Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'learnr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tomas Johannesson <tj@vedur.is>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Tomas", "Johannesson", "&", "Halldor"),
                      family = "Bjornsson",
                      role = "aut"),
               person(given = c("Icelandic", "Met.", "Office;", "Gabor"),
                      family = "Grothendieck",
                      role = "aut"),
               person(given = "Tomas",
                      family = "Johannesson",
                      role = "cre",
                      email = "tj@vedur.is"))
as necessary.
Maintainer: ‘Dan Zangri <dzangri@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dan",
                      family = "Zangri",
                      role = c("aut", "cre"),
                      email = "dzangri@gmail.com"),
               person(given = "Dustin",
                      family = "Tingley",
                      role = "ctb"),
               person(given = "Brandon",
                      family = "Stewart",
                      role = "ctb"))
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘stmgui-package.Rd’:
    \keyword{ stm, shiny }
Package required but not available: ‘stm’

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

Packages suggested but not available for checking:
  'quanteda', 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Andres Villegas <andresmauriciovillegas@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Andres",
                      family = "Villegas",
                      role = c("aut", "cre"),
                      email = "andresmauriciovillegas@gmail.com"),
               person(given = "Pietro",
                      family = "Millossovich",
                      role = "aut",
                      email = "Pietro.Millossovich.1@city.ac.uk"),
               person(given = "Vladimir",
                      family = "Kaishev",
                      role = "aut",
                      email = "Vladimir.Kaishev.1@city.ac.uk"))
as necessary.

Found the following (possibly) invalid file URI:
  URI: www.mortality.org
    From: man/EWMaleData.Rd
Cannot process vignettes
Packages suggested but not available for checking:
  'demography', 'knitr', 'MTS'

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘Matthias Salvisberg <matthias.salvisberg@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Matthias",
                    family = "Salvisberg",
                    role = c("aut", "cre"),
                    email = "matthias.salvisberg@gmail.com")
as necessary.
Specified C++11: support will be removed soon
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘quanteda’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Devin S. Johnson <devin.johnson@noaa.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Devin", "S."),
                    family = "Johnson",
                    role = c("aut", "cre"),
                    email = "devin.johnson@noaa.gov")
as necessary.
Maintainer: ‘Grant Humphries <grwhumphries@blackbawks.net>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'spelling', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Author field differs from that derived from Authors@R
  Author:    ‘Grant Humphries [aut, cre] (<https://orcid.org/0000-0001-5783-9892>), Bruno Caneco [aut], Aonghais Cook [aut], Elizabeth Masden [aut], Marine Scotland [fnd, cph], HiDef [cph], DMPstats [cph], Kelly Street [rev] (@kstreet13)’
  Authors@R: ‘Grant Humphries [aut, cre] (ORCID: <https://orcid.org/0000-0001-5783-9892>), Bruno Caneco [aut], Aonghais Cook [aut], Elizabeth Masden [aut], Marine Scotland [fnd, cph], HiDef [cph], DMPstats [cph], Kelly Street [rev] (GITHUB: @kstreet13)’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘David Cortes <david.cortes.rivera@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "David",
                    family = "Cortes",
                    role = c("aut", "cre"),
                    email = "david.cortes.rivera@gmail.com")
as necessary.

The Description field contains
  2016 <arXiv:1401.7020>), adaQN (adaptive quasi-Newton) (Keskar, N.S.,
  Berahas, A.S., 2016, <arXiv:1511.01169>).  Provides functions for
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package suggested but not available for checking: ‘knitr’

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/article.Rnw’
   ‘inst/doc/article2.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'fGarch', 'fBasics'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/stockR.rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Dane R. Van Domelen <vandomed@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Dane", "R."),
                    family = "Van Domelen",
                    role = c("aut", "cre"),
                    email = "vandomed@gmail.com")
as necessary.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘stocks.Rd’:
    https://doi.org/10.7287/peerj.preprints.3188v1
Packages required but not available: 'dvmisc', 'Hmisc'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'printr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Peter Reichert <peter.reichert@emeriti.eawag.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Peter",
                    family = "Reichert",
                    role = c("aut", "cre"),
                    email = "peter.reichert@emeriti.eawag.ch")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'tidyverse', 'knitr', 'rmarkdown', 'gt', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘stpp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Allen Day <allenday@allenday.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Allen",
                    family = "Day",
                    role = c("aut", "cre"),
                    email = "allenday@allenday.com")
as necessary.
Malformed Title field: should not end in a period.
Maintainer: ‘Thomas Arsouze <thomas.arsouze@cirad.fr>’

The BugReports field in DESCRIPTION has
  https://github.com/umr-amap/StormR/issues/new/choose
which should likely be
  https://github.com/umr-amap/StormR/issues/new/choose/issues
instead.
Package required but not available: ‘leaflet’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘tidyjson’

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Deniz Akdemir <deniz.akdemir.work@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Deniz",
                    family = "Akdemir",
                    role = c("aut", "cre"),
                    email = "deniz.akdemir.work@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'leaflet', 'rmarkdown', 'rsgeo', 'tmap'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "I.",
                      family = "Zhbannikov",
                      role = "aut"),
               person(given = "Liang",
                      family = "He",
                      role = "aut"),
               person(given = "K.",
                      family = "Arbeev",
                      role = "aut"),
               person(given = "I.",
                      family = "Akushevich",
                      role = "aut"),
               person(given = "A.",
                      family = "Yashin.",
                      role = "aut"),
               person(given = c("Ilya", "Y."),
                      family = "Zhbannikov",
                      role = "cre",
                      email = "ilya.zhbannikov@duke.edu"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Edith Gabriel <edith.gabriel@inrae.fr>’

The BugReports field in DESCRIPTION has
  https://github.com/stpp-GitHub-community
which should likely be
  https://github.com/stpp-GitHub-community/issues
instead.
Package required but not available: ‘rgl’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Monsuru Adepeju <monsuur2010@yahoo.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Monsuru",
                    family = "Adepeju",
                    role = c("cre", "aut"),
                    email = "monsuur2010@yahoo.com")
as necessary.

The BugReports field in DESCRIPTION has
  https://github.com/Manalytics/stppSim/issues/new/choose
which should likely be
  https://github.com/Manalytics/stppSim/issues/new/choose/issues
instead.
Package required but not available: ‘leaflet’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Samuel Soubeyrand <samuel.soubeyrand@inra.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(family = "Soubeyrand",
                      role = "aut"),
               person(family = "S.",
                      role = "aut"),
               person(family = "Tollenaere",
                      role = "aut"),
               person(family = "C.",
                      role = "aut"),
               person(family = "Haon-Lasportes",
                      role = "aut"),
               person(family = "E.",
                      role = "aut"),
               person(family = "Laine",
                      role = "aut"),
               person(family = "A.-L.",
                      role = "aut"),
               person(given = "Samuel",
                      family = "Soubeyrand",
                      role = "cre",
                      email = "samuel.soubeyrand@inra.fr"))
as necessary.
checkRd: (-1) powderymildew.Rd:14-16: Lost braces
    14 | \code{$demographic.coord}{
       |                          ^
checkRd: (-1) powderymildew.Rd:18-20: Lost braces
    18 | \code{$genetic.coord}{
       |                      ^
checkRd: (-1) powderymildew.Rd:22-24: Lost braces
    22 | \code{$demographic.measures}{
       |                             ^
checkRd: (-1) powderymildew.Rd:26-28: Lost braces
    26 | \code{$genetic.frequencies}{
       |                            ^
Package required but not available: ‘yaml’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'DT', 'flextable', 'plotly'

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Rachael C. Aikens <rockyaikens@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jose Brito <jambrito@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jose",
                      family = "Brito",
                      role = c("aut", "cre"),
                      email = "jambrito@gmail.com"),
               person(given = "Pedro",
                      family = "Silva",
                      role = "aut"),
               person(given = "Tomas",
                      family = "Veiga",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Miles Ott <miles_ott@alumni.brown.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Miles",
                    family = "Ott",
                    role = c("aut", "cre"),
                    email = "miles_ott@alumni.brown.edu")
as necessary.
Maintainer: ‘Julian Busch <jb@quants.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Julian",
                    family = "Busch",
                    role = c("aut", "cre"),
                    email = "jb@quants.ch")
as necessary.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Found the following files/directories:
  ‘myNewStrat.R’
Maintainer: ‘Michael Heath <m.heath@strath.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Michael",
                      family = "Heath",
                      role = c("aut", "cre"),
                      email = "m.heath@strath.ac.uk"),
               person(given = "Ian",
                      family = "Thurlbeck",
                      role = "ctb"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'StrathE2E2examples'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) StrathE2E2-package.Rd:70: Lost braces; missing escapes or markup?
    70 | {Basic model operations:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:79: Lost braces; missing escapes or markup?
    79 | {Parameter estimation:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:88: Lost braces; missing escapes or markup?
    88 | {Sensitivity and Monte Carlo analyses:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:98: Lost braces; missing escapes or markup?
    98 | {Compare model runs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:105: Lost braces; missing escapes or markup?
   105 | {Fishery yield analysis:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:111: Lost braces; missing escapes or markup?
   111 | {Visualize model inputs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:117: Lost braces; missing escapes or markup?
   117 | {Visualize model outputs:} \cr
       | ^
Maintainer: ‘Amr ElRafey <aelrafey@gmu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Farrokh",
                      family = "Alemi",
                      role = "aut",
                      email = "falemi@gmu.edu"),
               person(given = "Amr",
                      family = "ElRafey",
                      role = c("aut", "cre"),
                      email = "aelrafey@gmu.edu"))
as necessary.
Maintainer: ‘Thomas Jemielita <thomasjemielita@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thomas",
                    family = "Jemielita",
                    role = c("aut", "cre"),
                    email = "thomasjemielita@gmail.com")
as necessary.

The Description field contains
  2019 <arXiv:1912.03337>. This package is in beta and will be
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘David Cortes <david.cortes.rivera@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "David",
                    family = "Cortes",
                    role = c("aut", "cre"),
                    email = "david.cortes.rivera@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Sebastien Wouters <wouterseb@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Sebastien",
                      family = "Wouters",
                      role = c("aut", "cre"),
                      email = "wouterseb@gmail.com"),
               person(given = c("Adam", "D."),
                      family = "Smith",
                      role = "ctb"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'FossilSim', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Xiang Zhou <xiang_zhou@fas.harvard.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘Hmisc’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Xiangdong Gu <ustcgxd@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xiangdong",
                      family = "Gu",
                      role = c("aut", "cre"),
                      email = "ustcgxd@gmail.com"),
               person(given = "Raji",
                      family = "Balasubramanian",
                      role = "aut"))
as necessary.
Maintainer: ‘Priyanga Dilini Talagala <pritalagala@gmail.com>’

The Description field contains
  <arXiv:1908.04000> for detecting anomalies in high-dimensional data
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Korbinian Strimmer <strimmerlab@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rainer",
                      family = "Opgen-Rhein",
                      role = "aut"),
               person(given = "Verena",
                      family = "Zuber",
                      role = "aut"),
               person(given = "Korbinian",
                      family = "Strimmer.",
                      role = "aut"),
               person(given = "Korbinian",
                      family = "Strimmer",
                      role = "cre",
                      email = "strimmerlab@gmail.com"))
as necessary.
Packages required but not available: 'Seurat', 'SPECK'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Nele Schuwirth <nele.schuwirth@eawag.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Nele",
                      family = "Schuwirth",
                      role = c("aut", "cre"),
                      email = "nele.schuwirth@eawag.ch"),
               person(given = "Peter",
                      family = "Reichert",
                      role = "aut"),
               person(given = "Mikolaj",
                      family = "Rybinski",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'mapview', 'knitr', 'rmarkdown', 'devtools'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown', 'devtools'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/alpha-centrality.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘apportion_inverse.R’ ‘apportion_polygon.R’ ‘apportion_web.R’
    ‘prep_reach_dist.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Stephen A Sefick Jr. <ssefick@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Stephen", "A"),
                    family = "Sefick Jr.",
                    role = c("aut", "cre"),
                    email = "ssefick@gmail.com")
as necessary.
Maintainer: ‘Michael Hahsler <mhahsler@lyle.smu.edu>’

The BugReports field in DESCRIPTION has
  https://github.com/mhahsler/streamMOA
which should likely be
  https://github.com/mhahsler/streamMOA/issues
instead.
Package required but not available: ‘rJava’

