.Rd:64-65: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ODEsensitivity.Rd: sensitivity
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ODT.Rd: as.party
  PPO.Rd: nnet, Pursuit
  as.party.ODT.Rd: party
  plot.ODT.Rd: as.party
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NanoIndent.OEFPIL.Rd: nlsLM
  OEFPIL.Rd: nlsLM
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:
    ‘oes_plot.Rd’ ‘oes_prep.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:
    ‘assign_rates.R’ ‘diagnose.R’ ‘utility_spatial.R’
    ‘write_trial_files.R’
checkRd: (-1) formula.oglmx.Rd:49: Lost braces
    49 |   \code{\link{oglmx}}, code{\link[lmtest]{lrtest}}, code{\link{formula}}.
       |                            ^
checkRd: (-1) formula.oglmx.Rd:49: Lost braces
    49 |   \code{\link{oglmx}}, code{\link[lmtest]{lrtest}}, code{\link{formula}}.
       |                                                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  oglmx.Rd: maxNR, maxLik, polr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘set_parameters.Rd’
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:
    ‘01-opIndicators.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:
    ‘OLStraj.R’ ‘cbc_lm.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_server.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mlmer.Rd: lmer
  ranef.ranks.Rd: lmer
  var.components.Rd: lmer
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:
    ‘span_table.R’
checkRd: (-1) dot-discoveryRequest.Rd:15-16: Lost braces
    15 | \item{service}{One of {"locations", "deployments", "deviceCategories", "devices",
       |                       ^
checkRd: (-1) dot-discoveryRequest.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{method}{One of {"get", "getTree"}}
       |                      ^
checkRd: (-1) dot-saveAsFile.Rd:19: Lost braces; missing escapes or markup?
    19 | (numeric) Result code from {0: done, -1: error, -2: fileExists}
       |                            ^
checkRd: (-1) oncotree.fit.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:67: 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:
    ‘global.R’
checkRd: (-1) one_sample.Rd:40: Lost braces; missing escapes or markup?
    40 | In two sided or one sided interval estimation of \code{sigma^2} of one normal sample, {side} is a parameter used to control whether to compute two sided or one sided interval estimation. When computing the one sided upper limit, input \code{side = -1}; when computing the one sided lower limit, input \code{side = 1}; when computing the two sided limits, input \code{side = 0} (default).
       |                                                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  onls.Rd: nls.lm.control, nls.lm
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:
    ‘tab_onsv.R’ ‘tab_onsv.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘1onto.R’ ‘edit_matches.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  drawOpenKey.Rd: draw.colorkey
  smoothTrend.Rd: gam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
License stub is invalid DCF.
File ‘OpenCL/libs/R_OpenCL.so’:
  Found non-API call to R: ‘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.
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’ [3s/5s]
  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 Rd file(s) with Rd \link{} targets missing package
anchors:
  AnyOf.Rd: R6Class
  Argument.Rd: R6Class
  Array.Rd: R6Class
  BasicAuth.Rd: R6Class
  Boolean.Rd: R6Class
  BoundingBox.Rd: R6Class
  CollectionId.Rd: R6Class
  Date.Rd: R6Class
  DateTime.Rd: R6Class
  EPSGCode.Rd: R6Class
  GeoJson.Rd: R6Class
  Graph.Rd: R6Class
  Integer.Rd: R6Class
  JobId.Rd: R6Class
  Kernel.Rd: R6Class
  MetadataFilter.Rd: R6Class
  Number.Rd: R6Class
  OutputFormat.Rd: R6Class
  OutputFormatOptions.Rd: R6Class
  Parameter.Rd: R6Class
  Process.Rd: R6Class
  ProcessGraphArgument.Rd: R6Class
  ProcessGraphId.Rd: R6Class
  ProcessGraphParameter.Rd: R6Class
  ProjDefinition.Rd: R6Class
  RasterCube.Rd: R6Class
  String.Rd: R6Class
  TemporalInterval.Rd: R6Class
  TemporalIntervals.Rd: R6Class
  Time.Rd: R6Class
  UdfCodeArgument.Rd: R6Class
  UdfRuntimeArgument.Rd: R6Class
  UdfRuntimeVersionArgument.Rd: R6Class
  VectorCube.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:
    ‘format_search_term.R’ ‘openFDA.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:
    ‘create.R’ ‘og_validate.Rd’ ‘parse.R’ ‘property.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:
    ‘acs12.Rd’ ‘arbuthnot.Rd’ ‘ask.Rd’ ‘biontech_adolescents.Rd’
    ‘birds.Rd’ ‘blizzard_salary.Rd’ ‘census.Rd’ ‘cia_factbook.Rd’
    ‘climber_drugs.Rd’ ‘comics.Rd’ ‘daycare_fines.Rd’ ‘dotPlot.Rd’
    ‘drone_blades.Rd’ ‘epa2021.Rd’ ‘exam_grades.Rd’ ‘fact_opinion.Rd’
    ‘family_college.Rd’ ‘fish_age.Rd’ ‘friday.Rd’ ‘gdp_countries.Rd’
    ‘gss_wordsum_class.Rd’ ‘house.Rd’ ‘iowa.Rd’ ‘ipo.Rd’ ‘iran.Rd’
    ‘labor_market_discriminiation.Rd’ ‘lecture_learning.Rd’
    ‘lego_population.Rd’ ‘lego_sample.Rd’ ‘lizard_run.Rd’
    ‘london_boroughs.Rd’ ‘london_murders.Rd’ ‘malaria.Rd’ ‘mariokart.Rd’
    ‘mlb_teams.Rd’ ‘mlbbat10.Rd’ ‘mn_police_use_of_force.Rd’
    ‘nba_finals.Rd’ ‘nba_finals_teams.Rd’ ‘nycflights.Rd’ ‘orings.Rd’
    ‘oscars.Rd’ ‘paralympic_1500.Rd’ ‘piracy.Rd’ ‘race_justice.Rd’
    ‘simpsons_paradox_covid.Rd’ ‘soda.Rd’ ‘sowc_child_mortality.Rd’
    ‘sowc_demographics.Rd’ ‘sowc_maternal_newborn.Rd’ ‘ssd_speed.Rd’
    ‘twins.Rd’ ‘ucla_textbooks_f18.Rd’ ‘us_temperature.Rd’ ‘usb_admit.Rd’
    ‘world_pop.Rd’
Missing dependency on R >= 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’ ‘weather_now.R’
File ‘OpenMx/libs/OpenMx.so’:
  Found non-API calls to R: ‘IS_S4_OBJECT’, ‘Rf_isFrame’

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:
    ‘OpenRange_api_load_species.Rd’ ‘OpenRange_api_species.Rd’
    ‘OpenRange_load_species.Rd’ ‘OpenRange_sf.R’ ‘OpenRange_species.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘oscai.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ADSBDecoder.Rd: R6Class
  clusterRoutes.Rd: dbscan, cluster
  openSkiesAircraft.Rd: R6Class
  openSkiesAirport.Rd: R6Class
  openSkiesFlight.Rd: R6Class
  openSkiesRoute.Rd: R6Class
  openSkiesStateVector.Rd: R6Class
  openSkiesStateVectorSet.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) loss.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mixture.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mixture.Rd:34: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mixture-opera.Rd: auglag
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) word_imp.Rd:14: Lost braces
    14 | number of individual records. An \code{n} x code{2} dataframe can
       |                                                 ^
checkRd: (-1) MonteCarlo.Rd:23: Lost braces
    23 | N is computed from \code{p} length. M is code{10^4} by default.
       |                                              ^
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.ProjectProblem.Rd: ggplot
  plot_feature_persistence.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:
  graphoptbd.mae.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
Malformed Title field: should not end in a period.
checkRd: (-1) drawdesign.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gnu_style.Rd:24: Lost braces
    24 | [GNU Command Line Standards]{http://www.gnu.org/prep/standards/standards.html}
       |                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  graphoptrcd.mae.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ordDisp.Rd: vglm, VGAM
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) internal.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:62-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:15: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ordAOV.Rd: LRTSim, RLRTSim, RLRsim, exactLRT, exactRLRT
  ordGene.Rd: LRTSim, RLRTSim
  ordSmooth.Rd: gam, mgcv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) lra-ord.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lra-ord.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lra-ord.Rd:57-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lra-ord.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lra-ord.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ordinate.Rd: tidyr_tidy_select
  supplementation.Rd: fortify
  tbl_ord.Rd: fortify
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  join_multireader_data.Rd: bind_rows
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) orf.Rd:74: Lost braces
    74 | matrix of covariates \code{X} and a vector of outcomes 'code{Y} to the \code{orf}
       |                                                             ^
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  predictionMap.Rd: generateCVRuns, tuneParetoClassifier
  tunePareto.occ.Rd: tunePareto.knn, tuneParetoClassifier,
    trainTuneParetoClassifier
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) hillEquation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:84-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:88-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:91-93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) polynomial.derivatives.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.derivatives.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.derivatives.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:21: 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:
    ‘fitS4.R’ ‘helpers.R’
checkRd: (-1) oscar.Rd:44: Lost braces; missing escapes or markup?
    44 | \item{print}{Level of verbosity in Fortran (may not be visible on all terminals); should be an integer between {range, range}, Default: 3}
       |                                                                                                                ^
checkRd: (-1) oscar.control.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{start}{Starting point generation method, see vignettes for details; should be an integer between {range,range}, Default: 2}
       |                                                                                                        ^
checkRd: (-1) RLum.OSL_decomposition.Rd:90-91: Lost braces
    90 | \item \link{optimise_OSLintervals}: {Approximates the optimal integration intervals. Uses the global
       |                                     ^
checkRd: (-1) RLum.OSL_decomposition.Rd:92-94: Lost braces
    92 | \item \link{decompose_OSLcurve}: {Calculates component intensities for \strong{all} \code{record_type} measurements.
       |                                  ^
checkRd: (-1) fit_OSLcurve.Rd:97: Lost braces; missing escapes or markup?
    97 | fitting with the \emph{RSS_{K-1}} value of the previous fitting and calculates
       |                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RLum.OSL_correction.Rd: RLum.Analysis-class, Luminescence-package
  RLum.OSL_decomposition.Rd: RLum.Analysis-class, Luminescence-package,
    rmarkdown, rmarkdown-package, RLum.Data.Curve-class
  RLum.OSL_global_fitting.Rd: RLum.Analysis-class,
    Luminescence-package, rmarkdown, rmarkdown-package
  decompose_OSLcurve.Rd: RLum.Data.Curve-class
  fit_OSLcurve.Rd: RLum.Data.Curve-class
  optimise_OSLintervals.Rd: RLum.Data.Curve-class
  plot_OSLcurve.Rd: RLum.Data.Curve-class, ggplot2, ggplot2-package
  plot_PhotoCrosssections.Rd: ggplot2-package
  sum_OSLcurves.Rd: RLum.Analysis-class, 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:
  equidistPoints.Rd: approx2
  pointsMap.Rd: openmap
  randomPoints.Rd: distance
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) otp_create_surface.Rd:33: Lost braces; missing escapes or markup?
    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                ^
checkRd: (-1) otp_create_surface.Rd:33: Lost braces; missing escapes or markup?
    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                                ^
checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
Specified C++11: please drop specification unless essential
checkRd: (-1) fmat.Rd:15: Lost braces; missing escapes or markup?
    15 | \item outcome: codes {I, P, R, NC, O, UH, UO, eUH, eUO, NE}
       |                      ^
checkRd: (-1) fmat.Rd:24: Lost braces; missing escapes or markup?
    24 | The input parameters given by the user are {I, P, R, NC, O, UH, UO} and
       |                                            ^
checkRd: (-1) fmat.Rd:25: Lost braces; missing escapes or markup?
    25 | the parameter 'e'. The parameter e is multiplied by {UH, UO} internally so as to
       |                                                     ^
checkRd: (-1) fmat.Rd:26: Lost braces; missing escapes or markup?
    26 | produce {eUH, eUO}.
       |         ^
checkRd: (-1) middleearth.Rd:14: Lost braces; missing escapes or markup?
    14 | \item \strong{code:} one of the outcome codes {I, P, R, NC, O, UH, UO, UH, UO, NE}
       |                                               ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘method.r’ ‘outqrf.r’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  InitMcmc.Rd: big.matrix, bigmemory
  LoadMcmc.Rd: big.matrix, attach.big.matrix
  Peek.Rd: big.matrix
  Resume.Rd: big.matrix
  ToMemory.Rd: big.matrix
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:
    ‘owid.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  heart2.Rd: heart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) lint_package.Rd:20: Lost braces
    20 | code{\link[lintr:lint_package]{lintr::lint_package}} where we hardcode the
       |     ^
checkRd: (-1) provide_news_rd.Rd:22: Lost braces
    22 | Christian Vonderach uses the index thus wants file{inst/NEWS.rd} to
       |                                                   ^
checkRd: (-1) provide_news_rd.Rd:23: Lost braces
    23 | automatically be in sync with file{./NEWS.md}.
       |                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  check_usage.Rd: checkUsagePackage
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.PAFit_net.Rd: plot.network.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:
  Gb_lab.Rd: ggplot2
  plot_coverage.Rd: ggplot2
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:
  ‘gclus’ ‘irr’ ‘seriation’
checkRd: (-1) MICS2014Ch.Rd:296: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Ch.Rd:297: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HH.Rd:214: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HH.Rd:215: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HL.Rd:109: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HL.Rd:110: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Wm.Rd:336: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Wm.Rd:337: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018bh.Rd:88: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018bh.Rd:89: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018fs.Rd:308: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018fs.Rd:309: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018hh.Rd:362: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018hh.Rd:363: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mm.Rd:69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mm.Rd:70: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mn.Rd:243: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mn.Rd:244: Lost braces in \enumerate; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Hill.N2.core.Rd: Hill.N2
  palaeoSig-package.Rd: rda
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pbdb_map.Rd: map
  pbdb_map_occur.Rd: map
  pbdb_map_richness.Rd: map
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.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  confint.palm.Rd: boot
  fit.ns.Rd: bobyqa
  fit.void.Rd: bobyqa
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pampe-internal.Rd: leaps
  pampe.Rd: leaps
  robustness.Rd: leaps
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  doUniqueCJ.Rd: CJ
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_panels.R’ ‘clean_raw.Rd’ ‘create_means.R’ ‘helper_functions.R’
    ‘panelsummary.R’ ‘panelsummary_raw.R’
checkRd: (-1) panelsummary.Rd:112: Lost braces; missing escapes or markup?