Package suggested but not available for checking: ‘RMOA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Pablo Barbera <pablo.barbera@nyu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Pablo",
                    family = "Barbera",
                    role = c("aut", "cre"),
                    email = "pablo.barbera@nyu.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘mapview’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Sebastian Henz <bastihz.dev@posteo.de>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘ecxsys.Rd’:
    https://doi.org/10.1038/s41598-019-51645-4
  File ‘multi_tox.Rd’:
    https://doi.org/10.1186/s12302-020-00394-7
  File ‘multiple_stress.Rd’:
    https://doi.org/10.1021/acs.est.9b04293
    https://doi.org/10.1186/s12302-020-00394-7
  File ‘stressaddition-package.Rd’:
    https://doi.org/10.1038/s41598-019-51645-4
    https://doi.org/10.1186/s12302-020-00394-7
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Matt Barry <mrb@softisms.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Matt",
                    family = "Barry",
                    role = c("aut", "cre"),
                    email = "mrb@softisms.com")
as necessary.
Malformed Title field: should not end in a period.
Maintainer: ‘Alessandro Barbiero <alessandro.barbiero@unimi.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alessandro",
                      family = "Barbiero",
                      role = c("aut", "cre"),
                      email = "alessandro.barbiero@unimi.it"),
               person(given = "Riccardo",
                      family = "Inchingolo",
                      role = "aut",
                      email = "dott.inchingolo_r@libero.it"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Specified C++11: support will be removed soon
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tom Drake <t.drake@ed.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tom",
                    family = "Drake",
                    role = c("aut", "cre"),
                    email = "t.drake@ed.ac.uk")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'usethis'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Alexander Hoyle <alexander@alexanderhoyle.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alexander",
                    family = "Hoyle",
                    role = c("aut", "cre"),
                    email = "alexander@alexanderhoyle.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'gt', 'htmlwidgets', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Bert Gunter <bgunter@comcast.net>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘strucplot.Rd’:
    \concept{
      structured plots,structured trellis plot [TRUNCATED]
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rlist’

Package suggested but not available for checking: ‘knitr’

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling', 'usethis', 'pak', 'roxygen2',
  'devtools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'demography', 'knitr', 'rgl', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
Maintainer: ‘Moritz Berger <Moritz.Berger@imbie.uni-bonn.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Moritz",
                    family = "Berger",
                    role = c("aut", "cre"),
                    email = "moritz.berger@imbie.uni-bonn.de")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yifu Liu <2012johnnyliu@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yifu",
                      family = "Liu",
                      role = c("aut", "cre"),
                      email = "2012johnnyliu@gmail.com"),
               person(given = "Anru",
                      family = "Zhang",
                      role = "aut"))
as necessary.
Packages required but not available: 'DT', 'plotly'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/vignette.Rnw’
(Is a VignetteBuilder field missing?)

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘quanteda’

Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘I. Manjula Schou <im.schou@yahoo.com.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("I.", "Manjula"),
                    family = "Schou",
                    role = c("aut", "cre"),
                    email = "im.schou@yahoo.com.au")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jerome Collet <jeromepcollet@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jerome",
                    family = "Collet",
                    role = c("aut", "cre"),
                    email = "jeromepcollet@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'DT', 'bsplus', 'colourpicker'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

Packages suggested but not available for checking: 'gam', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Andrew Chapple <achapp@lsuhsc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Andrew",
                    family = "Chapple",
                    role = c("aut", "cre"),
                    email = "achapp@lsuhsc.edu")
as necessary.
Maintainer: ‘Junwei Han <hanjunwei1981@163.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xudong",
                      family = "Han",
                      role = "aut"),
               person(given = "Junwei",
                      family = "Han",
                      role = c("aut", "cre"),
                      email = "hanjunwei1981@163.com"),
               person(given = "Chonghui",
                      family = "Liu",
                      role = "aut"))
as necessary.
Package required but not available: ‘ChemmineR’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Scott Barlowe <sabarlowe@email.wcu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Scott",
                    family = "Barlowe",
                    role = c("aut", "cre"),
                    email = "sabarlowe@email.wcu.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'DT', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Bill Venables <Bill.Venables@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Bill",
                    family = "Venables",
                    role = c("aut", "cre"),
                    email = "Bill.Venables@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘David Brahm <brahm@alum.mit.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "David",
                      family = "Brahm",
                      role = c("aut", "cre"),
                      email = "brahm@alum.mit.edu"),
               person(given = "Greg",
                      family = "Snow",
                      role = "aut",
                      email = "Greg.Snow@intermountainmail.org"),
               person(given = c("with", "contributions", "from", "Curt"),
                      family = "Seeliger",
                      role = "aut",
                      email = "Seeliger.Curt@epamail.epa.gov"),
               person(given = "Henrik",
                      family = "Bengtsson.",
                      role = "aut",
                      email = "hb@maths.lth.se"))
as necessary.
Package required but not available: ‘gam’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Dianne Cook <dicook@monash.edu>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'pkgdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) fp19.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:12-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:25: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse', 'kableExtra', 'ggiraph'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘geom_glyph_ribbon.R’ ‘geom_glyph_ribbon.Rd’ ‘geom_glyph_segment.Rd’
    ‘theme_glyph.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) suggests.Rd:14: Lost braces; missing escapes or markup?
    14 | {suggests} aims to make that workflow as minimal and painless as possible,
       | ^
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'plotly', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ting-Huei Chen <tingstat22@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ting-Huei",
                    family = "Chen",
                    role = c("aut", "cre"),
                    email = "tingstat22@gmail.com")
as necessary.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SummaryLasso.Rcheck/00install.out’ for details.
Packages required but not available: 'Hmisc', 'gtsummary', 'flextable'

Packages suggested but not available for checking: 'knitr', 'tidyverse'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘shadowtext’

Packages suggested but not available for checking:
  'INLA', 'knitr', 'rmarkdown'

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

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

Package suggested but not available for checking: ‘flextable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Anna Vesely <anna.vesely@phd.unipd.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Anna",
                    family = "Vesely",
                    role = c("aut", "cre"),
                    email = "anna.vesely@phd.unipd.it")
as necessary.

The Description field contains
  may be found in Vesely, Finos, and Goeman (2020) <arXiv:2102.11759>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Running examples in ‘sumup-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: run_sumup
> ### Title: Run Sum Up
> ### Aliases: run_sumup
> 
> ### ** Examples
> 
> data(example_data)
> ex_data <- example_data
> ex_settings  <- set_default_settings()
> ex_settings  <- update_setting(ex_settings , "language", "en")
> ex_settings  <- update_setting(ex_settings , "use_sentiment_analysis", "sentimentr")
> result <- run_sumup(ex_data, ex_settings )
UDPipe model not available. Please download manually using udpipe_download_model() and set setting udpipe_model_file if you want to use that.
Sum-up continues running with an alternative tagging package.
Error in alternative_tagging(sentences) : 
  Please install tokenizers, textstem, and openNLP packages.
Calls: run_sumup -> lemmatize -> alternative_tagging
Execution halted
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2', 'covr', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Roel Braekers <roel.braekers@uhasselt.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Leen",
                      family = "Prenen",
                      role = "aut"),
               person(given = "Roel",
                      family = "Braekers",
                      role = c("aut", "cre"),
                      email = "roel.braekers@uhasselt.be"),
               person(given = "Luc",
                      family = "Duchateau",
                      role = "aut"),
               person(given = "Ewoud",
                      family = "De Troyer",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Martin Maechler <maechler@stat.math.ethz.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Marcel",
                      family = "Dettling",
                      role = "aut",
                      email = "marcel.dettling@zhaw.ch"),
               person(given = "Martin",
                      family = "Maechler",
                      role = c("aut", "cre"),
                      email = "maechler@stat.math.ethz.ch"))
as necessary.
Maintainer: ‘Tatsiana Khamiakova <t.tavita@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tatsiana",
                    family = "Khamiakova",
                    role = c("aut", "cre"),
                    email = "t.tavita@gmail.com")
as necessary.
checkRd: (-1) BiclustSet-class.Rd:19: Lost braces
    19 |     \item{\code{Number}:}{code{"numeric"}, number of biclusters in the set}
       |                               ^
Cannot process vignettes
Packages suggested but not available for checking:
  'fMultivar', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'weights', 'Hmisc'

Packages suggested but not available for checking:
  'Seurat', 'knitr', 'rmarkdown', 'velocyto.R'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Le Bao <lbaole17@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(family = "Le Bao",
                      role = c("aut", "cre"),
                      email = "lbaole17@gmail.com"),
               person(given = "Jeff",
                      family = "Gill",
                      role = "aut",
                      email = "jgill@mac.com"),
               person(given = "Tsung-han",
                      family = "Tsai",
                      role = "aut",
                      email = "thtsai@nccu.edu.tw"),
               person(given = "Jonathan",
                      family = "Rapkin",
                      role = "aut"))
as necessary.
Maintainer: ‘Minghui Wang <minghui.wang@mssm.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Minghui",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "minghui.wang@mssm.edu"),
               person(given = "Yongzhong",
                      family = "Zhao",
                      role = "aut"),
               person(given = "Bin",
                      family = "Zhang",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) plot.Rd:42: Lost braces; missing escapes or markup?
    42 |  \item{color.off}{color code; specifying the color for set(s) which are "{absent}" for an intersection.}
       |                                                                          ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘gam’

Packages suggested but not available for checking:
  'bartMachine', 'devtools', 'knitr', 'prettydoc', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jean-Eudes Dazard <jean-eudes.dazard@case.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Hideo Aizaki <azk-r@spa.nifty.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hideo",
                    family = "Aizaki",
                    role = c("aut", "cre"),
                    email = "azk-r@spa.nifty.com")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Hideo Aizaki <azk-r@spa.nifty.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hideo",
                    family = "Aizaki",
                    role = c("aut", "cre"),
                    email = "azk-r@spa.nifty.com")
as necessary.
Maintainer: ‘Hideo Aizaki <azk-r@spa.nifty.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hideo",
                    family = "Aizaki",
                    role = c("aut", "cre"),
                    email = "azk-r@spa.nifty.com")
as necessary.
Maintainer: ‘Hideo Aizaki <azk-r@spa.nifty.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hideo",
                    family = "Aizaki",
                    role = c("aut", "cre"),
                    email = "azk-r@spa.nifty.com")
as necessary.
Package required but not available: ‘rmarkdown’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ethan Alt <ethanalt@live.unc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ethan",
                    family = "Alt",
                    role = c("aut", "cre"),
                    email = "ethanalt@live.unc.edu")
as necessary.
Package required but not available: ‘rlist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) getFittedProbs.Rd:6-8: Lost braces
     6 | getFittedValues <- function(object) {
       |                                     ^
checkRd: (-1) getFittedProbs.Rd:14-16: Lost braces
    14 | getFittedValues <- function(object) {
       |                                     ^
Packages required but not available: 'FactoMineR', 'factoextra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'matlib', 'clusterProfiler', 'tidyverse', 'DT'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘Layla Parast <parast@austin.utexas.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Layla",
                    family = "Parast",
                    role = c("aut", "cre"),
                    email = "parast@austin.utexas.edu")
as necessary.
Maintainer: ‘Yunro Chung <yunro.chung@asu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yunro",
                    family = "Chung",
                    role = c("cre", "aut"),
                    email = "yunro.chung@asu.edu")
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘surrosurvROC-package.Rd’:
    \keyword{biomarkers, inverse probability weighing, [TRUNCATED]
  File ‘surrosurvROC.Rd’:
    \keyword{biomarkers, inverse probability weighing, [TRUNCATED]
Maintainer: ‘Miki Horiguchi <horiguchimiki@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Lu",
                      family = "Tian",
                      role = "aut"),
               person(given = "Hajime",
                      family = "Uno",
                      role = "aut"),
               person(given = "Miki",
                      family = "Horiguchi",
                      role = c("aut", "cre"),
                      email = "horiguchimiki@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Miki Horiguchi <horiguchimiki@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Miki",
                      family = "Horiguchi",
                      role = c("aut", "cre"),
                      email = "horiguchimiki@gmail.com"),
               person(given = "Hajime",
                      family = "Uno",
                      role = "aut"))
as necessary.
Maintainer: ‘Joao Pinto <joao.pinto@tecnico.ulisboa.pt>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Joao",
                      family = "Pinto",
                      role = c("aut", "cre"),
                      email = "joao.pinto@tecnico.ulisboa.pt"),
               person(given = "Andre",
                      family = "Verissimo",
                      role = "aut",
                      email = "andre.verissimo@tecnico.ulisboa.pt"),
               person(given = "Alexandra",
                      family = "Carvalho",
                      role = "aut",
                      email = "alexandra.carvalho@tecnico.ulisboa.pt"),
               person(given = "Susana",
                      family = "Vinga",
                      role = "aut",
                      email = "susanavinga@tecnico.ulisboa.pt"))
as necessary.
Maintainer: ‘Hajime Uno <huno@jimmy.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hajime",
                    family = "Uno",
                    role = c("aut", "cre"),
                    email = "huno@jimmy.harvard.edu")
as necessary.
Packages required but not available: 'timeROC', 'randomForestSRC'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages suggested but not available for checking: 'INLA', 'knitr'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/hhh4_spacetime.Rnw’
   ‘inst/doc/monitoringCounts.Rnw’
   ‘inst/doc/twinSIR.Rnw’
   ‘inst/doc/twinstim.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Guo-You Lan <jj6020770416jj@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hsin-wen",
                    family = "Chang",
                    role = c("aut", "cre"),
                    email = "hwchang@stat.sinica.edu.tw")
as necessary.
Package required but not available: ‘pec’

Packages suggested but not available for checking:
  'covr', 'knitr', 'randomForestSRC', 'rmarkdown', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'SHELF', 'survminer'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘candisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘DT’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'spelling'

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

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

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

Packages suggested but not available for checking: 'knitr', 'leaflet'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'SUMMER', 'tidyverse'

Packages suggested but not available for checking:
  'INLA', 'knitr', 'rmarkdown', 'kableExtra'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'gt', 'kableExtra', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'roxygen2', 'rmarkdown', 'gurobi'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'rms', 'xlsx'

Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Hajime Uno <huno@jimmy.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hajime",
                      family = "Uno",
                      role = c("aut", "cre"),
                      email = "huno@jimmy.harvard.edu"),
               person(given = "Tianxi",
                      family = "Cai",
                      role = "aut"))
as necessary.
Maintainer: ‘Marta Sestelo <sestelo@uvigo.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Luis",
                      family = "Meira-Machado",
                      role = "aut"),
               person(given = "Marta",
                      family = "Sestelo",
                      role = c("aut", "cre"),
                      email = "sestelo@uvigo.es"),
               person(given = "Gustavo",
                      family = "Soutinho",
                      role = "aut"))
as necessary.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) coxph_mpl_dc.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{mpl_h0t}{MPL estimates of the baseline hazard for T, i.e. h_{0T}(x_i)}
       |                                                                   ^
checkRd: (-1) coxph_mpl_dc.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{mpl_h0c}{MPL estimates of the baseline hazard for C, i.e. h_{0C}(x_i)}
       |                                                                   ^
checkRd: (-1) coxph_mpl_dc.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{mpl_H0t}{MPL estimates of the baseline cumulative hazard for T, i.e. H_{0T}(x_i)}
       |                                                                              ^
checkRd: (-1) coxph_mpl_dc.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{mpl_H0c}{MPL estimates of the baseline cumulative hazard for C, i.e. H_{0c}(x_i)}
       |                                                                              ^
checkRd: (-1) coxph_mpl_dc.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{mpl_S0t}{MPL estimates of the baseline survival for T, i.e. S_{0T}(x_i)}
       |                                                                     ^
checkRd: (-1) coxph_mpl_dc.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{mpl_S0c}{MPL estimates of the baseline survival for C, i.e. S_{0C}(x_i)}
       |                                                                     ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘RISCA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Paramita Saha-Chaudhuri <paramita.sahachaudhuri.work@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Patrick", "J."),
                      family = "Heagerty",
                      role = "aut",
                      email = "heagerty@u.washington.edu"),
               person(given = c("packaging", "by", "Paramita"),
                      family = "Saha-Chaudhuri",
                      role = "aut",
                      email = "paramita.sahachaudhuri.work@gmail.com"),
               person(given = "Paramita",
                      family = "Saha-Chaudhuri",
                      role = "cre",
                      email = "paramita.sahachaudhuri.work@gmail.com"))
as necessary.
Packages required but not available: 'randomForestSRC', 'survivalPLANN'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Michael Komodromos <mk1019@ic.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Michael",
                    family = "Komodromos",
                    role = c("aut", "cre"),
                    email = "mk1019@ic.ac.uk")
as necessary.

The Description field contains
  information see Komodromos et al. (2021) <arXiv:2112.10270>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Specified C++11: support will be removed soon
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘DT’

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'randomForestSRC'

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Chris Dardis <christopherdardis@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Chris",
                    family = "Dardis",
                    role = c("aut", "cre"),
                    email = "christopherdardis@gmail.com")
as necessary.
Package required but not available: ‘knitr’

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/plots.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Marta Bofill Roig <marta.bofillroig@meduniwien.ac.at>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Marta", "Bofill"),
                      family = "Roig",
                      role = c("aut", "cre"),
                      email = "marta.bofillroig@meduniwien.ac.at"),
               person(given = c("Guadalupe", "Gomez"),
                      family = "Melis",
                      role = "ctb"),
               person(given = "Yu",
                      family = "Shen",
                      role = "ctb"))
as necessary.

The Description field contains
  found in Bofill, Shen & Gómez (2021) <arXiv:2008.12887>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘SuperLearner’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'gam'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘censor_event.Rd’ ‘survival_class.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Xuefei Jia <xuefeij.ai@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Xuefei",
                    family = "Jia",
                    role = c("aut", "cre"),
                    email = "xuefeij.ai@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'survminer'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Miki Horiguchi <horiguchimiki@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Miki",
                      family = "Horiguchi",
                      role = c("aut", "cre"),
                      email = "horiguchimiki@gmail.com"),
               person(given = "Hajime",
                      family = "Uno",
                      role = "aut"))
as necessary.
Maintainer: ‘Hajime Uno <huno@jimmy.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hajime",
                      family = "Uno",
                      role = c("aut", "cre"),
                      email = "huno@jimmy.harvard.edu"),
               person(given = "Lu",
                      family = "Tian",
                      role = "aut"),
               person(given = "Miki",
                      family = "Horiguchi",
                      role = "aut"),
               person(given = "Angel",
                      family = "Cronin",
                      role = "aut"),
               person(given = "Chakib",
                      family = "Battioui",
                      role = "aut"),
               person(given = "James",
                      family = "Bell",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Rong Huang <roh019@ucsd.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rong",
                      family = "Huang",
                      role = c("aut", "cre"),
                      email = "roh019@ucsd.edu"),
               person(given = "Ronghui",
                      family = "Xu",
                      role = "aut",
                      comment = "Lily"))
as necessary.
Maintainer: ‘David Moriña Soler <dmorina@ub.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Alexander Sibley <dcibioinformatics@duke.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Kouros",
                      family = "Owzar",
                      role = "aut"),
               person(given = "Zhiguo",
                      family = "Li",
                      role = "aut"),
               person(given = "Nancy",
                      family = "Cox",
                      role = "aut"),
               person(given = "Sin-Ho",
                      family = "Jung",
                      role = "aut"),
               person(given = "Chanhee",
                      family = "Yi",
                      role = "aut"),
               person(given = "Alexander",
                      family = "Sibley",
                      role = "cre",
                      email = "dcibioinformatics@duke.edu"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package suggested but not available for checking: ‘knitr’

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/survSNP.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Zhuowei Sun <sunzw21@mails.jlu.edu.cn>’

The Description field contains
  <arXiv:2310.15877> and Sun, D. et al. (2023) <arXiv:2308.15549>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Lior Rennert <liorr@clemson.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Lior",
                      family = "Rennert",
                      role = c("aut", "cre"),
                      email = "liorr@clemson.edu"),
               person(given = "Yidan",
                      family = "Shi",
                      role = "aut",
                      email = "yidan.shi@pennmedicine.upenn.edu"))
as necessary.
checkRd: (-1) coxDT.Rd:76: Lost braces; missing escapes or markup?
    76 | The estimation procedure here is performed using coxph {survival} and inserting these estimated
       |                                                        ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘suso_gql_helpers.R’ ‘suso_gql_uploadMap.R’
Package suggested but not available for checking: ‘knitr’

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/sValues.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking:
  'rmarkdown', 'quarto', 'knitr', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Aaron M Olsen <aarolsen@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Aaron", "M"),
                      family = "Olsen",
                      role = c("aut", "cre"),
                      email = "aarolsen@gmail.com"),
               person(given = c("Alejandro", "J"),
                      family = "Romero",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Philippe Grosjean <phgrosjean@sciviews.org>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘createSyntaxFile.Rd’:
    \concept{ Syntax highlighting, code coloring }
  File ‘guiDDEInstall.Rd’:
    \concept{ Interprocess DDE communication, call tip [TRUNCATED]
  File ‘svIDE-package.Rd’:
    \concept{ GUI API IDE and code editor, language sy [TRUNCATED]
Packages required but not available: 'univariateML', 'fGarch'

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Philippe Grosjean <phgrosjean@sciviews.org>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) koInstall.Rd:24: Lost braces; missing escapes or markup?
    24 | set, svKomodo loads {svSocket}, starts the socket server listening to the
       |                     ^
checkRd: (-1) svKomodo-package.Rd:18: Lost braces; missing escapes or markup?
    18 | Komodo and (2) the present {svKomodo} R package that work hand in hand to
       |                            ^
checkRd: (-1) svKomodo-package.Rd:28: Lost braces; missing escapes or markup?
    28 | Nevertheless, the SciViews-K Komodo addin and the {svKomodo} R package
       |                                                   ^
checkRd: (-1) svKomodo-package.Rd:31: Lost braces; missing escapes or markup?
    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                          ^
checkRd: (-1) svKomodo-package.Rd:31: Lost braces; missing escapes or markup?
    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                                         ^
checkRd: (-1) svKomodo-package.Rd:37: Lost braces; missing escapes or markup?
    37 | Both SciViews-K and {svKomodo} should be considered archived items. I keep
       |                     ^
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Trevor Hastie <hastie@stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Trevor",
                    family = "Hastie",
                    role = c("aut", "cre"),
                    email = "hastie@stanford.edu")
as necessary.
Maintainer: ‘Damien Challet <damien.challet@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Damien",
                    family = "Challet",
                    role = c("aut", "cre"),
                    email = "damien.challet@gmail.com")
as necessary.
Maintainer: ‘Uditha Amarananda Wijesuriya <u.wijesuriya@usi.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Uditha", "Amarananda"),
                    family = "Wijesuriya",
                    role = c("aut", "cre"),
                    email = "u.wijesuriya@usi.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'covr', 'rmarkdown', 'prettydoc'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Philippe Grosjean <phgrosjean@sciviews.org>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Packages required but not available: 'knitr', 'rmarkdown'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Philippe Grosjean <phgrosjean@sciviews.org>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘bibRNews.Rd’:
    \concept{ BibTeX bibliography, R News }
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Philippe Grosjean <phgrosjean@sciviews.org>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Thomas Lumley <t.lumley@auckland.ac.nz>’

The Description field contains
  likelihood, as described in Lumley & Huang (2023) <arXiv:2311.13048>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Mithat Gonen <gonenm@mskcc.org>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Packages required but not available: 'Hmisc', 'rms'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) eff_n.Rd:32: Lost braces; missing escapes or markup?
    32 | \code{\link[survey:surveysummary]{survey::svymean()}} and related functions from the {survey}
       |                                                                                      ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
No examples, no tests, no vignettes
Maintainer: ‘Martin Lauss <martin.lauss@med.lu.se>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Martin",
                    family = "Lauss",
                    role = c("aut", "cre"),
                    email = "martin.lauss@med.lu.se")
as necessary.
Maintainer: ‘Xingye Qiao <qiao@math.binghamton.edu>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘swa.Rd’:
    \keyword{classification,}
    \keyword{selection,}
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Chung-hong Chan <chainsawtiney@gmail.com>’

The Description field contains
  (Mazini et al., 2019) <arXiv:1904.04047>, SemAxis (An et al., 2018)
  <arXiv:1806.05521>, Relative Negative Sentiment Bias (Sweeney &
  Test (Dev & Phillips, 2019) <arXiv:1901.07656>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘quanteda’

Package suggested but not available for checking: ‘covr’