   112 | \item `"{exp(estimate) * std.error}"
       |         ^
checkRd: (-1) panelsummary_raw.Rd:90: Lost braces; missing escapes or markup?
    90 | \item `"{exp(estimate) * std.error}"
       |         ^
checkRd: (-1) hvidovre.Rd:11: Lost braces
    11 |     \item{\code{roof_tile}}{a numeric vector, roof_tile}{dummy, roof made out of tiles =1}
       |                                                         ^
checkRd: (-1) hvidovre.Rd:25: Lost braces
    25 |     \item{\code{railways}}{a numeric vector, railways}{distance to nearest railway in meters}
       |                                                       ^
checkRd: (-1) hvidovre.Rd:26: Lost braces
    26 |     \item{\code{nature_SLD}}{a numeric vector, nature_SLD}{distance to nearest nature area in meters}
       |                                                           ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘mod_control_form.R’ ‘mod_leaflet_map.R’
checkRd: (-1) agreement.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:39: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  agreement.Rd: binom.confint
  papciUI.Rd: binom.confint
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘parameter_summary.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.linkdat.Rd: plot.pedigree
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) returns.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{...}{Other options including {type} which refers to the
       |                                      ^
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) PPS.fit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forbes400.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forbes400.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:11: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  parfm.Rd: Surv, optimx
  select.parfm.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
File ‘paropt/libs/paropt.so’:
  Found ‘__vsprintf_chk’, possibly from ‘vsprintf’ (C)
    Object: ‘../inst/libsundials.a’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘../inst/libsundials.a’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘../inst/libsundials.a’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘../inst/libsundials.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) summary.parsec.Rd:13-14: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  parsec2igraph.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:
    ‘evolve.Rd’ ‘genesis.Rd’ ‘simulate.Rd’ ‘wield.Rd’
Found the following files/directories:
  ‘co2’ ‘co2.1’ ‘co2.2’ ‘co2s.1’ ‘co2s.2’ ‘ctm.1’ ‘ctm.2’ ‘m’ ‘m.1’
  ‘m.2’ ‘test’ ‘test.1’ ‘test.2’ ‘testa.1’ ‘testa.2’ ‘xfile.1’
  ‘xfile.2’
Running ‘partsm_examples.R’ [1s/1s]
  Comparing ‘partsm_examples.Rout’ to ‘partsm_examples.Rout.save’ ...899,904c899,904
<  Min.   :-0.676   Min.   :0.0095   Min.   :-4.44   Min.   :0.00000  
<  1st Qu.:-0.198   1st Qu.:0.0309   1st Qu.:-1.13   1st Qu.:0.00000  
<  Median : 0.338   Median :0.1204   Median : 2.26   Median :0.00109  
<  Mean   : 0.242   Mean   :0.0996   Mean   :25.41   Mean   :0.10129  
<  3rd Qu.: 0.689   3rd Qu.:0.1534   3rd Qu.:46.76   3rd Qu.:0.02555  
<  Max.   : 1.025   Max.   :0.1950   Max.   :95.99   Max.   :0.95332  
---
>  Min.   :-0.676   Min.   :0.0095   Min.   :-4.4   Min.   :0.000  
>  1st Qu.:-0.198   1st Qu.:0.0309   1st Qu.:-1.1   1st Qu.:0.000  
>  Median : 0.338   Median :0.1204   Median : 2.3   Median :0.001  
>  Mean   : 0.242   Mean   :0.0996   Mean   :25.4   Mean   :0.101  
>  3rd Qu.: 0.689   3rd Qu.:0.1534   3rd Qu.:46.8   3rd Qu.:0.026  
>  Max.   : 1.025   Max.   :0.1950   Max.   :96.0   Max.   :0.953
Missing dependency on R >= 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_parttree.Rd’ ‘parttree.Rd’ ‘plot.parttree.Rd’
Specified C++11: please drop specification unless essential
checkRd: (-1) PAS-package.Rd:30: Lost braces
    30 |     {\code{bin model}}{\cr Zhiqiu Hu, Zhiquan Wang, and Shizhong Xu (2012) An infinitesimal model for quantitative trait genomic value prediction. PloS ONE 7: e41336.}
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) plotHeat.Rd:113: Lost braces
   113 | code{\link[patternize]{patPCA}}, as 'one' when visualizing single image or as 'multi' for multi
       |     ^
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gt1mAccFile.Rd: as.matrix.csr
  gt3xAccFile.Rd: as.matrix.csr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) pbd_loglik.Rd:31: Lost braces
    31 |     \code{pars2[1]} {set the conditioning on non-extinction of the clade (1) or not (0) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:32: Lost braces
    32 |     \code{pars2[2]} {sets whether the likelihood is for the branching times (0) or the phylogeny (1) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:33: Lost braces
    33 |     \code{pars2[3]} {sets whether the first element of the branching times is the stem (1) or the crown (2) age \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:34: Lost braces
    34 |     \code{pars2[4]} {sets whether the parameters and likelihood should be shown on screen (1) or not (0) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:35: Lost braces
    35 |     \code{pars2[5]} {sets which method should be used in the ode-solver. Default is 'lsoda'. See package deSolve for details. \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:36: Lost braces
    36 |     \code{pars2[6]}{Sets the lower bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}
       |                    ^
checkRd: (-1) pbd_loglik.Rd:37: Lost braces
    37 |     \code{pars2[7]}{Sets the upper bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}  
       |                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  perProb.Rd: pMvdc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘PBSddesolve/libs/PBSddesolve.so’:
  Found non-API call to R: ‘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.
File ‘PBSmodelling/libs/PBSmodelling.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.
Malformed Description field: should contain one or more complete sentences.
possible bashism in configure.ac line 40 (test -a/-o):
  if test [ -n "$PKG_CPPFLAGS" -a -n "$PKG_LIBS" ] ; then
  possible bashism in configure.ac line 43 (test -a/-o):
      if test [ -n "$PKG_CPPFLAGS" -o -n "$PKG_LIBS" ] ; then
  possible bashism in configure.ac line 80 (test -a/-o):
              if test [ -z "$CLP_LIBS" -a -z "$CLP_CFLAGS" ] ; then
  possible bashism in configure.ac line 106 (test -a/-o):
      if test [ -n "$CLP_INCLUDE" -a -n "$CLP_LIB" ] ; then
  possible bashism in configure.ac line 139 (test -a/-o):
              if test [ -d "/usr/include" -o -d "/usr/local/include" ] ; then
  possible bashism in configure.ac line 145 (test -a/-o):
              if test [ -d "/usr/local/lib" -o -d "/usr/local/lib64" -o -d "/usr/lib" -o -d "/usr/lib64"] ; then
  possible bashism in configure.ac line 189 (test -a/-o):
              if test [ -d "$prefix/lib" -o -d "$prefix/lib64" ] ; then
checkRd: (-1) twoby2Calibrate.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:85-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:87-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:97-100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:101-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:104-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:108-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:111-116: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pcdpca.Rd: spectral.density
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:
  ‘MASS’ ‘freqdom.fda’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pchreg.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) PCM_ABC.Rd:106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:108-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:114: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:205-207: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:208-211: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:212-216: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:221-224: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:225-228: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:229-231: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:232: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:233: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:234: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:235: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:236: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:237: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:238: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:239: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:240: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:67: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) MiniBenchmarkRvsCpp.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MiniBenchmarkRvsCpp.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MiniBenchmarkRvsCpp.Rd:18: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BenchmarkRvsCpp.Rd: PCMApplyTransformation
  MiniBenchmarkRvsCpp.Rd: PCMApplyTransformation
  PCMInfoCpp.Rd: PCMPresentCoordinates
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PCMOptions.Rd: vcv
  PCMTreeVCV.Rd: vcv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  person.posterior.Rd: adaptIntegrate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  define.clade.Rd: makeNodeLabel
  matrix.p.null.Rd: vegdist, matrix.p
  organize.pcps.Rd: organize.syncsa
  pcoa.sig.Rd: vegdist, pcoa, procrustes
  pcps.Rd: vegdist, matrix.p, ordispider, wcmdscale, ordilabel
  pcps.curve.Rd: vegdist, matrix.p
  pcps.sig.Rd: vegdist, matrix.p, mantel, adonis, adonis2, gls, lme,
    rda, procrustes, anova.gls, anova.lme
  self.belonging.Rd: belonging
  wcmdscale.org.Rd: wcmdscale, vegdist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) getPCRAData.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getPCRAData.Rd:29: Lost braces in \itemize; meant \describe ?
'::' or ':::' imports not declared from:
  ‘MASS’ ‘tensr’
'library' or 'require' calls not declared from:
  ‘MASS’ ‘facmodCS’ ‘fit.models’ ‘sandwich’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) pcvpcr.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
checkRd: (-1) pcvpls.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fitModel.Rd: nsga2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) pdkMeans.Rd:63: Lost braces
    63 | \cite{C18}{pdSpecEst} for more details. Note that this comes at the cost of increased computation time in comparison to one
       |           ^
checkRd: (-1) embedded.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) embedded.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
checkRd: (-1) ensemble.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) ensemble.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
checkRd: (-1) staged.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) staged.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calPlot.Rd: SmartControl, dpik
  coxboost.Rd: Hist
  plot.pec.Rd: prodlim
  plotPredictEventProb.Rd: SmartControl, prodlim
  plotPredictSurvProb.Rd: SmartControl, prodlim
  predictRestrictedMeanTime.Rd: survfit
  predictSurvProb.Rd: survfit
  selectCox.Rd: fastbw
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) variogramGuess.Rd:94: Lost braces
    94 | Method \code{"b"} was proposed by \doi{10.1016/0098-3004(95)00095-X}{Jian et al. (1996)} and
       |                                                                     ^
checkRd: (-1) variogramGuess.Rd:98: Lost braces
    98 | \doi{10.1016/j.cageo.2008.10.011}{Hiemstra et al. (2009)}.
       |                                  ^
checkRd: (-1) variogramGuess.Rd:100: Lost braces
   100 | Method \code{"d"} was developed by \doi{10.1007/s11004-012-9434-1}{Desassis & Renard (2012)}.
       |                                                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pq_plot.Rd: e_theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) breslow.Rd:27: Escaped LaTeX specials: \# \#
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
'library' or 'require' call not declared from: ‘mgcv’
checkRd: (-1) my.bspline.Rd:21: Escaped LaTeX specials: \$ \$ \$ \$ \$ \$
checkRd: (-1) my.bspline.Rd:27: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) pendensity.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:57: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:82: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:96: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:100: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:105: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘cv_pensynth.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tw_complex.Rd: glmer, lmer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) classificationMetrics.Rd:85: Lost braces; missing escapes or markup?
    85 |   will use some extra notation, namely: TP = #{p == + & t == +} ; FP =
       |                                               ^
checkRd: (-1) classificationMetrics.Rd:86: Lost braces; missing escapes or markup?
    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |    ^
checkRd: (-1) classificationMetrics.Rd:86: Lost braces; missing escapes or markup?
    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |                              ^
checkRd: (-1) classificationMetrics.Rd:86: Lost braces; missing escapes or markup?
    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |                                                       ^
checkRd: (-1) classificationMetrics.Rd:87: Lost braces; missing escapes or markup?
    87 |   ; P = #{t == +} ; N = #{t == -}; Finally, for some descriptions
       |          ^
checkRd: (-1) classificationMetrics.Rd:87: Lost braces; missing escapes or markup?
    87 |   ; P = #{t == +} ; N = #{t == -}; Finally, for some descriptions
       |                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bootEstimates.Rd: cluster
  cvEstimates.Rd: cluster
  hldEstimates.Rd: cluster
  loocvEstimates.Rd: cluster
  mcEstimates.Rd: cluster
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  exactLR.Rd: coxph
  nextStage.Rd: coxph
  permHeinze.Rd: coxph
  permIPT.Rd: coxph
  permIPZ.Rd: coxph
  permLR.Rd: coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
checkRd: (-1) read_PN.Rd:15: Lost braces
    15 | A code{\link{marked_petrinet}}
       |       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cc.manip.Rd: vegan
  comparative.comm.Rd: vegan
  drop_tip.Rd: drop.tip
  eco.xxx.regression.Rd: picante, rq
  fingerprint.regression.Rd: picante
  generic.metrics.Rd: picante
  laja.Rd: phylo
  pez.dispersion.Rd: picante
  pez.metrics.Rd: picante, caper, FD, ape
  phy.signal.Rd: pgls
  scape.Rd: phylo, corGrafen, corBlomberg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRD.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRDUS.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) DTV.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘animation.gif’
checkRd: (-1) PhageCocktail.Rd:100-103: Lost braces
   100 | "Result": {
       |           ^
checkRd: (-1) PhageCocktail.Rd:105-112: Lost braces
   105 | "BacteriaLysed": {
       |                  ^
checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^
checkRd: (-1) phasePlaneAnalysis.Rd:84: Lost braces; missing escapes or markup?