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyquant'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Mans Magnusson <mons.magnusson@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mans",
                      family = "Magnusson",
                      role = c("aut", "cre"),
                      email = "mons.magnusson@gmail.com"),
               person(given = "Erik",
                      family = "Bulow",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder packages required for checking but not installed:
  'rmarkdown', 'knitr'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'swephRdata', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘swfscMisc’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Juan Xiong <jxiong@szu.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Juan",
                      family = "Xiong",
                      role = c("aut", "cre"),
                      email = "jxiong@szu.edu.cn"),
               person(given = c("Grace", "Y."),
                      family = "Yi",
                      role = "aut",
                      email = "yyi@uwaterloo.ca"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jessica Weiss <jessica.weiss@uhnresearch.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jessica",
                      family = "Weiss",
                      role = c("aut", "cre"),
                      email = "jessica.weiss@uhnresearch.ca"),
               person(given = "Wei",
                      family = "Xu",
                      role = "aut",
                      email = "Wei.Xu@uhnresearch.ca"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Silvana M. Pesenti <swimpackage@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown', 'bookdown'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Gabriel Becker <gabembecker@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Gabriel",
                    family = "Becker",
                    role = c("aut", "cre"),
                    email = "gabembecker@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Josef Fruehwald <jofrhwld@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Josef",
                    family = "Fruehwald",
                    role = c("aut", "cre"),
                    email = "jofrhwld@gmail.com")
as necessary.
checkRd: (-1) hyph.support.en.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hyph.support.en.Rd:20: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'sylly.de', 'sylly.es'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) kRp.hyphen-methods.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kRp.hyphen-methods.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kRp.hyphen-methods.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kRp.hyphen-methods.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manage.hyph.pat.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manage.hyph.pat.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manage.hyph.pat.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manage.hyph.pat.Rd:56: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Vinicius Quintas Souto Maior <vinicius@de.ufpe.br>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Vinicius", "Quintas", "Souto"),
                      family = "Maior",
                      role = c("aut", "cre", "cph"),
                      email = "vinicius@de.ufpe.br"),
               person(given = c("Francisco", "Jose", "A"),
                      family = "Cysneiros",
                      role = "aut"))
as necessary.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘elliptical.ts.Rd’:
    https://doi.org/10.1007/s00362-016-0753-z
  File ‘influence.Rd’:
    https://doi.org/10.1080/03610929308831105
    https://doi.org/10.2307/3109764
    https://doi.org/10.1198/073500104000000217
  File ‘predict.Rd’:
    https://doi.org/10.1007/s00362-016-0753-z
  File ‘sym.arma-package.Rd’:
    https://doi.org/10.1007/s00362-016-0753-z
checkRd: (-1) elliptical.ts.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{epsilon}{positive convergence tolerance \emph{e}; the iterations converge when |fit - fit_{old}|/|fit| < \emph{e}. Default is \emph{e=1e-04}.}
       |                                                                                                   ^
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'shapes', 'RSDA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'Hmisc'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Alexander Grueneberg <cran@agrueneberg.info>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Blagoje Ivanović <blagoje.ivanovic@matf.bg.ac.rs>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Blagoje",
                    family = "Ivanović",
                    role = c("aut", "cre"),
                    email = "blagoje.ivanovic@matf.bg.ac.rs")
as necessary.
Running examples in ‘symmetry-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: symmetry_test
> ### Title: Perform symmetry tests
> ### Aliases: symmetry_test symmetry_test.default symmetry_test.lm
> ###   symmetry_test.fGARCH
> 
> ### ** Examples
> 
> set.seed(1)
> 
> # IID samples
> x <- rnorm(50)
> symmetry_test(x, "MOI", bootstrap = FALSE, k = 3, mu = 0)

	Symmetry test
	Null hypothesis: Data is symmetric around 0

data:  x
MOI = 0.60574, k = 3, p-value = 0.1379

> symmetry_test(x, "MOI", bootstrap = TRUE, k = 3, mu = 0)

	Symmetry test
	Null hypothesis: Data is symmetric around 0

data:  x
MOI = 0.60574, k = 3, B = 1000, p-value = 0.15

> symmetry_test(x, "MOI", bootstrap = TRUE, k = 3)

	Symmetry test
	Null hypothesis: Data is symmetric

data:  x
MOI = 0.27738, k = 3, B = 1000, p-value = 0.043
sample estimates:
       mu 
0.1004483 

> x <- rsl(50, alpha = 1.5)
> symmetry_test(x, "MOI", bootstrap = FALSE, k = 3, mu = 0)

	Symmetry test
	Null hypothesis: Data is symmetric around 0

data:  x
MOI = 1.1368, k = 3, p-value = 0.00536

> symmetry_test(x, "MOI", bootstrap = TRUE, k = 3, mu = 0)

	Symmetry test
	Null hypothesis: Data is symmetric around 0

data:  x
MOI = 1.1368, k = 3, B = 1000, p-value = 0.001

> symmetry_test(x, "MOI", bootstrap = TRUE, k = 3)

	Symmetry test
	Null hypothesis: Data is symmetric

data:  x
MOI = -0.32892, k = 3, B = 1000, p-value = 0.029
sample estimates:
      mu 
1.294132 

> 
> # Linear models
> lin_model <- lm(dist ~ speed, cars)
> symmetry_test(lin_model, "B1")

	Symmetry test of linear model residuals
	Null hypothesis: The residuals are symmetric around 0

data:  Residuals from model lin_model
B1 = 0.85863, B = 1000, p-value = 0.025

> 
> # Garch models
> library(fGarch)
Error in library(fGarch) : there is no package called ‘fGarch’
Execution halted
Maintainer: ‘Kem Phillips <kemphillips@comcast.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kem",
                    family = "Phillips",
                    role = c("aut", "cre"),
                    email = "kemphillips@comcast.net")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
No examples, no tests, no vignettes
Maintainer: ‘Michael Grabchak <mgrabcha@uncc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Michael",
                      family = "Grabchak",
                      role = c("aut", "cre"),
                      email = "mgrabcha@uncc.edu"),
               person(given = "Lijuan",
                      family = "Cao",
                      role = "aut",
                      email = "lcao2@uncc.edu"))
as necessary.
Maintainer: ‘Tarik C. Gouhier <tarik.gouhier@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Tarik", "C."),
                    family = "Gouhier",
                    role = c("aut", "cre"),
                    email = "tarik.gouhier@gmail.com")
as necessary.
checkRd: (-1) coord2dist.Rd:14: Lost braces; missing escapes or markup?
    14 | \code{n} x 4 matrix of coordinates consisting of {lat or y, lon or x} pairs for each each site
       |                                                  ^
Maintainer: ‘Donghoh Kim <donghoh.kim@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Matlab", "original", "by", "Eugene", "Brevdo;", "R", "port", "by", "Dongik"),
                      family = "Jang",
                      role = "aut"),
               person(given = "Hee-Seok",
                      family = "Oh",
                      role = "aut"),
               person(given = "Donghoh",
                      family = "Kim",
                      role = c("aut", "cre"),
                      email = "donghoh.kim@gmail.com"))
as necessary.
Maintainer: ‘Gertjan van den Burg <gertjanvandenburg@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Gertjan",
                    family = "van den Burg",
                    role = c("aut", "cre"),
                    email = "gertjanvandenburg@gmail.com")
as necessary.
Maintainer: ‘Michael Kleinsasser <mkleinsa@umich.edu>’

The Description field contains
  populations <arXiv:2106.06835>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘knitr’

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'plotly'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Alix Lahuec <alix.lahuec@mail.mcgill.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alix",
                    family = "Lahuec",
                    role = c("aut", "cre"),
                    email = "alix.lahuec@mail.mcgill.ca")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘broman’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Merlin Kopfmann <mghncd+cran@posteo.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Merlin",
                    family = "Kopfmann",
                    role = c("aut", "cre"),
                    email = "mghncd+cran@posteo.jp")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yixuan Qiu <yixuan.qiu@cos.name>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yixuan",
                      family = "Qiu",
                      role = c("aut", "cre"),
                      email = "yixuan.qiu@cos.name"),
               person(given = c("authors/contributors", "of", "the", "included", "fonts.", "See", "file", "AUTHORS", "for"),
                      family = "details.",
                      role = "aut"))
as necessary.
Maintainer: ‘Suraj Yerramilli <surajyerramilli@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Suraj",
                      family = "Yerramilli",
                      role = c("aut", "cre"),
                      email = "surajyerramilli@gmail.com"),
               person(given = "Arun",
                      family = "Tangirala",
                      role = "aut"))
as necessary.
Found the following files/directories:
  ‘test.csv’
Package required but not available: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Arne Henningsen <arne.henningsen@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Arne",
                      family = "Henningsen",
                      role = c("aut", "cre"),
                      email = "arne.henningsen@gmail.com"),
               person(given = c("Jeff", "D."),
                      family = "Hamann",
                      role = "aut"))
as necessary.
Package suggested but not available for checking: ‘knitr’

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/systemfit.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Stéphane Laurent <laurent_step@outlook.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Stéphane",
                    family = "Laurent",
                    role = c("aut", "cre"),
                    email = "laurent_step@outlook.fr")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Thomas Hoffelder <thomas.hoffelder@boehringer-ingelheim.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thomas",
                    family = "Hoffelder",
                    role = c("aut", "cre"),
                    email = "thomas.hoffelder@boehringer-ingelheim.com")
as necessary.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘T2EQ-package.Rd’:
    http://dx.doi.org/10.1080/10543406.2014.920344
    http://dx.doi.org/10.1177/009286159603000427
  File ‘T2EQ.Rd’:
    http://dx.doi.org/10.1080/10543406.2014.920344
  File ‘T2EQ.dissolution.profiles.hoffelder.Rd’:
    http://dx.doi.org/10.1177/009286159603000427
  File ‘ex_data_JoBS.Rd’:
    http://dx.doi.org/10.1080/10543406.2014.920344
Packages required but not available: 'highcharter', 'tables'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Philip C Schouten <philip.schouten@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Philip", "C"),
                    family = "Schouten",
                    role = c("aut", "cre"),
                    email = "philip.schouten@gmail.com")
as necessary.
Packages required but not available: 'knitr', 'yaml'

Packages suggested but not available for checking:
  'rmarkdown', 'printr', 'kableExtra', 'flextable', 'Hmisc'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'gt'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Alon Kipnis <kipnisal@stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alon",
                    family = "Kipnis",
                    role = c("aut", "cre"),
                    email = "kipnisal@stanford.edu")
as necessary.

The Description field contains
  frequency tables described in Kipnis (2019) <arXiv:1911.01208>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘tableone-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kableone
> ### Title: Export TableOne Objects to Markdown
> ### Aliases: kableone
> 
> ### ** Examples
> 
> 
> library(survival)
> data(pbc)
> 
> tableOne <- CreateTableOne(data = pbc)
> 
> kableone(tableOne)
Error in loadNamespace(x) : there is no package called ‘knitr’
Calls: kableone ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘tables’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

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

Packages suggested but not available for checking:
  'kableExtra', 'Hmisc', 'bookdown', 'rmarkdown', 'pkgdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'yamlet', 'kableExtra', 'spork', 'reactable'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'yaml', 'sortable'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Dane R. Van Domelen <vandomed@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Dane", "R."),
                    family = "Van Domelen",
                    role = c("aut", "cre"),
                    email = "vandomed@gmail.com")
as necessary.
Packages required but not available: 'knitr', 'kableExtra'

Package suggested but not available for checking: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'htmlwidgets', 'leaflet', 'leaftime', 'leaflet.extras', 'mapedit'

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

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

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Austin Nar <austin.nar@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Austin",
                    family = "Nar",
                    role = c("aut", "cre"),
                    email = "austin.nar@gmail.com")
as necessary.
Package required but not available: ‘yaml’

Package suggested but not available for checking: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Katarina Domijan <domijank@tcd.ie>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Katarina",
                    family = "Domijan",
                    role = c("aut", "cre"),
                    email = "domijank@tcd.ie")
as necessary.
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘kableExtra’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Eric Brown <eb@ericebrown.com>’

The BugReports field in DESCRIPTION has
  https://github.com/ropensci/tacmagic
which should likely be
  https://github.com/ropensci/tacmagic/issues
instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr', 'pkgdown', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Li-Hsiang Lin <llin79@gatech.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Li-Hsiang",
                      family = "Lin",
                      role = c("aut", "cre"),
                      email = "llin79@gatech.edu"),
               person(given = c("V.", "Roshan"),
                      family = "Joseph",
                      role = "aut"))
as necessary.
Specified C++11: support will be removed soon
Package required but not available: ‘plotly’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Anna Kiriliouk <anna.kiriliouk@unamur.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Anna",
                    family = "Kiriliouk",
                    role = c("aut", "cre"),
                    email = "anna.kiriliouk@unamur.be")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

Packages suggested but not available for checking: 'rmarkdown', 'pkgdown'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Nanne Aben <nanne.aben@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Nanne",
                    family = "Aben",
                    role = c("aut", "cre"),
                    email = "nanne.aben@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'kableExtra', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

Packages suggested but not available for checking:
  'rms', 'rmarkdown', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Alexey Shipunov <dactylorhiza@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alexey",
                    family = "Shipunov",
                    role = c("aut", "cre"),
                    email = "dactylorhiza@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘auth0.R’ ‘config.R’ ‘entra_id.R’ ‘google.R’ ‘utils.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
Maintainer: ‘Fabrizio Cipollini <cipollini.fabrizio@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Francesco",
                      family = "Calvori",
                      role = "aut"),
               person(given = "Fabrizio",
                      family = "Cipollini",
                      role = c("aut", "cre"),
                      email = "cipollini.fabrizio@gmail.com"),
               person(given = c("Giampiero", "M."),
                      family = "Gallo",
                      role = "aut"),
               person(given = "'gzstream'",
                      family = "authors.",
                      role = "aut"))
as necessary.
checkRd: (-1) TAQ-functions.Rd:119: Lost braces
   119 | Brownlees, C. T., and Gallo, G. M. (2006). Financial Econometric Analysis at Ultra{--}High Frequency: Data Handling Concerns, \emph{Computational Statistics and Data Analysis} \bold{51}, 2232--2245.
       |                                                                                   ^
checkRd: (-1) TAQ-package.Rd:59: Lost braces
    59 | Brownlees, C. T., and Gallo, G. M. (2006). Financial Econometric Analysis at Ultra{--}High Frequency: Data Handling Concerns, \emph{Computational Statistics and Data Analysis} \bold{51}, 2232--2245.
       |                                                                                   ^
Package required but not available: ‘targets’

Packages suggested but not available for checking:
  'knitr', 'quarto', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'SuperLearner', 'knitr', 'polle', 'randomForestSRC',
  'riskRegression', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘targeted-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estimate_truncatedscore
> ### Title: Estimation of mean clinical outcome truncated by event process
> ### Aliases: estimate_truncatedscore
> 
> ### ** Examples
> 
> data(truncatedscore)
> mod1 <- learner_glm(y ~ a * (x1 + x2))
> mod2 <- learner_glm(r ~ a * (x1 + x2), family = binomial)
> a <- estimate_truncatedscore(
+   data = truncatedscore,
+   mod.y = mod1,
+   mod.r = mod2,
+   mod.a = a ~ 1,
+   mod.event = mets::Event(time, status) ~ x1+x2,
+   time = 2
+ )
Error in loadNamespace(x) : there is no package called ‘riskRegression’
Calls: estimate_truncatedscore ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'knitr', 'yaml'

Packages suggested but not available for checking:
  'DT', 'googleCloudStorageR', 'gt', 'keras', 'rmarkdown', 'reprex',
  'shinybusy', 'tarchetypes', 'usethis', 'visNetwork'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Zehang Li <lizehang@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zehang",
                      family = "Li",
                      role = c("aut", "cre"),
                      email = "lizehang@uw.edu"),
               person(given = "Tyler",
                      family = "McCormick",
                      role = "aut"),
               person(given = "Sam",
                      family = "Clark",
                      role = "aut"))
as necessary.
Maintainer: ‘Hanwen Zhang <hanwengutierrez@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hanwen",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "hanwengutierrez@gmail.com"),
               person(given = c("Fabio", "H."),
                      family = "Nieto",
                      role = "aut"))
as necessary.
Maintainer: ‘Kartikeya Bolar <kartikeya.bolar@tapmi.edu.in>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kartikeya",
                    family = "Bolar",
                    role = c("aut", "cre"),
                    email = "kartikeya.bolar@tapmi.edu.in")
as necessary.
Package required but not available: ‘wordcloud2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tashudata'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘shadowtext’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'patternplot'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Yuan-De Tan <tanyuande@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yuan-De",
                    family = "Tan",
                    role = c("aut", "cre"),
                    email = "tanyuande@gmail.com")
as necessary.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘depreciation_interest.R’ ‘friction_period.R’ ‘nl_med_prices.R’
    ‘nl_pat_fam_prices.R’ ‘nl_ppp.R’ ‘nl_price_index.R’
    ‘nl_prod_oth_prices.R’
Cannot process vignettes
Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘tatoo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as_latex
> ### Title: Convert a Table to Latex Code
> ### Aliases: as_latex save_pdf view_pdf
> 
> ### ** Examples
> 
>   as_latex(iris)
Error: requireNamespace(package = "knitr", quietly = TRUE) is not TRUE
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Lukas Burk <lukas@quantenbrot.de>’

Found the following (possibly) invalid file URI:
  URI: CODE_OF_CONDUCT.md
    From: README.md
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘parse_schema.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Carl Boettiger <cboettig@gmail.com>’

The BugReports field in DESCRIPTION has
  https://github.com/cboettig/taxalight
which should likely be
  https://github.com/cboettig/taxalight/issues
instead.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jacques Allard <jacques.allard@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jacques",
                      family = "Allard",
                      role = c("aut", "cre"),
                      email = "jacques.allard@gmail.com"),
               person(given = "Vartan",
                      family = "Choulakian",
                      role = "aut"))
as necessary.
Package required but not available: ‘wikitaxa’

Package suggested but not available for checking: ‘vcr’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'taxize', 'wikitaxa', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'bookdown', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION 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:
    ‘TaylorRussell.Rd’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘shinybusy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Zhixuan Shao <shaozhixuansh@pku.edu.cn>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘sace.Rd’:
    https://doi.org/10.1093/biomet/asx034
  File ‘simulated_data.Rd’:
    https://doi.org/10.1093/biomet/asx034
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Guoli Sun <guolisun87@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Guoli",
                      family = "Sun",
                      role = c("aut", "cre"),
                      email = "guolisun87@gmail.com"),
               person(given = "Alex",
                      family = "Krasnitz",
                      role = "aut"))
as necessary.
Package suggested but not available for checking: ‘knitr’

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/TBFmultinomial.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package suggested but not available for checking: ‘knitr’

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/tbm_supplement.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Elior Rahmani <elior.rahmani@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘config’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Huaiyu Zhang <huaiyuzhang1988@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Huaiyu",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "huaiyuzhang1988@gmail.com"),
               person(given = "Haiyan",
                      family = "Wang",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'config', 'DT', 'golem', 'plotly'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Boris P Hejblum <boris.hejblum@u-bordeaux.fr>’

Found the following (possibly) invalid URLs:
  URL: https://docs.gsea-msigdb.org/#GSEA/Data_Formats/#gmt-gene-matrix-transposed-file-format-gmt/
    From: inst/doc/TcGSA_userguide.html
    Message: Invalid URL: '#' not allowed in fragment
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

Package suggested but not available for checking: ‘rmarkdown’

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'DT', 'tcpl', 'prettydoc', 'htmlTable',
  'rmdformats'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'plotly', 'gt'

Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'prettydoc', 'rmarkdown', 'htmlTable',
  'kableExtra', 'rmdformats'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxyglobals'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'T4cluster', 'maotai'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Raoul Wadhwa <raoulwadhwa@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Specified C++11: support will be removed soon
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘mobius-strips.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Guangchuang Yu <guangchuangyu@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'lintr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Mikael Lucas <mikael.lucas@ird.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Julien",
                      family = "Lavenus",
                      role = "aut"),
               person(given = "Mikael",
                      family = "Lucas",
                      role = "cre",
                      email = "mikael.lucas@ird.fr"))
as necessary.
Packages required but not available: 'gt', 'furniture'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘tdigest/libs/tdigest.so’:
  Found non-API call to R: ‘DATAPTR’
This entry point may be removed soon.

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Package required but not available: ‘rmarkdown’

Package suggested but not available for checking: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Maxime Durand <duran1211@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Maxime",
                    family = "Durand",
                    role = c("aut", "cre"),
                    email = "duran1211@gmail.com")
as necessary.
Package required but not available: ‘survidm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Dirk Eddelbuettel <edd@debian.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dirk",
                      family = "Eddelbuettel",
                      role = c("aut", "cre"),
                      email = "edd@debian.org"),
               person(given = "Kenneth",
                      family = "Rose",
                      role = "aut"))
as necessary.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Found the following HTML validation problems:
tdsa.html:232:1 (state_sens.Rd:7): Warning: <script> anchor "MathJax-script" already defined
Maintainer: ‘Jing Hua Zhao <jinghuazhao@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "David",
                      family = "Clayton",
                      role = "aut"),
               person(given = c("Jing", "Hua"),
                      family = "Zhao",
                      role = "cre",
                      email = "jinghuazhao@hotmail.com"))
as necessary.
Maintainer: ‘Greg Snow <538280@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Greg",
                    family = "Snow",
                    role = c("aut", "cre"),
                    email = "538280@gmail.com")
as necessary.
Maintainer: ‘Hugo Andres Gutierrez Rojas <hagutierrezro@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Hugo", "Andres", "Gutierrez"),
                    family = "Rojas",
                    role = c("aut", "cre"),
                    email = "hagutierrezro@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'random.cdisc.data', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'teal', 'DT', 'rmarkdown', 'teal.reporter', 'tern.gee', 'vistime'

Packages suggested but not available for checking:
  'knitr', 'roxy.shinylive', 'shinytest2'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'teal', 'colourpicker', 'DT', 'ggExtra', 'ggpmisc', 'htmlwidgets',
  'rmarkdown', 'shinyTree', 'sparkline', 'teal.reporter'

Packages suggested but not available for checking:
  'knitr', 'roxy.shinylive', 'shinytest2'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxy.shinylive', 'shinytest2', 'yaml'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'flextable', 'gtsummary', 'knitr', 'rmarkdown', 'rtables.officer',
  'shinybusy', 'sortable', 'yaml'

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

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

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

Packages suggested but not available for checking:
  'DT', 'knitr', 'rmarkdown', 'shinytest2'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxy.shinylive'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'DT', 'knitr', 'rmarkdown', 'shinytest2'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Johannes Ossberger <johannes.ossberger@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Johannes",
                    family = "Ossberger",
                    role = c("aut", "cre"),
                    email = "johannes.ossberger@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'SuperLearner', 'randomForestSRC'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jeffrey L. Andrews <jeff.andrews@ubc.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Jeffrey", "L."),
                      family = "Andrews",
                      role = c("aut", "cre"),
                      email = "jeff.andrews@ubc.ca"),
               person(given = c("Jaymeson", "R."),
                      family = "Wickins",
                      role = "aut"),
               person(given = c("Nicholas", "M."),
                      family = "Boers",
                      role = "aut"),
               person(given = c("Paul", "D."),
                      family = "McNicholas",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘arulesViz’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Marcos Fernández-Martínez <marcos.fernandez-martinez@uantwerpen.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Marcos",
                      family = "Fernández-Martínez",
                      role = c("aut", "cre"),
                      email = "marcos.fernandez-martinez@uantwerpen.be"),
               person(given = "Joan",
                      family = "Maspons",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Etienne Low-Decarie <etienne.decarie@gmail.com>’

Found the following (possibly) invalid file URI:
  URI: to_be_added
    From: man/Emiliania_huxleyi.Rd
Unavailable namespace imported from by a ':::' call: ‘ciftiTools’
  See the note in ?`:::` about the use of this operator.
Running ‘run_templateICAr_tests.R’ [0s/1s]
  Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/run_templateICAr_tests.R’ failed.
Complete output:
  > # Build --> Install and Restart
  > 
  > # [Edit these]
  > ## path to your Connectome Workbench
  > my_wb <- "~/Applications"
  > ## path to test data
  > dir_data <- "tests/data"
  > ## path to results from tests
  > dir_results <- file.path(dir_data, "results")
  > 
  > library(testthat)
  > library(ciftiTools)
  Error in library(ciftiTools) : there is no package called 'ciftiTools'
  Execution halted
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Siddhartha Kundu <siddhartha_kundu@aiims.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Siddhartha",
                    family = "Kundu",
                    role = c("aut", "cre"),
                    email = "siddhartha_kundu@aiims.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Till Massing <till.massing@uni-due.de>’

The Description field contains
  (Massing (2023) <arXiv:2303.07060>).  The following references form the
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘StableEstim’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Pixu Shi <pixu.shi@duke.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Pixu",
                    family = "Shi",
                    role = c("aut", "cre"),
                    email = "pixu.shi@duke.edu")
as necessary.
Package required but not available: ‘plotly’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘K. Gerald van den Boogaart <boogaart@math.tu-freiberg.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("K.", "Gerald"),
                    family = "van den Boogaart",
                    role = c("aut", "cre"),
                    email = "boogaart@uni-greifswald.de")
as necessary.
Maintainer: ‘Suleiman A Khan <khan.suleiman@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'config', 'tfruns', 'yaml'

Package suggested but not available for checking: ‘keras3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

Package in Depends/Imports which should probably only be in LinkingTo: ‘RcppEigen’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Weilin Chen <w.chen56@lse.ac.uk>’

The Description field contains
  projected data.  See Chen and Lam (2023) <arXiv:2208.04012> for more
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yuchen Zeng <yzeng58@wisc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Miaoyan",
                      family = "Wang",
                      role = "aut"),
               person(given = "Yuchen",
                      family = "Zeng",
                      role = c("aut", "cre"),
                      email = "yzeng58@wisc.edu"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rtracklayer’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘M. Suzette Blanchard <sblanchard@coh.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("M.", "Suzette"),
                    family = "Blanchard",
                    role = c("aut", "cre"),
                    email = "sblanchard@coh.org")
as necessary.
Packages required but not available: 'ergm', 'tergm'

Package suggested but not available for checking: ‘EpiModel’

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

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'covr'