    84 | identified {see (3) above}, if this point is a saddle then the manifolds are
       |            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  numericalSolution.Rd: 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:
  pheatmap.Rd: gtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘test.pdf’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cor.par.Rd: pcor, pcor.test
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:29: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:31: Escaped LaTeX specials: \_ \_
checkRd: (-1) maxConnectedSet.Rd:35: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:37: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:39: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:41: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:45: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:47: Escaped LaTeX specials: \_ \_
Specified C++11: please drop specification unless essential
Missing dependency on R >= 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_station_step.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  interactionMeans.Rd: Anova, linearHypothesis
  testFactors.Rd: linearHypothesis, Anova
  testInteractions.Rd: Anova, linearHypothesis
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:
    ‘df_to_tier.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Blue.Rd: new_waveband, waveband
  DNA_GM.Rd: new_waveband, waveband
  DNA_N.Rd: new_waveband, waveband
  DNA_P.Rd: new_waveband, waveband
  GEN_M.Rd: new_waveband, waveband
  IR.Rd: new_waveband, waveband
  Purple.Rd: new_waveband, waveband
  UV.Rd: new_waveband, waveband
  UVC.Rd: new_waveband, waveband
  UV_health_hazard.Rd: new_waveband, waveband
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:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-par.R’ ‘fit_aq_response.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
checkRd: (-1) 11_d.init.method.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:21-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:24-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:27-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:31-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:29: 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:
    ‘phylepic.R’ ‘plot.phylepic.R’ ‘plot_tree.R’
checkRd: (-1) GarlandJanis.IC.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.IC.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:7: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.DAG.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) fitgom.Rd:87: Lost braces
    87 |   \item \code{theta} The ncol{counts} by K matrix of estimated
       |                              ^
checkRd: (-1) fitgom.Rd:89: Lost braces
    89 |   \item \code{omega} The nrow{counts} by K matrix of estimated
       |                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  beta_diss.Rd: betapart.core, beta.pair, beta.multi, betapart
  phylobeta.Rd: phylo.betapart.core, phylo.beta.pair, phylo.beta.multi
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sub.taxa.label.Rd: read.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:
  makeEpiRecord.Rd: simNHP.fun
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) phylter.Rd:51: Lost braces; missing escapes or markup?
    51 | the output ({out$DiscardedGenes}).}
       |             ^
checkRd: (-1) pa-internal.Rd:11: Lost braces
    11 | code{l2df}: convert list to data.frame
       |     ^
checkRd: (-1) pa-internal.Rd:14: Lost braces
    14 | code{convertTZ}: force a new timezone on datetime
       |     ^
checkRd: (-1) pa-internal.Rd:16: Lost braces
    16 | code{createTime}: create datetime variable
       |     ^
checkRd: (-1) pa-internal.Rd:18: Lost braces
    18 | code{addDayIndex}: create ID_day variable from timestamp
       |     ^
checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) sample2matrix.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sample2matrix.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sample2matrix.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: 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:
    ‘exr-read.R’ ‘exr-types-read.R’ ‘exr-write.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:
    ‘piecenorm.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  anova.psem.Rd: Anova
  coefs.Rd: Anova
  summary.psem.Rd: Anova
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PerturbationClustering.Rd: pam
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:
    ‘aliases.Rd’ ‘bind.Rd’
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:
    ‘pipeline.R’
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘extract_col.Rd’ ‘na2empty.Rd’ ‘omit_na_cols.Rd’ ‘omit_na_rows.Rd’
    ‘pivot.R’ ‘pivot.Rd’ ‘utils.R’ ‘validate_col.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PivotBatch.Rd: R6Class
  PivotBatchCalculator.Rd: R6Class
  PivotBatchStatistics.Rd: R6Class
  PivotCalculation.Rd: R6Class
  PivotCalculationGroup.Rd: R6Class
  PivotCalculationGroups.Rd: R6Class
  PivotCalculator.Rd: R6Class
  PivotCell.Rd: R6Class
  PivotCells.Rd: R6Class
  PivotData.Rd: R6Class
  PivotDataGroup.Rd: R6Class
  PivotFilter.Rd: R6Class
  PivotFilterOverrides.Rd: R6Class
  PivotFilters.Rd: R6Class
  PivotHtmlRenderer.Rd: R6Class
  PivotLatexRenderer.Rd: R6Class
  PivotOpenXlsxRenderer.Rd: R6Class
  PivotOpenXlsxStyle.Rd: R6Class
  PivotOpenXlsxStyles.Rd: R6Class
  PivotStyle.Rd: R6Class
  PivotStyles.Rd: R6Class
  PivotTable.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) get_pixels.Rd:27-29: Lost braces
    27 | if (interactive()) {
       |                    ^
checkRd: (-1) sprinkle_colnames.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sprinkle_colnames.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:63-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:69-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:74-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:78-83: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 4.3.0 because package code uses the pipe
  placeholder at the head of a chain of extractions syntax added in R
  4.3.0.
  File(s) using such syntax:
    ‘plate.R’
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:
    ‘buildPackageGraph.Rd’ ‘collectFunNames.Rd’ ‘functions.r’
    ‘plotPackageGraph.Rd’ ‘utils.r’
possible bashism in configure.ac line 39 (test -a/-o):
     if test x"${PKG_CPPFLAGS}" = x -a x"${PKG_LIBS}" = x -a x"$PKGCONFIG" != x; 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:
    ‘class-summary_PKNCAresults.R’
checkRd: (-1) adjacency.Rd:27: Lost braces; missing escapes or markup?
    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                       ^
checkRd: (-1) adjacency.Rd:27: Lost braces; missing escapes or markup?
    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                                 ^
checkRd: (-1) adjacency.Rd:27: Lost braces; missing escapes or markup?
    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                                              ^
checkRd: (-1) rankings.Rd:127: Lost braces; missing escapes or markup?
   127 | rank skipped. For example {1, 0, 2, 1}, ranks the first and fourth items in
       |                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pltree.Rd: mob
  qvcalc.PlackettLuce.Rd: worstErrors, plot.qv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plainView.Rd: raster, levelplot, brick
  plainViewOutput.Rd: shinyWidgetOutput
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:
    ‘ingest.R’ ‘model_versions.R’ ‘supported_states.R’ ‘upload.R’
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
checkRd: (-1) one_design.Rd:125-126: Lost braces
   125 | function serves for the purpose of spot-testing for any pre-specified {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:
    ‘VDJ_build.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_season_form.R’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'library' or 'require' call not declared from: ‘MASS’
checkRd: (-1) plgraphics-internal.Rd:19: Lost braces
    19 |     \item{RNAMES}{code{row.names} if \code{x} is a matrix or data.frame,
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Tobit.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) check_hwe.Rd:103: Lost braces; missing escapes or markup?
   103 | {'ALL', 'AFF', 'UNAFF', 'ALL(QT)', 'ALL(NP)'}), A1 (Allele 1; usually minor),
       | ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PLmixed-package.Rd: lme4, optimx
  PLmixed.Rd: lme4, glmer, optimx, lmerControl, glmerControl, lmer
  coef.PLmod.Rd: coef.merMod
  fitted.PLmod.Rd: fitted.merMod
  fixef.PLmod.Rd: fixef.merMod
  plot.PLmod.Rd: plot.merMod
  predict.PLmod.Rd: predict.merMod
  ranef.PLmod.Rd: ranef.merMod
  residuals.PLmod.Rd: residuals.merMod
  simulate.PLmod.Rd: simulate.merMod
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) delta2a.Rd:21: Lost braces; missing escapes or markup?
    21 | delta_k = log(a_k - a_{k+1})
       |                       ^
checkRd: (-1) ordprob.mple.Rd:29: Lost braces
    29 | logical. If code{TRUE} all the q variable are assumed to have the same mean.
       |                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  slice3D.Rd: computeContour3d
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cutrgl.Rd: par3d, open3d, material3d, plotdev
  imagergl.Rd: contour2D, colkey, persp3D, perspbox, image3D,
    contour3D, scatter3D, arrows3D, segments3D, text3D, image2D,
    scatter2D, segments2D, text2D, arrows2D
  persp3Drgl.Rd: persp3D, ribbon3D, hist3D, scatter3D, points3D,
    lines3D, segments3D, slice3D, slicecont3D, isosurf3D, voxel3D,
    surf3D, spheresurf3D, box3D, border3D, rect3D, perspbox, plotdev
  plotrgl.Rd: material3d, par3d, open3d, arrows3D, scatter3D, plotdev,
    persp3D, slice3D, surf3D
Please provide package anchors for all Rd \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_griddap.Rd: griddap
  add_tabledap.Rd: tabledap
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) add_bars.Rd:15: Lost braces
    15 | When \\code{y0} is not specified, the lowest value of the y-axis is used.}
       |            ^
checkRd: (-1) add_bars.Rd:24: Lost braces
    24 | \\code{\\link[graphics]{par}}.}
       |       ^
checkRd: (-1) add_bars.Rd:24: Lost braces
    24 | \\code{\\link[graphics]{par}}.}
       |                        ^
checkRd: (-1) plotluck.Rd:129: Lost braces
   129 |  in factors are are shown as a special factor level code{"?"}. They can be
       |                                                         ^
'::' or ':::' imports not declared from:
  ‘DT’ ‘geojsonio’
'library' or 'require' calls not declared from:
  ‘gapminder’ ‘leaflet’ ‘tourr’
checkRd: (-1) domain_data.Rd:29: Lost braces
    29 | code{\link{help}}
       |     ^
checkRd: (-1) length_data.Rd:32: Lost braces
    32 | code{\link{help}}
       |     ^
checkRd: (-1) plotdomain.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotmutagensis.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotprotein-package.Rd:20: Lost braces
    20 | code{\link{help}}
       |     ^
checkRd: (-1) plotprotein.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotsite.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) site_data.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  innerplot.Rd: plotmat
  outerplot.Rd: plotmat
  plot.plspm.Rd: plotmat
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PLS_beta_wvc.Rd: PLS_glm_kfoldcv_formula, PLS_lm_wvc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  signpred.Rd: visweb
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:
  ‘plsRcox’ ‘plspm’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plte_builder.Rd: qi_builder
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:
    ‘plug.R’
checkRd: (-1) plu_more.Rd:16: Lost braces; missing escapes or markup?
    16 | Additional arguments are replaced with "{n} more".
       |                                         ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘edata_summary.R’ ‘filter_objects.R’ ‘protein_quant.R’
    ‘statRes_class.R’
checkRd: (-1) PMCMR-deprecated.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:41: 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:
    ‘earned_value.R’ ‘planned_value.R’ ‘pmevR6.R’
checkRd: (-1) pmledecon.Rd:113: Lost braces; missing escapes or markup?
   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                              ^
checkRd: (-1) pmledecon.Rd:113: Lost braces; missing escapes or markup?
   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                                                         ^
checkRd: (-1) ahp.Rd:16: Lost braces; missing escapes or markup?
    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                   ^
checkRd: (-1) ahp.Rd:16: Lost braces; missing escapes or markup?
    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                              ^
checkRd: (-1) plot_scm.Rd:106: Lost braces; missing escapes or markup?
   106 | \item{lookupDF}{A data frame containing a lookup table for node labels. By default, {plot_scm} will use the PSN model names. If a lookup table containing the fields `Model` and `Alias` is provided, model names in `Model` will be replaced in the output plots by mtaching labels in `Alias`.}
       |                                                                                     ^
checkRd: (-1) rnm.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:71: Lost braces in \itemize; meant \describe ?
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:
    ‘tasmania_ibra_data.Rd’ ‘thylacine_example_matrices.Rd’
checkRd: (-1) estimate.functional.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{bw}{function describing bandwidth selection (see ?gmm for alternatives). Standard is that the bandwidth depends on the sample length $T$ by $m(T)=T^{1/5}$.}
       |                                                                                                                                                           ^
checkRd: (-1) pois.fe.robust.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pois.fe.robust.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pois.fe.robust.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pp_measures.Rd: diversity
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:
    ‘hiperfrac.R’ ‘rice.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:
    ‘hits.R’ ‘size.R’ ‘utils.R’
checkRd: (-1) inputData.Rd:94: Lost braces
    94 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
checkRd: (-1) inputData.Rd:95: Lost braces
    95 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
checkRd: (-1) preprocessData.Rd:81: Lost braces
    81 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
checkRd: (-1) preprocessData.Rd:82: Lost braces
    82 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
checkRd: (-1) stat_quantile_prob.Rd:14: Lost braces; missing escapes or markup?
    14 | Number {25, 50, 75}
       |        ^
checkRd: (-1) calculateDIC.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculateDIC.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polySegratioMM-package.Rd:70-72: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bootPolywog.Rd: foreach, dgCMatrix-class
  cv.polywog.Rd: cv.ncvreg
  polywog.Rd: glmnet, ncvreg, foreach, Formula, dgCMatrix-class,
    cv.glmnet, cv.ncvreg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) MLM_Model.Rd:31: Lost braces; missing escapes or markup?
    31 |   the weight vectors \bold{{w}^{i}} corresponds to class \eqn{i}{i}.
       |                                ^
checkRd: (-1) MLM_Model.Rd:33: Lost braces; missing escapes or markup?