VignetteBuilder packages required for checking but not installed:
  'rmarkdown', 'knitr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'devtools', 'pkgdown', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'gt', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'colourpicker', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘geeasy’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) MC_CRUDE.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) MC_IS.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) PROB_BASEVAR-class.Rd:14: Lost braces
    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
checkRd: (-1) PROB_DETVAR-class.Rd:14: Lost braces
    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
checkRd: (-1) SORM.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) SYS_LSF-class.Rd:16: Lost braces
    16 | \item{\code{func}}{prepared for objective functions like SYS_LSF$func <- function(x){return(x[1] + x[2])}}
       |                                                                                     ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Author field differs from that derived from Authors@R
  Author:    ‘Nicolas Frerebeau [aut, cre] (<https://orcid.org/0000-0001-5759-4944>), Brice Lebrun [art] (<https://orcid.org/0000-0001-7503-8685>, Logo designer), Université Bordeaux Montaigne [fnd] (03pbgwk21), CNRS [fnd] (02feahw73)’
  Authors@R: ‘Nicolas Frerebeau [aut, cre] (ORCID: <https://orcid.org/0000-0001-5759-4944>), Brice Lebrun [art] (ORCID: <https://orcid.org/0000-0001-7503-8685>, Logo designer), Université Bordeaux Montaigne [fnd] (ROR: <https://ror.org/03pbgwk21>), CNRS [fnd] (ROR: <https://ror.org/02feahw73>)’
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘spelling.R’ [0s/0s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'EstCRM', 'DT', 'golem', 'officedown', 'bruceR', 'rmarkdown',
  'flextable', 'lordif', 'semPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michael C Sachs <sachsmc@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Michael", "C"),
                      family = "Sachs",
                      role = c("aut", "cre"),
                      email = "sachsmc@gmail.com"),
               person(given = c("Michael", "P"),
                      family = "Fay",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) lognormConstCVCI.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lognormConstCVCI.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lognormConstCVCI.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Gannaz Irene <irene.gannaz@insa-lyon.fr>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘TestCor-package.Rd’:
    https://doi.org/10.1111/j.2517-6161.1995.tb02031.x
    https://doi.org/10.1080/01621459.2014.999157
    https://doi.org/10.1214/088342307000000113
    https://doi.org/10.1198/016214504000000539
Package required but not available: ‘knitr’

Package suggested but not available for checking: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'gurobi', 'DT', 'knitr', 'rmarkdown', 'kableExtra', 'pkgdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘Morpho’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Dexter Cahoy <dexter.cahoy@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Dexter",
                    family = "Cahoy",
                    role = c("aut", "cre"),
                    email = "dexter.cahoy@gmail.com")
as necessary.
Package suggested but not available for checking: ‘knitr’

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/tester_introduction.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(testex)
  > 
  > test_check("testex")
  Failed with error:  'there is no package called 'roxygen2''
  Saving _problems/test-testthat-4.R
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 73 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • on R CMD check (1): 'test-options.R:27:3'
  • tests not installed (1): 'test-srcref-key.R:27:3'
  • {roxygen2} is not installed. (3): 'test-roxygen2-expect.R:17:3',
    'test-roxygen2-parse-text.R:17:3', 'test-roxygen2-testthat.R:17:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-testthat.R:2:3'): with_attached temporarily attaches a packages ──
  Expected `suppressPackageStartupMessages(...)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 73 ]
  Error:
  ! Test failures.
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘En-shuo Hsu <daviden1013@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Jeffrey", "C."),
                      family = "Miecznikowski",
                      role = "aut"),
               person(given = "En-shuo",
                      family = "Hsu",
                      role = c("aut", "cre"),
                      email = "daviden1013@gmail.com"),
               person(given = "Yanhua",
                      family = "Chen",
                      role = "aut"),
               person(given = "Albert",
                      family = "Vexler",
                      role = "aut"))
as necessary.
Package required but not available: ‘Hmisc’

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

Packages suggested but not available for checking: 'knitr', 'covr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Kathrin Moellenhoff <kathrin.moellenhoff@rub.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kathrin",
                    family = "Moellenhoff",
                    role = c("aut", "cre"),
                    email = "kathrin.moellenhoff@rub.de")
as necessary.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘bootstrap_test.Rd’:
    https://doi.org/10.1080/01621459.2017.1281813
Maintainer: ‘Manel Salamero <manelsalamero@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Manel",
                    family = "Salamero",
                    role = c("aut", "cre"),
                    email = "manelsalamero@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'diffviewer', 'knitr', 'rmarkdown', 'usethis'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'devtools', 'usethis'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Paul R. Rosenbaum <rosenbaum@wharton.upenn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Paul", "R."),
                    family = "Rosenbaum",
                    role = c("aut", "cre"),
                    email = "rosenbaum@wharton.upenn.edu")
as necessary.
Maintainer: ‘vincent guyader <vincent@thinkr.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "vincent",
                    family = "guyader",
                    role = c("aut", "cre"),
                    email = "vincent@thinkr.fr")
as necessary.
Package required but not available: ‘FactoMineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Giancarlo Vercellino <giancarlo.vercellino@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Giancarlo",
                    family = "Vercellino",
                    role = c("aut", "cre"),
                    email = "giancarlo.vercellino@gmail.com")
as necessary.
Package required but not available: ‘modeest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Juan Domingo Gonzalez <juanrst@hotmail.com>’

The Description field contains
  objects of arbitrary geometries. arXiv preprint <arXiv:2312.16721>).
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) permucycle.Rd:37: Lost braces; missing escapes or markup?
    37 |  {The 2 in the first row means there are two cycles;}
       |  ^
checkRd: (-1) permucycle.Rd:38: Lost braces; missing escapes or markup?
    38 |   {The second row means there is a cycle of length 2, with members  (1,3);}
       |   ^
checkRd: (-1) permucycle.Rd:39: Lost braces; missing escapes or markup?
    39 |  {The third row means  there is a cycle of length 1, with member  (2);}
       |  ^
checkRd: (-1) permucycle.Rd:40: Lost braces; missing escapes or markup?
    40 |  {The fourth row is redundant for this specific case.}
       |  ^
checkRd: (-1) permucycle.Rd:41: Lost braces; missing escapes or markup?
    41 |  {One can read from the output of permucycle() to obtain cycle notation (13)(2) of the permutation, and other information.}
       |  ^
Maintainer: ‘Alejandro Gonzalez Recuenco <alejandrogonzalezrecuenco@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Alejandro", "Gonzalez"),
                    family = "Recuenco",
                    role = c("aut", "cre"),
                    email = "alejandrogonzalezrecuenco@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'rmarkdown', 'yaml', 'rjtools'

Packages suggested but not available for checking:
  'bookdown', 'knitr', 'spelling'

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

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

Packages suggested but not available for checking:
  'covr', 'kableExtra', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Unknown package ‘oglmx’ in Rd xrefs
Running examples in ‘texreg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: knitreg
> ### Title: Flexibly choose the right table output format for use with
> ###   'knitr'
> ### Aliases: knitreg
> 
> ### ** Examples
> 
> require("nlme")
Loading required package: nlme
> model.1 <- lme(distance ~ age, data = Orthodont, random = ~ 1)
> model.2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)
> knitreg(list(model.1, model.2), center = FALSE, caption = "", table = FALSE)
Error in knitreg(list(model.1, model.2), center = FALSE, caption = "",  : 
  knitreg requires the 'knitr' package to be installed.
To do this, enter 'install.packages("knitr")'.
Execution halted
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘qgraph’

Package suggested but not available for checking: ‘quanteda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Dominik S. Meier <dominikmeier@outlook.com>’

The Description field contains
  'text2sdg' package. See Wulff, Meier and Mata (2023) <arXiv:2301.11353>
  and Meier, Wulff and Mata (2021) <arXiv:2110.05856> for reference.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘corpustools’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

Packages suggested but not available for checking: 'covr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘DT’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'plotly', 'quanteda',
  'quanteda.textstats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tyler Rinker <tyler.rinker@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following (possibly) invalid file URI:
  URI: CONDUCT.md
    From: README.md
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Christian Fong <christianfong@stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Christian",
                    family = "Fong",
                    role = c("aut", "cre"),
                    email = "christianfong@stanford.edu")
as necessary.
checkRd: (-1) infer_Z.Rd:16: Lost braces; missing escapes or markup?
    16 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variatioanl approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
checkRd: (-1) sibp.Rd:26: Lost braces
    26 | It is recommended to use link{sibp_param_search} instead of this function to search over multiple configurations of the most important parameters.  So long as only the training data is used, the analyst can freely experimient with as many parameter configurations as he likes without corrupting his causal inferences.  Once a parameter configuration is chosen, the user can then use \link{sibp_amce} on the test set to estimate the average marginal component effect (AMCE) for each treatment.}
       |                              ^
checkRd: (-1) sibp.Rd:28: Lost braces; missing escapes or markup?
    28 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variational approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
checkRd: (-1) sibp_amce.Rd:19: Lost braces
    19 |   \item{sibp.amce}{The table returned by code{sibp_amce}.}
       |                                              ^
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Matt Taddy <mataddy@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Matt",
                    family = "Taddy",
                    role = c("aut", "cre"),
                    email = "mataddy@gmail.com")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

The Description field contains
  Inverse Regression for Text Analysis <arXiv:1012.2098> and Taddy (2015,
  AoAS), Distributed Multinomial Regression, <arXiv:1311.6139>. A
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘congress109.Rd’:
    http://dx.doi.org/10.3886/ICPSR26242
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Matthieu Decorde <matthieu.decorde@ens-lyon.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Sylvain",
                      family = "Loiseau",
                      role = "aut"),
               person(given = "Lise",
                      family = "Vaudor",
                      role = "aut"),
               person(given = "Matthieu",
                      family = "Decorde",
                      role = c("aut", "cre"),
                      email = "matthieu.decorde@ens-lyon.fr"),
               person(given = "Serge",
                      family = "Heiden",
                      role = "aut"))
as necessary.
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking:
  'knitr', 'qgraph', 'ggalt'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/textplot-examples.Rnw’
(Is a VignetteBuilder field missing?)

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:
    ‘nlp_build_chunks.R’ ‘sem_search_corpus.R’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘textra.R’
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'reactable'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) textTrainNPlot.Rd:93: height/width attributes should be in pixels
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Luke Miratrix <lmiratrix@stat.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Luke",
                    family = "Miratrix",
                    role = c("aut", "cre"),
                    email = "lmiratrix@stat.harvard.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) make.phrase.matrix.Rd:20: Lost braces
    20 |  \\tabular{rrrrr}{
       |           ^
checkRd: (-1) make.phrase.matrix.Rd:20-23: Lost braces
    20 |  \\tabular{rrrrr}{
       |                  ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tyler Rinker <tyler.rinker@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘quanteda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Timothy Conwell <timconwell@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Timothy",
                    family = "Conwell",
                    role = c("aut", "cre"),
                    email = "timconwell@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'BiocStyle', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'tensorflow', 'keras'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘tensorflow’

Packages suggested but not available for checking:
  'knitr', 'keras3', 'rmarkdown'

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

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

Packages suggested but not available for checking:
  'cloudml', 'knitr', 'pixels', 'yaml'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘James Curran <j.curran@auckland.ac.nz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "James",
                      family = "Curran",
                      role = c("aut", "cre"),
                      email = "j.curran@auckland.ac.nz"),
               person(given = "TingYu",
                      family = "Huang",
                      role = "aut"))
as necessary.
Packages required but not available: 'tensorflow', 'tfruns'

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

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

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

Packages suggested but not available for checking:
  'knitr', 'tfestimators', 'keras', 'rmarkdown'

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

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

Package suggested but not available for checking: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Hong Zhang <hzhang@wpi.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hong",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "hzhang@wpi.edu"),
               person(given = "Zheyang",
                      family = "Wu",
                      role = "aut"))
as necessary.
Maintainer: ‘Ge Tan <ge_tan@live.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ge",
                    family = "Tan",
                    role = c("aut", "cre"),
                    email = "ge_tan@live.com")
as necessary.
Specified C++11: support will be removed soon
Packages required but not available: 'tensorflow', 'keras'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

Packages suggested but not available for checking:
  'tfdatasets', 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Paul Gilbert <pgilbert.ttv9z@ncf.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Paul",
                    family = "Gilbert",
                    role = c("aut", "cre"),
                    email = "pgilbert.ttv9z@ncf.ca")
as necessary.
Packages required but not available: 'tfrmt', 'DT', 'gt', 'sortable'

Package suggested but not available for checking: ‘shinytest2’