    33 | We set \eqn{{\bold{{w}}^{h}} = 0} and the parameters to be learned are the weight vectors \bold{{w}^{i}}
       |                                                                                                     ^
File ‘pomp/libs/pomp.so’:
  Found non-API call to R: ‘CLOENV’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  forceLocus.Rd: forcePool
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  p_dfa_xerrors2.Rd: hcubature
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:
    ‘getPrevalence.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  allel.rich.Rd: genind
  allele.dist.Rd: genind
  bilby.Rd: genind
  gd.kosman.Rd: genind
  gd.smouse.Rd: genind
  genleastcost.Rd: gdistance, rSPDistance
  landgenreport.Rd: gdistance, rSPDistance
  null.all.Rd: genind
  popgenreport.Rd: genind, import2genind, df2genind, read.fstat,
    read.structure, read.genetix, read.genepop, Mercator, dismo, knitr,
    adegenet, pegas, mmod
  read.genetable.Rd: genind-class, adegenet, import2genind, df2genind,
    read.fstat, read.structure, read.genetix, read.genepop
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MLG-accessors.Rd: genlight-class
  aboot.Rd: genind, genpop, genlight-class
  bitwise.dist.Rd: genlight-class, genind-class
  bitwise.ia.Rd: genlight-class
  bootgen-class.Rd: gen-class
  bruvo.boot.Rd: genind, boot.phylo, nancycats, nj, nodelabels, tab
  bruvo.dist.Rd: genind
  bruvo.msn.Rd: genind, nancycats
  bruvomat-methods.Rd: genind-class
  clonecorrect.Rd: genind-class
  coercion-methods.Rd: genind-class, splitStrata
  diss.dist.Rd: genind
  diversity_ci.Rd: genind
  filter_stats.Rd: genind, genlight
  fix_replen.Rd: genind
  genclone-class.Rd: genind-class, genlight-class
  genclone-method.Rd: genind-class
  genetic_distance.Rd: genind-class, dist.genpop
  genind2genalex.Rd: genind-class
  genotype_curve.Rd: genind-class
  ia.Rd: import2genind
  info_table.Rd: genind-class
  informloci.Rd: genind-class
  is.clone.Rd: genind-class, genlight-class
  missingno.Rd: genind-class, tab
  mlg.Rd: ggplot
  mlg.filter.Rd: genind-class
  pgen.Rd: strata
  plot_poppr_msn.Rd: genind-class, genlight-class
  poppr-package.Rd: genind-class, genlight-class
  poppr.Rd: tab, strata, last_plot
  poppr.amova.Rd: genind-class, genlight-class, strata, quasieuclid,
    lingoes, cailliez
  poppr.msn.Rd: genind, genlight, nancycats, nj, nodelabels, tab
  popsub.Rd: genind-class, genlight-class
  psex.Rd: strata
  read.genalex.Rd: genind, other, genind-class
  recode_polyploids.Rd: genind-class, genpop-class
  rraf.Rd: strata
  shufflepop.Rd: genind-class
  snpclone-coercion-methods.Rd: genlight-class
  snpclone-method.Rd: genlight-class
  test_replen.Rd: genind
  upgma.Rd: as.phylo
  win.ia.Rd: genlight-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:
  Lifetable.Rd: forecast, read.demogdata
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'::' or ':::' import not declared from: ‘RPESE’
'library' or 'require' calls not declared from:
  ‘TTR’ ‘doMC’
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SnP500Returns.Rd: zoo
  access.Rd: zoo
  portvol.Bayes.Rd: zoo
  portvol.Rd: zoo
  risk.attrib.Copula.Rd: zoo
  risk.attribution.Rd: zoo
  volatility.Rd: zoo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pow.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:
  posterdown_html.Rd: html_paged
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) summary.POUMM.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{stats}{a named list of functions of the form function(par) { number },
       |                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ebp.Rd: nlme
  write.excel.Rd: openxlsx
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) coalesce_xy.Rd:22: Lost braces; missing escapes or markup?
    22 | the \code{conflict} argument of {powerjoin}'s join functions. \code{coalesce_xy()} is
       |                                 ^
checkRd: (-1) power_left_join.Rd:67: Lost braces; missing escapes or markup?
    67 | \item{by}{As in {dplyr}, but extended so user can supply a formula or a list
       |                 ^
checkRd: (-1) power_left_join.Rd:79: Lost braces; missing escapes or markup?
    79 | \item{keep}{A boolean for compatibility with {dplyr}, or a value among "left",
       |                                              ^
checkRd: (-1) preprocess_inputs.Rd:37: Lost braces; missing escapes or markup?
    37 | only be used in the \code{x} and \code{y} arguments of {powerjoin} join functions. No
       |                                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.Method.Rd: patchwork
  plot.StepOne.Rd: patchwork
  plot.StepThree.Rd: patchwork
  plot.StepTwo.Rd: patchwork
  plot.Validation.Rd: patchwork
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:
    ‘FSR.R’ ‘SR.R’ ‘helper_functions_model.R’ ‘plot.powerNLSEM.R’
    ‘smart_search.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pn.hist.Rd: histogram
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:146: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:148: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:126: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:219: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:221: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:225: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:229: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:231: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:233: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:235: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:237: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:301: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:303: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:305: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:307: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:309: Escaped LaTeX specials: \&
checkRd: (-1) med_pn.Rd:129: 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:
    ‘save.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:
    ‘direct_match.R’ ‘direct_match_spp_genus.R’ ‘fuzzy_match_genus.R’
    ‘fuzzy_match_infraspp_within_species.R’
    ‘fuzzy_match_spp_within_genus.R’ ‘genus_match.R’ ‘internal.R’
    ‘matching_ppendemic.R’ ‘suffix_match_spp_within_genus.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.ppgmmga.Rd: ggplot
  ppgmmga.Rd: densityMclust, ga, gaisl
  ppgmmga.options.Rd: ga_Selection, ga_Crossover, ga_Mutation
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ProgPredLasso.Rd: cvCovEst
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  envelope-methods.Rd: envelope
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) ccp_ppm.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{model}{Determines of model fit is such that there are p_{it}s (model=1) or
       |                                                               ^
checkRd: (-1) curve_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
checkRd: (-1) gaussian_ppmx.Rd:143: Lost braces; missing escapes or markup?
   143 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
checkRd: (-1) gaussian_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
checkRd: (-1) ordinal_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
checkRd: (-1) ordinal_ppmx.Rd:147: Lost braces; missing escapes or markup?
   147 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each sujbects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  webtool.Rd: runApp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
File ‘praznik/libs/praznik.so’:
  Found non-API call to R: ‘Rf_isFrame’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Specified C++11: please drop specification unless essential
checkRd: (-1) PRDA.Rd:8: Lost braces; missing escapes or markup?
     8 | Given an hypothetical value of effect size, {PRDA} performs a prospective
       |                                             ^
checkRd: (-1) PRDA.Rd:22: Lost braces; missing escapes or markup?
    22 | In {PRDA} there are two main functions:
       |    ^
checkRd: (-1) PRDA.Rd:51: Lost braces; missing escapes or markup?
    51 | Alternatively, {PRDA} allows users to specify a distribution of plausible
       |                ^
checkRd: (-1) diagnose_expressions.Rd:39: Lost braces
    39 | \item wrapping a function argument in two curly braces (e.g. `{{arg}} > 0) means
       |                                                               ^
File ‘precondition/libs/precondition.so’:
  Found non-API calls to R: ‘PRENV’, ‘R_PromiseExpr’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PredCRG.Rd: AAStringSet, readAAStringSet
  PredCRG_Enc.Rd: AAStringSet, readAAStringSet
  PredCRG_data.Rd: AAStringSet, readAAStringSet
  PredCRG_training.Rd: AAStringSet, readAAStringSet, ksvm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) dev_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:58-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:61-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:26-27: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  llbt.worth.Rd: gnm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  prepplot.Rd: Arrows
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:
    ‘mi_pre.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gpe.Rd: cv.glmnet
  gpe_cv.glmnet.Rd: cv.glmnet
  gpe_trees.Rd: ctree, glmtree, ctree_control, earth, cv.glmnet
  rTerm.Rd: cv.glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) prereg_initialize.Rd:20: Lost braces; missing escapes or markup?
    20 | the (pre)registration form specification (in {preregr} format), see the
       |                                              ^
checkRd: (-1) prereg_initialize.Rd:23: Lost braces; missing escapes or markup?
    23 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
checkRd: (-1) prereg_initialize.Rd:26: Lost braces; missing escapes or markup?
    26 | For an introduction to working with {preregr} (pre)registrations,
       |                                     ^
checkRd: (-1) rmd_templates.Rd:75: Lost braces; missing escapes or markup?
    75 | This function creates an R Markdown template from a {preregr}
       |                                                     ^
checkRd: (-1) rmd_templates.Rd:77: Lost braces; missing escapes or markup?
    77 | Sheet holding the (pre)registration form specification (in {preregr}
       |                                                            ^
checkRd: (-1) rmd_templates.Rd:81: Lost braces; missing escapes or markup?
    81 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
checkRd: (-1) format_number.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) format_number.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) format_number.Rd:38: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
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:
    ‘estimate_risk.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  adjust.sigma2.Rd: pdist
  binomial.logistic.MCML.Rd: maxBFGS
  glgm.LA.Rd: maxBFGS
  linear.model.MLE.Rd: maxBFGS
  lm.ps.MCML.Rd: maxBFGS
  poisson.log.MCML.Rd: maxBFGS
  spat.corr.diagnostic.Rd: 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:
  cpd.Rd: nls.lm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  psm_analysis_weighted.rd: svydesign
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) alogistic.Rd:20: Lost braces
    20 | The user does not put these directly into this function, but rather uses code{ode} in the \code{deSolve} package.
       |                                                                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_sequence.Rd: DNAbin
  get_sequences.Rd: DNAbin
  layout_tree_ape.Rd: phylo, plot.phylo
  search_primer_pair.Rd: create_progress_bar, response
  tree_from_alignment.Rd: dist.dna, nj
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘PRIMME/libs/PRIMME.so’:
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘primme/libprimme.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) NesPrInDT.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTAll.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTAllparts.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTMulab.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTMulabAll.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTMulev.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTMulevAll.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTreg.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTregAll.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) RePrInDT.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) findbeta.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{lower.v}{logical, if TRUE the specified percentile.value is the upper limit for the mean (or the median or the mode) at the specified confidence level (percentile). If {FALSE} the specified percentile.value is the lower limit for the mean (or the median or the mode) at the specified confidence level (percentile). The default is FALSE.}
       |                                                                                                                                                                               ^
checkRd: (-1) proc.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) proc.Rd:28: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  animate_process.Rd: process_map, JS, createWidget, sizingPolicy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  prepare_examples.Rd: grouped_log, eventlog, activitylog
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lhmm.Rd: statmod
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  smooth.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:
  proc_print.Rd: reporter
  proc_reg.Rd: v
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) paasche.Rd:91: Lost braces
    91 |     \code{OSME} \tab Output-oriented scale-mix efficiency score \emph{(code{orientation = "out"})}\cr
       |                                                                            ^
checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  validate_profile.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) PS.Rd:9: Lost braces
     9 |                 \item{CD}{}{Character disorder scale score}
       |                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotData.Rd: zoo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) proftools-package.Rd:40: Lost braces
    40 |   by the code{kcachegrind} program available on some operating
       |              ^
checkRd: (-1) prolific_prescreener.Rd:254: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_prescreener.Rd:255: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:243: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:244: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_plot.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{global}{Logical. If \code{TRUE} ({default}), a global density plot is
       |                                        ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘complete_chat.R’ ‘complete_prompt.R’ ‘format_prompt.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:
    ‘build_url.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fitDistr.Rd: nls.lm
  predictNLS.Rd: rtmvt
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BBmm.Rd: multiroot
  HRQoLplot.Rd: radarchart
  summary.BBmm.Rd: multiroot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) computeResponseProbability.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{model}{the item model to use. Accepts \code{grm} or {gpcm}.}
       |                                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotInfo-methods.Rd: SingleGroupClass-class
  runCalibration.Rd: SingleGroupClass-class
  runEquateObserved.Rd: equate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) struc_addSimData.Rd:15: Lost braces
    15 | \item{value}{code{data.frame} or code{data.table}}
       |                  ^
checkRd: (-1) struc_addSimData.Rd:15: Lost braces
    15 | \item{value}{code{data.frame} or code{data.table}}
       |                                      ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘nba_data.R’ ‘nba_data.Rd’ ‘nfl_data.R’ ‘nhl_data.R’ ‘nhl_data.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.protoclust.Rd: protoclust
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) prototest.univariate.Rd:21: Lost braces
    21 | response variable. Vector of length emph{n}, assumed to be quantitative.
       |                                         ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘cell.R’ ‘command.R’ ‘instrument.R’ ‘io.R’ ‘modplug.R’ ‘note.R’
    ‘render.R’ ‘s3.R’ ‘select_ops.R’
checkRd: (-1) pr_stem_sentences.Rd:20: Lost braces; missing escapes or markup?
    20 | Implementation of the {SnowballC} stemmer. Note that punctuation and capital letters 
       |                       ^
checkRd: (-1) pr_stem_words.Rd:20: Lost braces; missing escapes or markup?
    20 | Implementation of the {SnowballC} stemmer. Note that punctuation and capitals letters 
       |                       ^
checkRd: (-1) proust_sentiments.Rd:7: Lost braces; missing escapes or markup?
     7 | See the {rfeel} package now: http://github.com/ColinFay/rfeel}
       |         ^
checkRd: (-1) proust_sentiments.Rd:20: Lost braces; missing escapes or markup?
    20 | See the {rfeel} package now: http://github.com/ColinFay/rfeel
       |         ^
Missing dependency on R >= 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_proverbs.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  colSds.Rd: Matrix
  colZeros.Rd: Matrix
  simil.Rd: Matrix, CsparseMatrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘proxy/libs/proxy.so’:
  Found non-API calls to R: ‘OBJECT’, ‘Rf_NonNullStringMatch’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
47c47
< This is mgcv 1.9-3. For overview type 'help("mgcv-package")'.
---
> This is mgcv 1.9-1. For overview type 'help("mgcv-package")'.
Running ‘basic.R’ [32s/40s]
  Comparing ‘basic.Rout’ to ‘basic.Rout.save’ ...34c34
< This is mgcv 1.9-3. For overview type 'help("mgcv-package")'.
---
> This is mgcv 1.9-1. For overview type 'help("mgcv-package")'.
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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  formatting.Rd: tbl_format_setup
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘pryr/libs/pryr.so’:
  Found non-API calls to R: ‘BODY’, ‘CLOENV’, ‘ENCLOS’, ‘EXTPTR_PROT’,
    ‘EXTPTR_TAG’, ‘FORMALS’, ‘FRAME’, ‘HASHTAB’, ‘NAMED’, ‘PRCODE’,
    ‘PRENV’, ‘PRVALUE’, ‘Rf_findVarInFrame3’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Missing dependency on R >= 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.weighting.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PSAboot.Rd: Match
  balance.matching.Rd: cv.trans.psa
  boot.ctree.Rd: cv.trans.psa
  boot.matching.Rd: cv.trans.psa, Match
  boot.matchit.Rd: cv.trans.psa
  boot.rpart.Rd: cv.trans.psa
  boot.strata.Rd: cv.trans.psa
  boot.weighting.Rd: cv.trans.psa
  boxplot.PSAboot.balance.Rd: facet_wrap
  hist.PSAboot.Rd: geom_histogram
Please provide package anchors for all Rd \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.CBS.DNAcopy.Rd: DNAcopy
  as.DNAcopy.CBS.Rd: DNAcopy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CountryID.Rd: countrycode
  DDGet.Rd: countrycode
  DpiGet.Rd: countrycode
  IMF_WBGet.Rd: countrycode
  PolityGet.Rd: countrycode
  RRCrisisGet.Rd: countrycode
  WinsetCreator.Rd: countrycode
  countrycode_data.Rd: countrycode
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) qpc.Rd:43: Lost braces
    43 | S{Sulewski, P. (2020). \emph{Normal Distribution with Plasticizing Component,} Communications in Statistics ? Theory and Method 51(11), 3806-3835.}
       |  ^
checkRd: (-1) riedsid.Rd:92-93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riedsid.Rd:94-96: 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:
    ‘pseudohouseholds.R’
checkRd: (-1) data1.Rd:14: Lost braces
    14 | The data set from {AbouRizk, S.M., Halpin, D.W., Wilson, J. R. (1994). \emph{Fitting beta distributions based on sample data.} Journal of Construction Engineering and Management 120(2), 288–305.}
       |                   ^
checkRd: (-1) data2.Rd:14: Lost braces; missing escapes or markup?
    14 | The data set presents the height of 99 five-year-old British boys in cm downloaded from {http://www.mas.ncl.ac.uk/njnsm/medfac/docs/intro.pdf.}
       |                                                                                         ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘psid_read.R’ ‘psid_reshape.R’ ‘psid_str.R’
checkRd: (-1) table1.Rd:14: Lost braces
    14 | The first data set from {Sulewski, P. (2017) \emph{A new test for independence in 2x2 contingency tables,} Acta Universitatis Lodziensis. Folia Oeconomica, 4(330), 55–75}
       |                         ^
checkRd: (-1) table3.Rd:14: Lost braces
    14 | The third data set from {Sulewski, P. (2021). \emph{Logarithmic Minimum Test for Independence in Three Way Con-tingency Table of Small Sizes.} Journal of Statistical Computation and Simulation 91(13), 2780-2799}
       |                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.Rd: ggplot2
  ps_aggregated.Rd: ggplot2
  ps_detailed.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:
  PStrata-package.Rd: 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:
  PSTf-class.Rd: TraMineR
  cprob.Rd: TraMineR
  generate.Rd: TraMineR
  plot-PSTr.Rd: seqdef
  pmine.Rd: TraMineR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) dprime.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
'::' or ':::' imports not declared from:
  ‘colorspace’ ‘psychomix’
'library' or 'require' calls not declared from:
  ‘car’ ‘lmtest’ ‘psychomix’ ‘psychotree’ ‘strucchange’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CEMSChoice.Rd: paircomp
  EuropeanValuesStudy.Rd: paircomp
  Topmodel2007.Rd: paircomp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) PTE_bootstrap_inference.Rd:39-42: Lost braces
    39 |                                                         continuous = function(Xytrain){ #defalt is OLS regression
       |                                                                                       ^
checkRd: (-1) PTE_bootstrap_inference.Rd:43-47: Lost braces
    43 |                                                         incidence = function(Xytrain){ #default is logistic regression
       |                                                                                      ^
checkRd: (-1) PTE_bootstrap_inference.Rd:48-52: Lost braces
    48 |                                                         survival = function(Xytrain){ #default is Weibull regression
       |                                                                                     ^
checkRd: (-1) PTE_bootstrap_inference.Rd:66-68: Lost braces
    66 |                                         function(mod, Xyleftout){
       |                                                                 ^
checkRd: (-1) PTE_bootstrap_inference.Rd:74-77: Lost braces
    74 |                                         function(results, indices_1_1, indices_0_0, indices_0_1, indices_1_0){
       |                                                                                                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ddist.Rd: extraDistr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ptw-package.Rd:20-28: Lost braces
    20 | @Article{Bloemberg2010,
       |         ^
checkRd: (-1) ptw-package.Rd:30-38: Lost braces
    30 | Article{Wehrens2015,
       |        ^
checkRd: (-1) ma.Rd:62: Lost braces
    62 | \item{yi}{Numeric vector of length code{k} with observed effect size
       |                                        ^
checkRd: (-1) ma.Rd:65: Lost braces
    65 | \item{vi}{Numeric vector of length code{k} with sampling variances.}
       |                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  followupTable.Rd: anova.coxph
  specialFrame.Rd: model.design, strata, strip.terms
  stripes.Rd: plot.prodlim
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) plotWordCloud.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{PubMed wordcloud using function 'wordcloud' of package {wordcloud}}
       |                                                               ^
checkRd: (-1) plotWordCloud.Rd:32: Lost braces; missing escapes or markup?
    32 | This function just call 'wordcloud' from package {wordcloud}. See package {wordcloud} for more details about the parameters.
       |                                                  ^
checkRd: (-1) plotWordCloud.Rd:32: Lost braces; missing escapes or markup?
    32 | This function just call 'wordcloud' from package {wordcloud}. See package {wordcloud} for more details about the parameters.
       |                                                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as_MonoClust.PULS.Rd: monoClust
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NA_summary.Rd: create_time_series
  blink_summary.Rd: create_time_series
  check_baseline.Rd: create_time_series
  compare_summary.Rd: create_time_series
  ppl_check_eye_recording.Rd: create_time_series
  ppl_plot_avg.Rd: create_time_series
  ppl_plot_avg_contour.Rd: create_time_series
  ppl_select_recorded_eye.Rd: create_time_series
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:
    ‘source_pmc.R’ ‘source_pubmed.R’ ‘source_pubtations.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:
    ‘check_api_key.R’ ‘get_organization_data.R’ ‘get_sensor_data.R’
    ‘get_sensor_history.R’ ‘get_sensors_data.R’ ‘purple_air_request.R’
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  by_row.Rd: invoke, lift
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘purrrlyr/libs/purrrlyr.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.
File ‘purrr/libs/purrr.so’:
  Found non-API call to R: ‘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:
  pva-class.Rd: dcmle-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) DataSets.Rd:10: Lost braces; missing escapes or markup?
    10 | \format{the \code{PvarQuantileDF} is a \code{data.frame} with fields \code{prob} an {Qaunt}. 
       |                                                                                     ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘da.Rd’ ‘da_object_oriented_functions.R’
    ‘higher_level_disprop_analysis.R’ ‘lower_level_disprop_analysis.R’
    ‘print.da.Rd’
checkRd: (-1) pvlrt.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{no_zi_idx}{List of pairs {(i, j)} where zero inflation is not allowed. To
       |                                ^
checkRd: (-1) r_contin_table_zip.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{no_zi_idx}{List of pairs {(i, j)} where zero inflation is not allowed. To
       |                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PWI.Rd: bibliometrix, convert2df
  PWI2.Rd: convert2df
  countries.Rd: biblioAnalysis
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:
  ‘Hmisc’ ‘car’ ‘dplyr’ ‘ggplot2’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘pwrFDR.R’
checkRd: (-1) aid_st2.Rd:6: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  predictpycno.Rd: SpatialGridDataFrame, SpatialPolygonsDataFrame
  pycno.Rd: SpatialPolygonsDataFrame, SpatialGridDataFrame
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) crosstab.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  univariate_plot.Rd: ggplot2, patchwork
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) srswrRe.Rd:10: Lost braces
    10 |   \item{listRanef}{{\emph{ranef(model)}} object where {\emph{model}} is an { \emph{lmer}} object.}
       |                                                                            ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘qb_records.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Qcoxph.Rd: coxph, coxph.object, predict.coxph
  Qest.control.Rd: pchreg
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:
    ‘qgis_run_algorithm_p.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  anova.cmprsk.Rd: rms
  crr.fit.Rd: rms
  nomogram.mk6.Rd: rms, plot.summary.rms
  summary.cmprsk.Rd: rms
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) qif.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  array.Rd: simple_sparse_array
  rKhatriRao.Rd: KhatriRao
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) qmethod-package.Rd:109: Lost braces
   109 |   \item Van Exel, J., and G. de Graaf, 2005. \emph{Q Methodology: A Sneak Preview}\cr \url{https://qmethodblog.files.wordpress.com/2016/01/qmethodologyasneakpreviewreferenceupdate.pdf}{Available at this link}.
       |                                                                                                                                                                                         ^
checkRd: (-1) qmethod-package.Rd:110: Lost braces
   110 |   \item Brown, S. R., 1980. \emph{Political subjectivity: Applications of Q methodology in political science}, New Haven, CT: Yale University Press.\cr \url{https://qmethodblog.files.wordpress.com/2016/01/brown-1980-politicalsubjectivity.pdf}{Available at this link}.
       |                                                                                                                                                                                                                                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pcrfit.Rd: nlsLM
  plot.pcrfit.Rd: plot3d, points3d, lines3d, axis3d, mtext3d
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_qqboxplot.Rd: geom_boxplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) hideLocation.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{trueLoc}{A vector of one or more numbers in the set {1, 2, ..., nSubjects} whose locations are to be hidden.}
       |                                                           ^
checkRd: (-1) hideLocation.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{nSubjects}{An integer larger than 1 used to define the set {1, 2, ..., nSubjects}.}
       |                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  piqr.Rd: slp, iqr, summary.iqr, test.fit
  predict.piqr.Rd: predict.iqr
  summary.piqr.Rd: summary.iqr
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:
    ‘qr_vcard.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AHeVT.Rd: truncSP
  AHeVXT.Rd: truncSP
  QRIndiv.Rd: truncSP
  QRSimul.Rd: truncSP
  QRStepwise.Rd: truncSP
  QRWSimul.Rd: truncSP
  simul_shapetest.Rd: truncSP
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  qde.Rd: rq
  qrjoint.Rd: rq
  summary.qde.Rd: geweke.diag
  summary.qrjoint.Rd: geweke.diag
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:
    ‘all_new_functions.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  commodities.Rd: xts
  crypto.Rd: xts
  default.Rd: xts
  fx.Rd: xts
  interest_rates.Rd: xts
  losses.Rd: xts
  stock_indices.Rd: xts
  stock_indices_constituents.Rd: xts
  stocks.Rd: xts
  volatility.Rd: xts
Please provide package anchors for all Rd \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_ARMA_GARCH.Rd: ugarchfit
  get_data.Rd: getSymbols, Quandl, Ad, Cl, Op, Hi, Lo, Vo, OpCl, ClCl,
    HiCl, LoCl, LoHi, OpHi, OpLo, OpOp
  matrix_plot.Rd: levelplot
  returns.Rd: xts
  tests.Rd: ad.test
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'::' or ':::' imports not declared from:
  ‘simsalapar’ ‘stabledist’
Malformed Description field: should contain one or more complete sentences.
File ‘qs/libs/qs.so’:
  Found non-API calls to R: ‘CLOENV’, ‘ENCLOS’, ‘FRAME’, ‘HASHTAB’,
    ‘IS_S4_OBJECT’, ‘LEVELS’, ‘OBJECT’, ‘PRENV’, ‘Rf_allocSExp’,
    ‘SETLEVELS’, ‘SET_CLOENV’, ‘SET_ENCLOS’, ‘SET_FRAME’,
    ‘SET_HASHTAB’, ‘SET_PRENV’, ‘SET_S4_OBJECT’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
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:
  ggplot_pxg.Rd: plot_coef
  ggplot_scan1.Rd: plot_snpasso
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) IPWE_mean_IndCen.Rd:54-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{case}{string. One of {"a", "b", "c"}, corresponding to three models.}
       |                            ^
checkRd: (-1) simJLSDdata.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:32-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  KhmaladzeFormat.Rd: KhmaladzeTest
  cmidecdf.Rd: npcdistbw
  mice.impute.rq.Rd: rq
  midrqControl.Rd: npcdistbw
  qlss.Rd: rq
  rq.counts.Rd: rq
  rrq.Rd: rq
  sparsity.rqt.Rd: rq
  summary.rqt.Rd: summary.rq, boot
  summary.rrq.Rd: boot
  tsrq.Rd: rq
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) find_lcp.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:63-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:18-19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:23-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) als_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) qualpal.Rd:22-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) qualpal.Rd:30-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cqs.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cqs.Rd:33-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cqs.Rd:37-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) llqr.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) llqr.Rd:38-41: 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:
    ‘char_select.R’ ‘char_select.Rd’ ‘convert-wrappers.Rd’ ‘convert.Rd’
    ‘corpus-addsummary-metadata.R’ ‘corpus_sample.Rd’ ‘dfm.Rd’
    ‘dfm_select.Rd’ ‘dfm_tfidf.Rd’ ‘dictionary.Rd’ ‘docfreq.Rd’
    ‘docnames.Rd’ ‘index.Rd’ ‘nsentence.Rd’ ‘tokens_compound.Rd’
    ‘tokens_replace.Rd’ ‘tokens_sample.Rd’ ‘tokens_split.Rd’
    ‘topfeatures.Rd’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘textplot_network.Rd’ ‘textplot_wordcloud.Rd’ ‘textplot_xray.Rd’
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  logLik.gcrq.Rd: logLik.rq
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) quarries.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:20-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:26-28: 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:
    ‘quax.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  quest-package.Rd: str2str
  ucfa.Rd: lavaan-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) display_table.Rd:37: Lost braces; missing escapes or markup?