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

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

Package suggested but not available for checking: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) shoulders.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) shoulders.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) shoulders.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ThankYouStars)
  > 
  > test_check("ThankYouStars")
  Saving _problems/test-starring-12.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-starring.R:3:1'): (code run outside of `test_that()`) ──────────
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: `with_mock()` was deprecated in testthat 3.2.0 and is now defunct.
  ℹ Please use `with_mocked_bindings()` instead.
  Backtrace:
      ▆
   1. └─testthat::with_mock(...) at test-starring.R:3:1
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted
Packages suggested but not available for checking: 'rms', 'knitr'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/blood_loss_report.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pkgdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pkgdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'worcs', 'knitr', 'yaml'

Packages suggested but not available for checking:
  'rmarkdown', 'pkgdown', 'webexercises', 'usethis', 'bookdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Glenn J. Tattersall <gtatters@brocku.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Glenn", "J."),
                    family = "Tattersall",
                    role = c("aut", "cre"),
                    email = "gtatters@brocku.ca")
as necessary.
Maintainer: ‘Francisco Jablinski Castelhano <fjcastelhano@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Francisco", "Jablinski", "Castelhano/Laboclima", "-", "Universidade", "Federal", "do"),
                      family = "Paraná",
                      role = "aut"),
               person(given = c("Francisco", "Jablinski"),
                      family = "Castelhano",
                      role = "cre",
                      email = "fjcastelhano@gmail.com"))
as necessary.
Maintainer: ‘Jose Gama <rxprtgama@gmail.com>’

Found the following (possibly) invalid file URIs:
  URI: www.madur.com
    From: man/RTDtemperatureFromResistance.Rd
  URI: www.betatherm.com
    From: man/ThermistorSlope.Rd
  URI: www.betatherm.com
    From: man/ThermistorSteinhartHartCoeffFromMeasurements.Rd
  URI: www.betatherm.com
    From: man/ThermistorVolumeResistivityFromR25.Rd
  URI: www.betatherm.com
    From: man/ThermistorVolumeResistivityFromRho.Rd
  URI: www.conaxbuffalo.com
    From: man/ThermocoupleLeadWireExternalResistanceUS.Rd
  URI: www.madur.com
    From: man/rtdResistivityAlpha.Rd
  URI: www.phoenixcontact.com
    From: man/thermocoupleExtensionCables.Rd
  URI: www.tempco.com
    From: man/thermocoupleWireColorUnitedStatesCanadaMexico.Rd
  URI: www.conaxbuffalo.com
    From: man/thermocoupleWireSizeResistanceImperial.Rd
Maintainer: ‘Amit Sasson <amitsasson1@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Amit",
                    family = "Sasson",
                    role = c("aut", "cre"),
                    email = "amitsasson1@gmail.com")
as necessary.
Maintainer: ‘Olgun Aydin <olgun.aydin@pg.edu.pl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Olgun",
                      family = "Aydin",
                      role = c("aut", "cre"),
                      email = "olgun.aydin@pg.edu.pl"),
               person(given = "Mustafa",
                      family = "Cavus",
                      role = "aut"))
as necessary.
Maintainer: ‘Thomas Hoffmann <tjhoffm@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thomas",
                    family = "Hoffmann",
                    role = c("aut", "cre"),
                    email = "tjhoffm@gmail.com")
as necessary.
Package required but not available: ‘devtools’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'knitr', 'htmlwidgets'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Holger L. Kern <hkern@fsu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Holger", "L."),
                    family = "Kern",
                    role = c("aut", "cre"),
                    email = "hkern@fsu.edu")
as necessary.
Package required but not available: ‘htmlwidgets’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Paolo Giordani <paolo.giordani@uniroma1.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Maria", "Antonietta", "Del"),
                      family = "Ferraro",
                      role = "aut"),
               person(given = c("Henk", "A.L."),
                      family = "Kiers",
                      role = "aut"),
               person(given = "Paolo",
                      family = "Giordani",
                      role = c("aut", "cre"),
                      email = "paolo.giordani@uniroma1.it"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3dimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
Maintainer: ‘Oliver Keyes <ironholds@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Oliver",
                    family = "Keyes",
                    role = c("aut", "cre"),
                    email = "ironholds@gmail.com")
as necessary.

Found the following (possibly) invalid file URI:
  URI: CONDUCT.md
    From: README.md

The Description field contains
  A connector to the 'What3Words' (http://what3words.com/) service, which
Please enclose URLs in angle brackets (<...>).
Maintainer: ‘Man-Hua Chen <mchen@mail.tku.edu.tw>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Man-Hua",
                    family = "Chen",
                    role = c("aut", "cre"),
                    email = "mchen@mail.tku.edu.tw")
as necessary.
Maintainer: ‘Tao Xiao <taoxiao1@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tao",
                    family = "Xiao",
                    role = c("aut", "cre"),
                    email = "taoxiao1@gmail.com")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'DiagrammeR', 'formattable', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
File ‘tibble/libs/tibble.so’:
  Found non-API call to R: ‘SET_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.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling', 'yaml'

VignetteBuilder package required for checking but not installed: ‘knitr’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  guess_tspec.Rd: abort
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File ‘tibblify/libs/tibblify.so’:
  Found non-API calls to R: ‘BODY’, ‘CLOENV’, ‘ENCLOS’, ‘EXTPTR_PROT’,
    ‘EXTPTR_TAG’, ‘FORMALS’, ‘FRAME’, ‘HASHTAB’, ‘OBJECT’, ‘PRENV’,
    ‘PRVALUE’, ‘R_PromiseExpr’, ‘Rf_allocSExp’, ‘Rf_findVarInFrame3’,
    ‘SETLENGTH’, ‘SET_BODY’, ‘SET_CLOENV’, ‘SET_FORMALS’,
    ‘SET_GROWABLE_BIT’, ‘SET_OBJECT’, ‘SET_TRUELENGTH’, ‘STRING_PTR’
These entry points may be removed soon:
‘EXTPTR_PROT’, ‘EXTPTR_TAG’, ‘FRAME’, ‘HASHTAB’, ‘BODY’, ‘FORMALS’, ‘CLOENV’, ‘ENCLOS’, ‘OBJECT’, ‘SET_FORMALS’, ‘SET_BODY’, ‘SET_CLOENV’, ‘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.
Running examples in ‘tibblify-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: parse_openapi_spec
> ### Title: Parse an OpenAPI spec
> ### Aliases: parse_openapi_spec parse_openapi_schema
> 
> ### ** Examples
> 
> file <- '{
+   "$schema": "http://json-schema.org/draft-04/schema",
+   "title": "Starship",
+   "description": "A vehicle.",
+   "type": "object",
+   "properties": {
+     "name": {
+       "type": "string",
+       "description": "The name of this vehicle. The common name, e.g. Sand Crawler."
+     },
+     "model": {
+       "type": "string",
+       "description": "The model or official name of this vehicle."
+     },
+     "url": {
+       "type": "string",
+       "format": "uri",
+       "description": "The hypermedia URL of this resource."
+     },
+     "edited": {
+       "type": "string",
+       "format": "date-time",
+       "description": "the ISO 8601 date format of the time this resource was edited."
+     }
+   },
+   "required": [
+     "name",
+     "model",
+     "edited"
+   ]
+ }'
> 
> parse_openapi_schema(file)
Error in read_spec(file) : The package "yaml" is required.
Calls: parse_openapi_schema -> read_spec -> <Anonymous>
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Sergei Izrailev <sizrailev@jabiruventures.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sergei",
                    family = "Izrailev",
                    role = c("aut", "cre"),
                    email = "sizrailev@jabiruventures.com")
as necessary.
Maintainer: ‘Alec Stephenson <alec_stephenson@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alec",
                      family = "Stephenson.",
                      role = "aut"),
               person(given = "Alec",
                      family = "Stephenson",
                      role = "cre",
                      email = "alec_stephenson@hotmail.com"))
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Tom Cox <tom.cox@uantwerp.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Tom",
                      family = "Cox",
                      role = c("aut", "cre"),
                      email = "tom.cox@uantwerp.be"),
               person(given = "Lennert",
                      family = "Schepers",
                      role = "aut",
                      email = "lennert.schepers@uantwerp.be"))
as necessary.
Maintainer: ‘Moritz Mueller-Navarra <muellernavarra@gmail.com>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘BuildTT.Rd’:
    https://doi.org/10.5194/os-15-1363-2019
  File ‘SynTT.Rd’:
    https://doi.org/10.5194/os-15-1363-2019
  File ‘TideTable.Rd’:
    https://doi.org/10.5194/os-15-1363-2019
Maintainer: ‘Steven Sanderson <spsanderson@gmail.com>’

Found the following (possibly) invalid URLs:
  URL: https://lifecycle.r-lib.org/articles/stages.html##experimental
    From: README.md
    Message: Invalid URL: '#' not allowed in fragment
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rstanarm'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rstanarm', 'covr', 'rmarkdown', 'pkgdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'rlist', 'framecleaner', 'badger', 'autostats'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'config', 'DT', 'golem', 'gt', 'plotly', 'rmarkdown', 'timevis',
  'tippy'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tmap'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'knitr', 'htmlwidgets'

Packages suggested but not available for checking:
  'rmarkdown', 'tidyverse', 'covr'

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

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

Packages suggested but not available for checking:
  'covr', 'knitr', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'yaml', 'visNetwork', 'htmlwidgets'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tidydelta
> ### Title: Delta Method implementation
> ### Aliases: tidydelta
> 
> ### ** Examples
> 
> # Equivalent ways to use tidydelta()
> library(tidyverse)
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
Package required but not available: ‘plotly’

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'quarto'

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'explore', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Author field differs from that derived from Authors@R
  Author:    ‘Tyson Barrett [aut, cre] (<https://orcid.org/0000-0002-2137-1391>), Mark Fairbanks [ctb], Ivan Leung [ctb], Indrajeet Patil [ctb] (<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets)’
  Authors@R: ‘Tyson Barrett [aut, cre] (ORCID: <https://orcid.org/0000-0002-2137-1391>), Mark Fairbanks [ctb], Ivan Leung [ctb], Indrajeet Patil [ctb] (ORCID: <https://orcid.org/0000-0003-1995-6531>, Twitter: @patilindrajeets)’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

Package suggested but not available for checking: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Robert Myles McDonnell <robertmylesmcdonnell@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Robert", "Myles"),
                    family = "McDonnell",
                    role = c("aut", "cre"),
                    email = "robertmylesmcdonnell@gmail.com")
as necessary.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘iterate.Rd’ ‘random_walk_rank.Rd’
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown', 'covr', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘SuperLearner’

Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr', 'rmarkdown', 'vimp'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 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_paras.Rd’ ‘checks.R’ ‘compute-idx.Rd’ ‘compute-indexes.R’
    ‘dimension-reduction.R’ ‘dimension-reduction.Rd’ ‘dist-fit.Rd’
    ‘distribution-fit.R’ ‘drought-idx.Rd’ ‘drought-indexes.R’ ‘init.R’
    ‘normalise.R’ ‘normalise.Rd’ ‘rescale.Rd’ ‘rescaling.R’
    ‘swap-values.R’ ‘swap.Rd’ ‘temporal-aggregate.Rd’
    ‘temporal-aggregation.R’ ‘theme_benchmark.Rd’
    ‘variable-transformation.R’ ‘variable-transformation.Rd’
'::' or ':::' imports not declared from:
  ‘here’ ‘janitor’ ‘ozmaps’ ‘readxl’ ‘rmapshaper’ ‘sf’ ‘tibble’
'library' or 'require' calls not declared from:
  ‘GGally’ ‘ozmaps’ ‘tidyverse’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'listviewer', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tidyjson.Rcheck/00install.out’ for details.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'quanteda', 'spelling', 'covr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Joshua M Rosenberg <jmrosenberg@utk.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
checkRd: (-1) single_imputation.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) single_imputation.Rd:23-27: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘kableExtra’

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘FactoMineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Michael Milton <michael.r.milton@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Michael",
                    family = "Milton",
                    role = c("aut", "cre"),
                    email = "michael.r.milton@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'quarto', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘tidy_plate.R’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [64s/71s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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:
    ‘summarise2.Rd’
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'admixtools', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rstanarm’

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

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

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

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'yaml'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'skimr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘tidyprompt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: skim_with_labels_and_levels
> ### Title: Skim a dataframe and include labels and levels
> ### Aliases: skim_with_labels_and_levels
> 
> ### ** Examples
> 
> # First add some labels to 'mtcars':
> mtcars$car <- rownames(mtcars)
> mtcars$car <- factor(mtcars$car, levels = rownames(mtcars))
> attr(mtcars$car, "label") <- "Name of the car"
> 
> # Then skim the data:
> mtcars |>
+   skim_with_labels_and_levels()
Error in skim_with_labels_and_levels(mtcars) : 
  The 'skimr' package is required to use skim_with_labels_and_levels()
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘timetk’

Packages suggested but not available for checking:
  'alphavantager', 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'redcapAPI', 'rmarkdown', 'skimr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘import_instruments.R’ ‘make_choose_all_table.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rgee’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
File ‘tidyr/libs/tidyr.so’:
  Found non-API call to R: ‘DATAPTR’
This entry point may be removed soon.

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'covr', 'umx', 'yaml', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'ttservice', 'Seurat', 'plotly'

Package suggested but not available for checking: ‘knitr’

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'spelling', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'fBasics', 'tidyplots'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'mallet', 'quanteda', 'rmarkdown', 'stm'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'kableExtra', 'usethis'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘tidytlg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gentlg
> ### Title: Output a tidytlg table
> ### Aliases: gentlg
> 
> ### ** Examples
> 
> 
> final <- data.frame(
+   label = c(
+     "Overall", "Safety Analysis Set",
+     "Any Adverse event{\\super a}", "- Serious Adverse Event"
+   ),
+   Drug_A = c("", "40", "10 (25%)", "0"),
+   Drug_B = c("", "40", "10 (25%)", "0"),
+   anbr = c(1, 2, 3, 4),
+   roworder = c(1, 1, 1, 1),
+   boldme = c(1, 0, 0, 0),
+   newrows = c(0, 0, 1, 0),
+   indentme = c(0, 0, 0, 1),
+   newpage = c(0, 0, 0, 0)
+ )
> 
> # Produce output in rtf format
> gentlg(
+   huxme = final,
+   wcol = c(0.70, 0.15, 0.15),
+   file = "TSFAEX",
+   title = "This is Amazing Demonstration 1",
+   footers = c(
+     "Note: For demonstrative purposes only",
+     "{\\super a} Subjects are counted once for any given event."
+   )
+ )
Error in loadNamespace(x) : there is no package called ‘usethis’
Calls: gentlg ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'leaflet'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'usethis', 'yaml'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling', 'usethis'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘reprex’

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Simon Urbanek <Simon.Urbanek@r-project.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Simon",
                      family = "Urbanek",
                      role = c("aut", "cre"),
                      email = "Simon.Urbanek@r-project.org"),
               person(given = "Kent",
                      family = "Johnson",
                      role = "ctb",
                      email = "kjohnson@akoyabio.com"))
as necessary.
Maintainer: ‘Will Kuan <aiien61will@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Will",
                    family = "Kuan",
                    role = c("aut", "cre"),
                    email = "aiien61will@gmail.com")
as necessary.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Siyu Han <siyu.han@helmholtz-muenchen.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Siyu",
                      family = "Han",
                      role = c("aut", "cre"),
                      email = "siyu.han@helmholtz-muenchen.de"),
               person(given = "Jialing",
                      family = "Huang",
                      role = "aut"),
               person(given = "Francesco",
                      family = "Foppiano",
                      role = "aut"),
               person(given = "Cornelia",
                      family = "Prehn",
                      role = "aut"),
               person(given = "Jerzy",
                      family = "Adamski",
                      role = "aut"),
               person(given = "Karsten",
                      family = "Suhre",
                      role = "aut"),
               person(given = "Ying",
                      family = "Li",
                      role = "aut"),
               person(given = "Giuseppe",
                      family = "Matullo",
                      role = "aut"),
               person(given = "Freimut",
                      family = "Schliess",
                      role = "aut"),
               person(given = "Christian",
                      family = "Gieger",
                      role = "aut"),
               person(given = "Annette",
                      family = "Peters",
                      role = "aut"),
               person(given = "Rui",
                      family = "Wang-Sattler",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘alakazam’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Chi Song <song.1188@osu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("George", "C."),
                      family = "Tseng",
                      role = "aut",
                      email = "ctseng@pitt.edu"),
               person(given = c("Wing", "H."),
                      family = "Wong",
                      role = "aut",
                      email = "whwong@stanford.edu"),
               person(given = "Chi",
                      family = "Song",
                      role = "cre",
                      email = "song.1188@osu.edu"))
as necessary.
Package required but not available: ‘leaflet’

Packages suggested but not available for checking:
  'spelling', 'rmarkdown', 'knitr', 'pkgdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages suggested but not available for checking: 'knitr', 'covr'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/tikzDevice.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'leaflet'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'leaflet', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Hyungsuk Tak <hyungsuk.tak@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hyungsuk",
                      family = "Tak",
                      role = c("aut", "cre"),
                      email = "hyungsuk.tak@gmail.com"),
               person(given = "Kaisey",
                      family = "Mandel",
                      role = "aut"),
               person(given = c("David", "A."),
                      family = "van Dyk",
                      role = "aut"),
               person(given = c("Vinay", "L."),
                      family = "Kashyap",
                      role = "aut"),
               person(given = "Xiao-Li",
                      family = "Meng",
                      role = "aut"),
               person(given = "Aneta",
                      family = "Siemiginowska",
                      role = "aut"),
               person(given = "Zhirui",
                      family = "Hu",
                      role = "aut"))
as necessary.

The Description field contains
  <arXiv:2005.08049>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Peter Reichert <peter.reichert@emeriti.eawag.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Peter",
                    family = "Reichert",
                    role = c("aut", "cre"),
                    email = "peter.reichert@emeriti.eawag.ch")
as necessary.
Maintainer: ‘Toshihiro Umehara <toshi@niceume.com>’

The BugReports field in DESCRIPTION has
  https://github.com/niceume/timeDF
which should likely be
  https://github.com/niceume/timeDF/issues
instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Dahee Lee <dhlee99@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dahee",
                      family = "Lee",
                      role = c("aut", "cre"),
                      email = "dhlee99@gmail.com"),
               person(given = "Dustin",
                      family = "Tingley",
                      role = "aut"))
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘life_exp.Rd’:
    \keyword{durPlot,}
    \keyword{durSummary,}
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Paul Blanche <paulfblanche@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Paul",
                    family = "Blanche",
                    role = c("aut", "cre"),
                    email = "paulfblanche@gmail.com")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘pec’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Yifu Yan <yanyifu94@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yifu",
                    family = "Yan",
                    role = c("aut", "cre"),
                    email = "yanyifu94@hotmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
No news entries found.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'dygraphs', 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) setup_sql_functions.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} System Functions}
       |                ^
checkRd: (-1) setup_sql_functions.Rd:17: Lost braces; missing escapes or markup?
    17 | Installs functions needed to operated {timeseriesdb} in
       |                                       ^
checkRd: (-1) setup_sql_grant_rights.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Grant execute on {timeseriesdb} functions}
       |                         ^
checkRd: (-1) setup_sql_grant_rights.Rd:17: Lost braces; missing escapes or markup?
    17 | Grant execute on {timeseriesdb} functions
       |                  ^
checkRd: (-1) setup_sql_tables.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} System Tables}
       |                ^
checkRd: (-1) setup_sql_tables.Rd:17: Lost braces; missing escapes or markup?
    17 | Installs tables needed to operated {timeseriesdb} in
       |                                    ^
checkRd: (-1) setup_sql_triggers.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} Triggers}
       |                ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

Packages suggested but not available for checking:
  'modeltime', 'knitr', 'rmarkdown', 'trelliscopejs'

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

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:
    ‘tcor.Rd’
Packages required but not available: 'htmlwidgets', 'rmarkdown'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) alcohol.Rd:16-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:22-26: Lost braces in \itemize; meant \describe ?
Maintainer: ‘Joris Snellenburg <j.snellenburg@vu.nl>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Masami Saga <msaga@mtb.biglobe.ne.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("The", "Institute", "of", "Statistical"),
                      family = "Mathematics",
                      role = "aut"),
               person(given = "Masami",
                      family = "Saga",
                      role = "cre",
                      email = "msaga@mtb.biglobe.ne.jp"))
as necessary.
Maintainer: ‘Josef Leydold <josef.leydold@wu.ac.at>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Josef",
                      family = "Leydold",
                      role = c("aut", "cre"),
                      email = "josef.leydold@wu.ac.at"),
               person(given = "Carsten",
                      family = "Botts",
                      role = "aut"),
               person(given = "Wolfgang",
                      family = "H\\\"ormann",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'knitr', 'rmarkdown'

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

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

Packages suggested but not available for checking:
  'AnnoProbe', 'FactoMineR', 'factoextra', 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION 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:
    ‘base-lenses.R’ ‘where_il.Rd’
Maintainer: ‘Francois Guillem <guillem.francois@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Francois",
                    family = "Guillem",
                    role = c("aut", "cre"),
                    email = "guillem.francois@gmail.com")
as necessary.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tinyProject)
  > 
  > test_check("tinyProject")
  Saving _problems/test-commandArgs-41.R
  [ FAIL 1 | WARN 5 | SKIP 0 | PASS 73 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-commandArgs.R:3:1'): (code run outside of `test_that()`) ───────
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: `with_mock()` was deprecated in testthat 3.2.0 and is now defunct.
  ℹ Please use `with_mocked_bindings()` instead.
  Backtrace:
      ▆
   1. └─testthat::with_mock(...) at test-commandArgs.R:3:1
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 5 | SKIP 0 | PASS 73 ]
  Error:
  ! Test failures.
  Execution halted
Package required but not available: ‘gt’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: style_tt
> ### Title: Style a Tiny Table
> ### Aliases: style_tt tt_style
> 
> ### ** Examples
> 
> ## Don't show: 
> if (knitr::is_html_output()) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ ## Don't show: 
+ }) # examplesIf
Error in loadNamespace(x) : there is no package called ‘knitr’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'DHARMa'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Camilo Khatchikian <ckhatchikian@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Adrien",
                      family = "Rieux",
                      role = "aut"),
               person(given = "Camilo",
                      family = "Khatchikian",
                      role = c("aut", "cre"),
                      email = "ckhatchikian@gmail.com"))
as necessary.
Specified C++14: support will be removed soon
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) partition_undirected_graph.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{cutoff}{Numeric. The value max(0, g_{i,j} - cutoff) so that there are <\code{.num_components}> components in the graph.}
       |                                           ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Brian Salzer <brian.m.salzer@frb.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jeff",
                      family = "Hallman",
                      role = "aut",
                      email = "jeffhallman@gmail.com"),
               person(given = "Brian",
                      family = "Salzer",
                      role = "cre",
                      email = "brian.m.salzer@frb.gov"))
as necessary.
checkRd: (-1) tierChart.Rd:332: Lost braces
   332 |   If the input argument code{boxes} is \code{F}, the \code{lBox},
       |                             ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘leaflet’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ReDaMoR', 'visNetwork', 'DT', 'roxygen2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'BED'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Luke Tierney <luke-tierney@uiowa.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Luke",
                    family = "Tierney",
                    role = c("aut", "cre"),
                    email = "luke-tierney@uiowa.edu")
as necessary.
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
Maintainer: ‘Filipe Campelo <fcampelo@ci.uc.pt>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Filipe",
                    family = "Campelo",
                    role = c("aut", "cre"),
                    email = "fcampelo@ci.uc.pt")
as necessary.
Maintainer: ‘Jasin Machkour <jasin.machkour@tu-darmstadt.de>’

The Description field contains
  Machkour, Muma, and Palomar (2022) <arXiv:2110.06048>, Efron, Hastie,
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Author field differs from that derived from Authors@R
  Author:    ‘Lukas Soenning [aut, cre, cph] (<https://orcid.org/0000-0002-2705-395X>), German Research Foundation (DFG) [fnd] (018mejw64, Grant number 548274092)’
  Authors@R: ‘Lukas Soenning [aut, cre, cph] (ORCID: <https://orcid.org/0000-0002-2705-395X>), German Research Foundation (DFG) [fnd] (ROR: <https://ror.org/018mejw64>, Grant number 548274092)’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘fBasics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jona Lilienthal <lilienthal@statistik.tu-dortmund.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jona",
                    family = "Lilienthal",
                    role = c("aut", "cre"),
                    email = "lilienthal@statistik.tu-dortmund.de")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/tlm.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++14: support will be removed soon
checkRd: (-1) pmvn.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvn.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvn.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:25: Lost braces in \itemize; meant \describe ?
Maintainer: ‘Muhammed Ali Onder <muhammedalionder@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Muhammed", "Ali"),
                    family = "Onder",
                    role = c("aut", "cre"),
                    email = "muhammedalionder@gmail.com")
as necessary.
Package required but not available: ‘tmap’

Package suggested but not available for checking: ‘knitr’

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

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

Package suggested but not available for checking: ‘knitr’

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

Package suggested but not available for checking: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'htmlwidgets', 'leafem', 'leafgl', 'leaflegend', 'leaflet',
  'leafsync'

Packages suggested but not available for checking: 'knitr', 'widgetframe'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Kasper Kristensen <kaskr@dtu.dk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kasper",
                    family = "Kristensen",
                    role = c("aut", "cre"),