    37 | \item{normtest}{A character indicating test of normality, the default method is \code{\link{shapiro.test}} when sample size no more than 5000, otherwise \code{\link[nortest]{lillie.test}} {Kolmogorov-Smirnov} is used, see package \strong{nortest} for more methods.Use 'shapiro.test', 'lillie.test', 'ad.test', etc to specify methods.}
       |                                                                                                                                                                                             ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘2d.R’ ‘assign_data.Rd’ ‘avg_highd_data.Rd’ ‘compute_std_counts.Rd’
    ‘find_low_dens_hex.Rd’ ‘find_pts.Rd’ ‘geom_trimesh.R’ ‘highd.R’
    ‘model.R’ ‘parameters.R’ ‘prediction.R’ ‘show_langevitour.Rd’
    ‘stat_trimesh.R’
File ‘quotedargs/libs/quotedargs.so’:
  Found non-API calls to R: ‘ENCLOS’, ‘LEVELS’, ‘PRCODE’, ‘PRENV’,
    ‘PRVALUE’, ‘Rf_allocSExp’, ‘SETLEVELS’, ‘SET_NAMED’, ‘SET_PRCODE’,
    ‘SET_PRENV’, ‘SET_PRVALUE’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fl.drFitModel.Rd: nlsLM
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:
    ‘complex_check.R’ ‘create_interactions.R’ ‘estimate_payoffs.R’
    ‘mse.InteractionClassification.R’ ‘nearest_payoff.Rd’
    ‘summary.InteractionClassification.R’ ‘summary.payoffs.R’
checkRd: (-1) est.R0.ML.Rd:98: Lost braces
    98 | Supplementary Material S1 from \doi{10.1186/1472-6947-12-147}{Obadia et al., 2012}.
       |                                                              ^
checkRd: (-1) plot.R0.R.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from one estimation method.
       |                                                      ^
checkRd: (-1) plot.R0.sR.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from an
       |                                                      ^
checkRd: (-1) do_admb.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) do_admb.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) do_admb.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_pars.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pqlmer.Rd: glmmPQL
  r2beta.Rd: lmer, lme, glmmPQL
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  runMLwiN.Rd: mcmc.list
  sixway.Rd: mcmc, mcmc.list
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
checkRd: (-1) bugs.Rd:158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:166: Lost braces in \itemize; meant \describe ?
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
Unknown package ‘BRugs’ in Rd xrefs
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  html_doc.Rd: whisker-package
  ltx_doc.Rd: whisker-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) r4ss-package.Rd:9: Lost braces; missing escapes or markup?
     9 | A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks. This version of '{r4ss}' is compatible with Stock Synthesis versions 3.24 through 3.30 (specifically version 3.30.19.01, from April 2022).
       |                                                                                                                                                                                                                                                                                                                                                                                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  r6extended.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) extract_class.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extract_class.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extract_class.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) post_RA_fits.Rd:61: Lost braces; missing escapes or markup?
    61 |     \item{\code{H(po_{bm_{n.bm}}, po_act)}:}{ last benchmark prior bm_{n.bm} inducing the fit \code{fits.bm[[n.bm]]} and actual prior}
       |                                                                       ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ao_get_leaners_progress_by_course.R’
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:
    ‘add_element.Rd’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Communities.Rd: igraph
  DiffGraph.Rd: igraph
  GGMpathStats.Rd: igraph
  Ugraph.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:
  matrix_rank.Rd: rankMatrix, Matrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) makeDesignMatrix.Rd:16: Lost braces; missing escapes or markup?
    16 | is randomized to a certain treatment {j}, the entry of \code{(i,j)} of the
       |                                      ^
File ‘randomizr/libs/randomizr.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.
Problems with news in ‘NEWS.md’:
No news entries found.
Running examples in ‘randquotes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: randquote
> ### Title: Get Random Quotes
> ### Aliases: randquote
> 
> ### ** Examples
> 
> randquote()
Error in randquote() : Fetching failed. The API call returned 400 error
Execution halted
Running ‘test-all.R’ [1s/2s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("randquotes")
  Loading required package: randquotes
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-randquotes.R:4:3'): the functions of randquotes ────────────────
  Error in `randquote()`: Fetching failed. The API call returned 400 error
  Backtrace:
      ▆
   1. ├─testthat::expect_that(randquote(), is_a("data.frame")) at test-randquotes.R:4:3
   2. │ └─testthat (local) condition(object)
   3. │   └─testthat::expect_is(x, class)
   4. │     └─testthat::quasi_label(enquo(object), label, arg = "object")
   5. │       └─rlang::eval_bare(expr, quo_get_env(quo))
   6. └─randquotes::randquote()
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rdt.Rd: IndependenceTest-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:
  rankhazard-package.Rd: coxph
  rankhazardplot.Rd: coxph, predict.coxph, pspline
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) grottaBar.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rankL2R.Rd:18: Lost braces; missing escapes or markup?
    18 | where the vector dimension is 2^{response.number}.}
       |                                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rboost.Rd: gbm.object, gbm.more, gbm.perf
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:
    ‘evds_table_api.R’ ‘excel_internal.R’ ‘request_funcs.R’
    ‘sp_df_utils.R’
checkRd: (-1) user_log_dir.Rd:48: Lost braces
    48 | \\env{$XDG_CACHE_HOME} if defined
       |      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rasclass-class.Rd: randomForest, multinom, mlp, svm
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:
    ‘findblocks_bc.Rd’ ‘getdata_bc.Rd’ ‘listdata_bc.Rd’ ‘opendata_bc.Rd’
    ‘utils.R’
checkRd: (-1) RasterList-Package.Rd:20: Lost braces
    20 | {\code{\link{rasterList}}}{: it is the constructor of a  \code{\link{RasterList-class}} object from a generic \code{object}, it also transforms a \code{\link{RasterList-class}} into another one throungh a function argument. }
       |                           ^
checkRd: (-1) RasterList-Package.Rd:22: Lost braces
    22 | {\code{\link{rasterListFun}}}{: it is a function that constructs  a  particular \code{\link{RasterList-class}} object in which the objects are \code{function}-type. }
       |                              ^
checkRd: (-1) RasterList-Package.Rd:24: Lost braces
    24 | {\code{\link{RasterListApply}}}{: it is a function that allows to operate among two or more \code{\link{RasterList-class}} objects defined in the same spatial extent through a generic function \code{fun(x,y,...)} where \code{x} and \code{y} are each cell/element of two \code{\link{RasterList-class}} objects given as arguments \code{x} and \code{y} of \code{\link{RasterListApply}}.}
       |                                ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RasterList-Package.Rd: RasterLayer-class, RasterStack-class
  RasterList-class.Rd: RasterLayer-class, Raster-class
  raster.Rd: RasterLayer-class
  stack.Rd: RasterStack-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:
  bwplot-methods.Rd: panel.violin, panel.bwplot, sampleRandom,
    panel.stripplot
  chooseRegion.Rd: in.out
  densityplot-methods.Rd: sampleRandom
  hexbinplot.Rd: sampleRegular
  histogram-methods.Rd: sampleRandom
  horizonplot-methods.Rd: zonal
  hovmoller-methods.Rd: zonal, panel.2dsmoother
  levelplot-methods.Rd: sampleRegular, trellis.par.set, custom.theme,
    panel.levelplot, panel.levelplot.raster, ratify
  rasterTheme.Rd: custom.theme, custom.theme.2,
    yscale.components.default, xscale.components.default,
    trellis.par.get
  splom-methods.Rd: sampleRandom
  vectorplot.Rd: terrain, panel.arrows
  xyLayer.Rd: sampleRegular, spatSample
  xyplot-methods.Rd: zonal
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) as_mcmc.list.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Convert a rater_fit object to a {coda} \code{mcmc.list} object.}
       |                                        ^
checkRd: (-1) as_mcmc.list.Rd:16: Lost braces; missing escapes or markup?
    16 | Convert a rater_fit object to a {coda} \code{mcmc.list} object.
       |                                 ^
checkRd: (-1) as_mcmc.list.Rd:13: Lost braces; missing escapes or markup?
    13 | A {coda} mcmc.list object.
       |   ^
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:109-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:115-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:121-124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:125-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:128-138: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Query.Rd: DBIConnection-class
  dbClearResult.Rd: DBIResult-class
  dbColumnInfo.Rd: DBIResult-class
  dbConnect-AthenaDriver-method.Rd: DBIDriver-class,
    DBIConnection-class
  dbDataType.Rd: DBIDriver-class, DBIConnection-class
  dbDisconnect.Rd: DBIConnection-class
  dbExistsTable.Rd: DBIConnection-class
  dbFetch.Rd: DBIResult-class
  dbGetInfo.Rd: DBIObject-class, DBIDriver-class, DBIConnection-class,
    DBIResult-class
  dbGetPartition.Rd: DBIConnection-class
  dbGetQuery.Rd: DBIConnection-class
  dbGetStatement.Rd: DBIResult-class
  dbGetTables.Rd: DBIConnection-class
  dbHasCompleted.Rd: DBIResult-class
  dbIsValid.Rd: DBIObject-class, DBIDriver-class, DBIConnection-class,
    DBIResult-class
  dbListFields.Rd: DBIConnection-class
  dbListTables.Rd: DBIConnection-class
  dbQuote.Rd: DBIConnection-class
  dbRemoveTable.Rd: DBIConnection-class
  dbShow.Rd: DBIConnection-class
  dbStatistics.Rd: dbSendQuery, DBIResult-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) S1.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{m_bar}{the sample vector of moments for a specified vector $(h_{a,r},y)$}
       |                                                                      ^
checkRd: (-1) S1.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{N_k}{index of the $ h_{a,r}$ function considered}
       |                             ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘combine_n_pct.Rd’ ‘fmt_kbl_header.Rd’ ‘fmt_table.Rd’
    ‘table-format.R’
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) rbm.haplos.power.Rd:35: Lost braces; missing escapes or markup?
    35 |   \item{simus.haplos}{ Which method to simulate the data, if \code{simus.haplos="freqs"}, {rbm.haplos.freqs()} is used, otherwise \code{rbm.haplos.thresholds()} is used.}
       |                                                                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cmax.Rd: apply.yearly, apply.monthly
  rvn_rvi_process_diagrammer.Rd: render_graph
  rvn_write_Raven_table.Rd: write.fwf
  rvn_wyear_indices.Rd: endpoints
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:
    ‘render_model.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BayesianOptimization.Rd: GP_fit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘Rbeast/libs/Rbeast.so’:
  Found non-API call to R: ‘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:
  acceptance_rate.Rd: libbi, get_traces
  adapt_particles.Rd: libbi
  adapt_proposal.Rd: libbi
  get_mvn_params.Rd: libbi
  numeric_to_time.Rd: libbi
  update_proposal.Rd: bi_model
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) R.cache-package.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) R.cache-package.Rd:31-34: 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:
    ‘tests.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ewowin.Rd: owin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  carto_scale.Rd: discrete_scale, continuous_scale
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) mig_calculate_rc.Rd:28: Lost braces; missing escapes or markup?
    28 | \item pre-working age: {a1, alpha1}
       |                        ^
checkRd: (-1) mig_calculate_rc.Rd:29: Lost braces; missing escapes or markup?
    29 | \item working age: {a2, alpha2, mu2, lambda2}
       |                    ^
checkRd: (-1) mig_calculate_rc.Rd:30: Lost braces; missing escapes or markup?
    30 | \item retirement: {a3, alpha3, mu3, lambda3}
       |                   ^
checkRd: (-1) mig_calculate_rc.Rd:31: Lost braces; missing escapes or markup?
    31 | \item post retirement: {a4, lambda4}
       |                        ^
Found the following files/directories:
  ‘temp.RData’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get.fingerprint.Rd: fingerprint-class, featvec-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) nc_open_CGLS.Rd:29-32: Lost braces
    29 | if(resolution == "300m"){
       |                         ^
checkRd: (-1) nc_open_CGLS.Rd:33-36: Lost braces
    33 | if(resolution == "1km"){
       |                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  classify_DayTime.Rd: sunriset, crepuscule
  dy_DepthTS.Rd: dygraph, dyOptions
  get_DayTimeLimits.Rd: sunriset, crepuscule
  ggplot_geopos.Rd: SpatialPolygonsDataFrame, projection, cmap
  ggplotly_geopos.Rd: region_definitions, v, add.region, delete.region,
    ggplotly
  image_TempDepthProfiles.Rd: cmap, set.colorbarp
  leaflet_geopos.Rd: SpatialPolygonsDataFrame, cmap
  plot_DepthTempTS.Rd: oceanmap, cmap
  plot_data_coverage.Rd: oceanmap
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Rchoice.Rd:159: Lost braces; missing escapes or markup?
   159 |  \code{ranp}. If the parameters are assumed to be normally distributed \eqn{\beta_i ~ N(\beta, \Sigma)}, then the random parameter are constructed as: \deqn{\beta_{ir}=\beta+L\omega_{ir}} where \eqn{LL'=\Sigma} and \eqn{\omega_{ir}} is the {r}-th draw from standard normal distribution for individual \eqn{i}. 
       |                                                                                                                                                                                                                                                 ^
Found the following files/directories:
  ‘data.csv’
Found the following files/directories:
  ‘outcmaesdisp.dat’
checkRd: (-1) indexplot.Rd:28: Lost braces
    28 |   \item{legend}{keyword (see \code{link}[grapics]{legend}) giving location of the legend if \code{groups} are specified; 
       |                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Barplot.Rd: rainbow_hcl
  normalityTest.Rd: pearson.test, ad.test, cvm.test, lillie.test,
    sf.test
  readSAS.Rd: read_sas
  readSPSS.Rd: read_spss, read.spss
  readStata.Rd: read.dta13
  readXL.Rd: read_excel
  stepwise.Rd: stepAIC
  summarySandwich.Rd: hccm, vcovHAC
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BiclustGUI.Rd: biclust, fabia, iBBiG, BicARE, superbiclust,
    BcDiag-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:
  RcmdrPlugin.BWS1-package.Rd: crossdes, support.BWS, support.CEs,
    Rcmdr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RcmdrPlugin.BWS2-package.Rd: DoE.base, Rcmdr, support.BWS2,
    support.CEs, survival
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RcmdrPlugin.BWS3-package.Rd: support.BWS3, support.CEs, Rcmdr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RcmdrPlugin.cpd.Rd: cpd, Rcmdr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RcmdrPlugin.GWRM.Rd: GWRM, Rcmdr
  generalizedWaringModel.Rd: linearModel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) RcmdrPlugin.MA-package.Rd:23: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GUI_RandomANOVA.Rd: lmer
  RcmdrPlugin.TeachStat-package.Rd: Rcmdr
  Utilities.Rd: distr, DiscreteDistribution, AbscontDistribution
  aovreml.Rd: lmer
  aovremm.Rd: lmer
  characRV.Rd: E, skewness, kurtosis
  priceIndexNum.Rd: priceIndex
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) nonlinearAR1.sim.Rd:8: Lost braces; missing escapes or markup?
     8 | of the form z_n = g(z_{n-1}) + epsilon. A normal distribution is assumed for the innovations.
       |                       ^
Missing dependency on R >= 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’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  add_github_actions_citation.Rd: cffr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
possible bashism in configure.ac line 35 (test -a/-o):
  if test [-n "$PKG_CPPFLAGS" -a -n "$PKG_LIBS"] ; then
  possible bashism in configure.ac line 38 (test -a/-o):
     if test [-n "$PKG_CPPFLAGS" -o -n "$PKG_LIBS"] ; then
  possible bashism in configure.ac line 66 (test -a/-o):
     if test [-n "$CPLEX_INCLUDE" -a -n "$CPLEX_LIB" ] ; then
  possible bashism in configure.ac line 82 (test -a/-o):
        if test [-n "$CPLEX_INCLUDE" -o -n "$CPLEX_LIBS" ] ; then
  possible bashism in configure.ac line 89 (test -a/-o):
  if test ["$FOUND_ALL" = "no" -a -z "$CPLEX_DIR"] ; then
  possible bashism in configure.ac line 119 (test -a/-o):
     if test [-z "$LIBFORMAT" -a ! -d "${CPLEX_DIR}/lib/${SYSTEM}/${LIBFORMAT}"] ; then
  possible bashism in configure.ac line 173 (should be 'b = a'):
  if test "${ac_cv_header_ilcplex_cplex_h}" == no; then
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'library' or 'require' call not declared from: ‘rbenchmark’
Specified C++11: please drop specification unless essential
possible bashism in configure.ac line 37 (should be 'b = a'):
  if test x"${RSysinfoName}" == x"Darwin"; then
  possible bashism in configure.ac line 48 (should be 'b = a'):
     if test x"${hasOpenMP}" == x""; then
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
File ‘Rcpp/libs/Rcpp.so’:
  Found non-API call to R: ‘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.
checkRd: (-1) cSMCexamples.Rd:78-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cSMCexamples.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cSMCexamples.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cSMCexamples.Rd:90: 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:
    ‘print.rcpptimer.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cppXPtr.Rd: cppFunction
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++14: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘extract_smoking.R’ ‘extract_test_data_var.R’ ‘extract_time_until.R’
    ‘misc_functions.R’
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 "$FOUND_ALL" -a -n "$CSDP_DIR"] ; then
  possible bashism in configure.ac line 87 (should be 'b = a'):
      if test "${ac_cv_header_declarations_h}" == no; then
File ‘Rcsdp/libs/Rcsdp.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
    Object: ‘Csdp/lib/libsdp.a’
  Found ‘printf’, possibly from ‘printf’ (C)
    Object: ‘Csdp/lib/libsdp.a’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘Csdp/lib/libsdp.a’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘Csdp/lib/libsdp.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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:
    ‘00_console.R’ ‘02_helpers.R’ ‘exports.R’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mrd_est.Rd: vcovHC
  mrd_impute.Rd: vcovHC
  rd_est.Rd: vcovHC
  rd_impute.Rd: vcovHC
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RDestimate.Rd: vcovHC, ivreg
Please provide package anchors for all Rd \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.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.
Specified C++11: please drop specification unless essential
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) 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
File ‘Rdsdp/libs/Rdsdp.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
    Object: ‘dsdp/lib/libdsdp.a’
  Found ‘printf’, possibly from ‘printf’ (C)
    Object: ‘dsdp/lib/libdsdp.a’
  Found ‘putchar’, possibly from ‘putchar’ (C)
    Object: ‘dsdp/lib/libdsdp.a’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘dsdp/lib/libdsdp.a’
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
    Object: ‘dsdp/lib/libdsdp.a’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘dsdp/lib/libdsdp.a’
  Found ‘vsprintf’, possibly from ‘vsprintf’ (C)
    Object: ‘dsdp/lib/libdsdp.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Missing dependency on R >= 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’ ‘process_tracing_estimator.Rd’
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.
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) 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.
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.
Specified C++11: please drop specification unless essential
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.
Malformed Description field: should contain one or more complete sentences.
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
Specified C++11: please drop specification unless essential
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:
    ‘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.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘redist.diagplot.Rd’ ‘redist.segcalc.Rd’
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.
File ‘rEDM/libs/rEDM.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Objects: ‘cppEDM/lib/libEDM.a’, ‘cppEDM/src/libEDM.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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{\"}).}
       |                                         ^
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".}}
       |                                  ^
Specified C++11: please drop specification unless essential
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.
Specified C++11: please drop specification unless essential
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:
  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.
Problems with news in ‘NEWS.md’:
No news entries found.
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’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) repo_build.Rd:44-47: Lost braces
    44 | ## chunk "item 1" {
       |                   ^
checkRd: (-1) repo_dependencies.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repo_dependencies.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repo_dependencies.Rd:51-53: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 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 calls to R: ‘OBJECT’, ‘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’
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:
    ‘compute_orbital_speeds.Rd’ ‘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’ ‘resp_distributions.Rd’ ‘resp_styles.Rd’
    ‘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:
    ‘as_result.Rd’ ‘bind.R’ ‘bind.Rd’ ‘result.R’ ‘result.Rd’
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.}
       |               ^
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
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
       |                                                                         ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘define_an_exercise.Rd’ ‘define_exercises.Rd’
    ‘define_exercises_from_csv.Rd’ ‘define_exercises_from_excel.Rd’
'::' or ':::' import not declared from: ‘Matrix’
'library' or 'require' call not declared from: ‘Matrix’
Missing dependency on R >= 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’
File ‘Rfast/libs/Rfast.so’:
  Found non-API call to R: ‘R_lsInternal’

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) 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.
Problems with news in ‘NEWS.md’:
No news entries found.
'library' or 'require' calls not declared from:
  ‘rpanel’ ‘tkrplot’
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.
Problems with news in ‘NEWS.md’:
No news entries found.
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.
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:
    ‘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")) {
       |                                                   ^
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.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  authorize.Rd: oauth2.0_token
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}
       |     ^
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.
Specified C++11: please drop specification unless essential
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) iex.chart.Rd:23: Lost braces; missing escapes or markup?
    23 | r takes only of of the values accepted IN API request. {"5y", "2y", "1y", "ytd", "6m", "3m", "1m", "1d"}
       |                                                        ^
checkRd: (-1) descrip.Rd:122: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:123: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:124-125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:126-128: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:129-133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:134-135: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:136-138: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:139-140: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:141-144: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:145-146: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:147: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:148: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:149: Lost braces in \itemize; \value handles \item{}{} directly
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.
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:
    ‘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:
  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}}
       |                                                                                                                                                                                                                                                   ^
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-release-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: ‘EXTPTR_PROT’, ‘EXTPTR_PTR’,
    ‘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.
Specified C++11: please drop specification unless essential
possible bashism in configure.ac line 36 (should be 'b = a'):
  if test x"${RSysinfoName}" == x"Darwin"; then
  possible bashism in configure.ac line 47 (should be 'b = a'):
  if test x"${hasOpenMP}" == x""; then
License stub is invalid DCF.
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:
    ‘higher_order_metadata.R’
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: ‘ENCLOS’, ‘OBJECT’, ‘PRENV’, ‘PRVALUE’,
    ‘R_PromiseExpr’, ‘Rf_allocSExp’, ‘Rf_findVarInFrame3’, ‘SETLENGTH’,
    ‘SET_BODY’, ‘SET_CLOENV’, ‘SET_ENCLOS’, ‘SET_FORMALS’,
    ‘SET_GROWABLE_BIT’, ‘SET_TRUELENGTH’, ‘SET_TYPEOF’, ‘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.
File ‘rlas/libs/rlas.so’:
  Found non-API call to R: ‘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:
  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’
File ‘rlibkriging/libs/rlibkriging.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Objects: ‘../inst/lib/libKriging.a’,
      ‘libK/build/src/lib/libKriging.a’
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Objects: ‘../inst/lib/libKriging.a’,
      ‘libK/build/src/lib/libKriging.a’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optimizeNewLambda
> ### Title: Perform factorization for new lambda value
> ### Aliases: optimizeNewLambda
> 
> ### ** Examples
> 
> pbmc <- normalize(pbmc)
ℹ Normalizing datasets "ctrl"
ℹ Normalizing datasets "stim"
✔ Normalizing datasets "stim" ... done

ℹ Normalizing datasets "ctrl"
✔ Normalizing datasets "ctrl" ... done

> pbmc <- selectGenes(pbmc)
ℹ Selecting variable features for dataset "ctrl"
✔ ... 168 features selected out of 249 shared features.
ℹ Selecting variable features for dataset "stim"
✔ ... 166 features selected out of 249 shared features.
✔ Finally 173 shared variable features are selected.
> pbmc <- scaleNotCenter(pbmc)
ℹ Scaling dataset "ctrl"
✔ Scaling dataset "ctrl" ... done

ℹ Scaling dataset "stim"
✔ Scaling dataset "stim" ... done

> if (requireNamespace("RcppPlanc", quietly = TRUE)) {
+     # Only running a few iterations for fast examples
+     pbmc <- runINMF(pbmc, k = 20, nIteration = 2)
+     pbmc <- optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2)
+ }
INMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 43773
Error: Must provide 2 V matrices
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
createLiger   5.659  0.197   7.074
calcAgreement 4.726  1.103   8.372
Specified C++11: please drop specification unless essential
checkRd: (-1) basic_GS.Rd:42: Lost braces; missing escapes or markup?
    42 | \eqn{L} and {U} are strictly lower/upper triangular matrix respectively.
       |             ^
checkRd: (-1) basic_SOR.Rd:45: Lost braces; missing escapes or markup?
    45 | \eqn{L} and {U} are strictly lower/upper triangular matrix respectively.
       |             ^
checkRd: (-1) basic_SSOR.Rd:45: Lost braces; missing escapes or markup?
    45 | \eqn{L} and {U} are strictly lower/upper triangular matrix respectively.
       |             ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  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}
       |                                                                   ^
Specified C++11: please drop specification unless essential
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) 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’
Problems with news in ‘NEWS.md’:
No news entries found.
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.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
File ‘Rmixmod/libs/Rmixmod.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘mixmod.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘decrypt.Rd’ ‘encrypt.Rd’ ‘encrypt_raw.Rd’
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.
Problems with news in ‘NEWS.md’:
No news entries found.
File ‘rmumps/libs/rmumps.so’:
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘lib/MUMPS_5.2.1/lib/libdmumps.a’,
      ‘lib/MUMPS_5.2.1/lib/libmumps_common.a’, ‘lib/libdmumps.a’,
      ‘lib/libmumps_common.a’
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘lib/MUMPS_5.2.1/lib/libdmumps.a’, ‘lib/libdmumps.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) myTarGetClientList.Rd:33: Lost braces
    33 | {MyTarget API Documenation}{https://target.my.com/doc/api/detailed/#resource_agency_clients}
       |                            ^
Malformed Title field: should not end in a period.
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: \_
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘compare_documents.Rd’ ‘term_char_sim.Rd’ ‘term_union.Rd’
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘projectRoads.Rd’
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
File ‘robfilter/libs/robfilter.so’:
  Found non-API call to R: ‘Rf_isFrame’

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:
  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.
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.
Specified C++11: please drop specification unless essential
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.
Problems with news in ‘NEWS.md’:
No news entries found.
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: \# \#
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) ROI_plugin_build_equality_constraints.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_equality_constraints.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:29: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_solve.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
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,
       |                                                   ^
Problems with news in ‘NEWS.md’:
No news entries found.
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}".}
       |                                                                                                                                                                                                                                                                                                                                                               ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  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
       |                                                  ^
Specified C++11: please drop specification unless essential
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
       |                                                              ^
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)
       |                                                         ^
Specified C++11: please drop specification unless essential
checkRd: (-1) psel.Rd:83: Lost braces; missing escapes or markup?
    83 | For example, a \code{top=1} preference selection on the tuples {(a=1, b=1), (a=1, b=2)}
       |                                                                ^
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.
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’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ionosphere.Rd’
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}
       |                      ^
Unknown package ‘Bchron’ in Rd xrefs
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.Rd’ ‘sort_tips.r’ ‘tips.r’ ‘validate_rankedPhylo.r’
Specified C++11: please drop specification unless essential
checkRd: (-1) mrrr.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:69-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:71-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:74: Lost braces in \itemize; meant \describe ?
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.
       |                                                                                                                                                          ^
File ‘RSclient/libs/RSclient.so’:
  Found non-API calls to R: ‘BODY’, ‘EXTPTR_PTR’, ‘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.
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-release-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: ‘BODY’, ‘FORMALS’, ‘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:
    ‘calculate_indices.Rd’ ‘get_stac_data.R’ ‘get_stac_data.Rd’
    ‘landsat_mask_function.Rd’
'library' or 'require' call not declared from: ‘plot3D’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  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’
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.
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.
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
       |                                                     ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘lp.Rd’
Specified C++11: please drop specification unless essential
Missing dependency on R >= 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_row.Rd’ ‘delete_selected_rows.Rd’ ‘for_each_col.Rd’ ‘redo.Rd’
    ‘set_calculation.Rd’ ‘set_column_defaults.Rd’ ‘set_editor.Rd’
    ‘set_formatter_color.Rd’ ‘set_formatter_datetime.Rd’
    ‘set_formatter_html.Rd’ ‘set_formatter_image.Rd’
    ‘set_formatter_link.Rd’ ‘set_formatter_money.Rd’
    ‘set_formatter_plaintext.Rd’ ‘set_formatter_progress.Rd’
    ‘set_formatter_star.Rd’ ‘set_formatter_textarea.Rd’
    ‘set_formatter_tick_cross.Rd’ ‘set_formatter_toggle_switch.Rd’
    ‘set_formatter_traffic_light.Rd’ ‘set_header_filter.Rd’
    ‘set_multi_column_header.Rd’ ‘set_options_group_by.Rd’
    ‘set_options_pagination.Rd’ ‘set_tooltip.Rd’ ‘tabulatorContext.Rd’
    ‘titanic.Rd’ ‘trigger_download.Rd’ ‘trigger_get_data.Rd’
    ‘trigger_get_sheet_data.Rd’ ‘undo.Rd’
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 ?
Specified C++11: please drop specification unless essential
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.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘str_rtl.Rd’
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) 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’ ‘stapi.Rd’ ‘tiles.R’
Specified C++11: please drop specification unless essential
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}}.
       |                                                                                                       ^
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘Tsttwalk.dat’
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.
Running examples in ‘rusquant-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getSymbols.Moex
> ### Title: Get financial data from MOEX Exchange
> ### Aliases: getSymbols.Moex
> 
> ### ** Examples
> 
> data <- getSymbols.Moex('GAZP', from='2022-01-01', to='2022-01-10', period='day', auto.assign=FALSE)
Error in if (engine == "stock" & market != "bonds") market <- "shares" : 
  missing value where TRUE/FALSE needed
Calls: getSymbols.Moex
Execution halted
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’
Problems with news in ‘NEWS.md’:
No news entries found.
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.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Malformed Title field: should not end in a period.
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’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘rxFun.Rd’
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.
Specified C++11: please drop specification unless essential
'library' or 'require' call not declared from: ‘Ryacas’
Specified C++14: please drop specification unless essential
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}}.}
       |                              ^
Specified C++14: please drop specification unless essential
Missing dependency on R >= 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.Rd’ ‘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.
File ‘S7/libs/S7.so’:
  Found non-API calls to R: ‘FORMALS’, ‘Rf_allocSExp’

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) 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.
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Missing dependency on R >= 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’ ‘dualFun1.Rd’
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
Specified C++11: please drop specification unless essential
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
checkRd: (-1) ModelHMMR-class.Rd:37: Lost braces; missing escapes or markup?
    37 |         class {StatHMMR}).
       |               ^
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:
    ‘cmc_psat.Rd’ ‘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.
Specified C++11: please drop specification unless essential
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.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘as_SpatRaster.Rd’ ‘clip_bands.Rd’ ‘get_band_names.Rd’
    ‘get_spatial_resolution.Rd’ ‘get_spectral_band_names.Rd’
    ‘merge_tiles.Rd’ ‘save_by_resolution.Rd’ ‘select_bands.Rd’
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 ?
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
'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.
License stub is invalid DCF.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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’
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.
Specified C++11: please drop specification unless essential
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.
Specified C++11: please drop specification unless essential
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.
Specified C++11: please drop specification unless essential
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.}
       |                                                                               ^
Missing dependency on R >= 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}
       |    ^
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.}
       |                 ^
Problems with news in ‘NEWS.md’:
No news entries found.
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.
Specified C++11: please drop specification unless essential
checkRd: (-1) msdpd.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hyperpar.Rd:17: Lost braces
    17 | \item{c}{denotes the expected range of eqn{f} .}
       |                                           ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘assign_meta_data.Rd’
Missing dependency on R >= 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"}.}
       |                                                                                                                                   ^
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’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘as.list.selenider_elements.Rd’ ‘elem_ancestors.Rd’ ‘elem_attr.Rd’
    ‘elem_cache.Rd’ ‘elem_click.Rd’ ‘elem_css_property.Rd’
    ‘elem_equal.Rd’ ‘elem_expect.Rd’ ‘elem_expect_all.Rd’
    ‘elem_filter.Rd’ ‘elem_flatten.Rd’ ‘elem_hover.Rd’ ‘elem_name.Rd’
    ‘elem_scroll_to.Rd’ ‘elem_select.Rd’ ‘elem_size.Rd’ ‘elem_text.Rd’
    ‘find_each_element.Rd’ ‘find_element.Rd’ ‘find_elements.Rd’
    ‘get_actual_element.Rd’ ‘s.Rd’
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.
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:
    ‘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.
Found the following significant warnings:
  Warning: replacing previous import ‘mgcv::lp’ by ‘gamlss::lp’ when loading ‘semsfa’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/semsfa.Rcheck/00install.out’ for details.
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.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
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.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                               ^
checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                                                          ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                              ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                                                     ^
Found the following files/directories:
  ‘assocpointpair_result.csv’ ‘foundereffectfinder_result.csv’
  ‘getfreqs_result.csv’ ‘getfreqs_result.png’ ‘orPlot.pdf1_1.pdf’
  ‘orPlot.pdf2_1.pdf’ ‘orPlot.pdf3_1.pdf’ ‘orPlot.pdf4_1.pdf’
  ‘orPlot.pdf5_1.pdf’ ‘orPlot.pdf6_1.pdf’ ‘orPlot.pdf7_1.pdf’
  ‘orPlot.pdf8_1.pdf’ ‘q-values_result.csv’ ‘rewritetuple_result.csv’
  ‘tartan_plot.pdf’ ‘vispair_plot.pdf’ ‘vispairfeat_plot.pdf’
  ‘volcano_plot.pdf’
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.
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:
    ‘Joiner.Rd’ ‘Splitter.Rd’ ‘add_node.Rd’ ‘print.sewage_pipeline.Rd’
    ‘pull_output.Rd’ ‘run.Rd’
Missing dependency on R >= 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.
Specified C++11: please drop specification unless essential
Missing dependency on R >= 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_curve.Rd’ ‘sfc_4x4_meander.Rd’ ‘sfc_generator.Rd’
    ‘spacefilling.Rd’
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’
Specified C++11: please drop specification unless essential
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.
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sgat)
  > 
  > test_check("sgat")
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 1 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test-initialization_sgat.R:1:1', 'test-sgat.R:1:1',
    'test-sgat_day.R:1:1', 'test-tripadvisor_places.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-ushuaia_restaurants.R:3:3'): gives vector ────────────────────
  length(restaurants) is not strictly more than 100. Difference: -25
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 1 ]
  Error: Test failures
  Execution halted
'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.
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.}
       |                    ^
Missing dependency on R >= 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.
       |                                                                                                    ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘lottie_addEventListener.Rd’ ‘lottie_button.Rd’
    ‘lottie_removeEventListener.Rd’
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}
       |            ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘fabs.Rd’
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.
Problems with news in ‘NEWS.md’:
No news entries found.
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 ?
Problems with news in ‘NEWS.md’:
No news entries found.
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’
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’
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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘slimSelectInput.Rd’
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.
Specified C++11: please drop specification unless essential
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
       |              ^
Specified C++11: please drop specification unless essential
Missing dependency on R >= 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.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) sig.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
Found the following files/directories:
  ‘ExportFigtree1.tre’
Missing dependency on R >= 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 ?
checkRd: (-1) sim_Y_Binary_X.Rd:51: Lost braces
    51 |     \item \code{dist = "binomial"} is drawn from eqn{Bin(XB, XB(1-XB))}
       |                                                     ^
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.
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’ ‘bootstrap_CIs.Rd’ ‘bundle_sim.R’
    ‘calc_coverage.R’ ‘calc_rejection.R’ ‘extrapolate_coverage.Rd’
    ‘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.
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’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘si_calculate.Rd’
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’ ‘anonymise.Rd’
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’
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.
Specified C++11: please drop specification unless essential
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘glimpse_na.Rd’
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’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘addCorGen.Rd’
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.
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
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:
  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 ?
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Missing dependency on R >= 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.
       |                                                                                                  ^
Malformed Description field: should contain one or more complete sentences.
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.
       |                                        ^
Missing dependency on R >= 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.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘prop.Rd’
Missing dependency on R >= 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:
  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’
    ‘calculate_power_curves.Rd’ ‘eval_design_custom_mc.R’
    ‘eval_design_survival_mc.R’ ‘skprGUI.R’
Specified C++11: please drop specification unless essential
checkRd: (-1) outliers.hdts.Rd:44: Lost braces; missing escapes or markup?
    44 |   \item I.cov.rob - The matrix (V'GnV)^{-1} used to compute the statistics to detect the idiosyncratic outliers.
       |                                        ^
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
       |                                                                                     ^
File ‘slider/libs/slider.so’:
  Found non-API call to R: ‘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:
  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] +
       |          ^
Problems with news in ‘NEWS.md’:
No news entries found.
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. 
       |                         ^
Problems with news in ‘NEWS.md’:
No news entries found.
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.
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
File ‘smcryptoR/libs/smcryptoR.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
    Object: ‘smcrypto/target/release/libsmcrypto.a’
  Found ‘abort’, possibly from ‘abort’ (C)
    Object: ‘smcrypto/target/release/libsmcrypto.a’
  Found ‘exit’, possibly from ‘exit’ (C)
    Object: ‘smcrypto/target/release/libsmcrypto.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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},....}
       |                                                                                ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) SMMA.Rd:115: Lost braces
   115 |  is the empirical explained variance from \cite{Meinshausen and B{u}hlmann, 2015}.  See \cite{Lund et al., 2020} for more details and references.
       |                                                                  ^
checkRd: (-1) SMMA.Rd:170: Lost braces
   170 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
Specified C++11: please drop specification unless essential
checkRd: (-1) estimMk.Rd:44: Lost braces; missing escapes or markup?
    44 | estimMk returns the transition probability matrix of size (S^{k})xS (with S = length(E)) 
       |                                                              ^
Specified C++11: please drop specification unless essential
checkRd: (-1) getKernel.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getKernel.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smoof_function.Rd:10: Lost braces
    10 | or code{smoof_multi_objective_function}. Both single- and multi-objective functions share the following attributes.
       |        ^
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.
Problems with news in ‘NEWS.md’:
No news entries found.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
Found the following files/directories:
  ‘my_new_social_media_plot.png’
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’
    ‘sk_plot.Rd’ ‘sk_sub.Rd’ ‘sk_var.Rd’ ‘sk_var_mult.Rd’
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                  ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                           ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                                      ^
checkRd: (-1) sk_GLS.Rd:40: Lost braces; missing escapes or markup?
    40 | Operations with V^{-1} are computed using the factorization \code{fac} (see \code{sk_var}), or
       |                   ^
checkRd: (-1) sk_LL.Rd:37: Lost braces; missing escapes or markup?
    37 | \code{quad_form} is z^T V^{-1} z, for the observed response vector z, which is constructed
       |                           ^
checkRd: (-1) sk_var.Rd:41: Lost braces; missing escapes or markup?
    41 | returns the quadratic form X^T V^{-1} X.
       |                                  ^
checkRd: (-1) sk_var.Rd:33: Lost braces; missing escapes or markup?
    33 | either matrix \code{V}, or X^T V^{-1} X, or a factorization ('chol' or 'eigen')
       |                                  ^
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
checkRd: (-1) knockoffGenotypes.Rd:32: Lost braces; missing escapes or markup?
    32 | This function efficiently constructs group-knockoffs of {0,1,2} variables distributed
       |                                                         ^
checkRd: (-1) knockoffGenotypes.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{X}{a {0,1,2} matrix of size n-by-p containing the original variables.}
       |            ^
checkRd: (-1) knockoffGenotypes.Rd:29: Lost braces; missing escapes or markup?
    29 | A {0,1,2} matrix of size n-by-p containing the knockoff variables.
       |   ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘gtable_ld_associations_combine.Rd’ ‘gtable_ld_grobs.Rd’
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’ ‘doRanking.Rd’
    ‘elementLookup.Rd’ ‘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’
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:
    ‘soundSpeed.Rd’
Missing dependency on R >= 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 ?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘SouthPark_Script_Data.Rd’ ‘app_server.R’
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.
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
       |                             ^
Specified C++11: please drop specification unless essential
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.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
checkRd: (-1) Coord.to.Pointers.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{triangle=TRUE}{Input \code{rows} and {cols} represent lower
       |                                            ^
checkRd: (-1) Coord.to.Pointers.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{triangle=FALSE}{Input \code{rows} and {cols} represent a full
       |                                             ^
checkRd: (-1) cholsolveAQinvAT.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Solve the equation X = AQ^{-1}t(A) under permutations}
       |                                  ^
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.
Missing dependency on R >= 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’
Missing dependency on R >= 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’
Specified C++11: please drop specification unless essential
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’
Specified C++14: please drop specification unless essential
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.
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: \$
Missing dependency on R >= 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’
Specified C++11: please drop specification unless essential
Missing dependency on R >= 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’
Specified C++11: please drop specification unless essential
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
    61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc}, 
       |                                                   ^
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})
       |                                                                                                                                                                  ^
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes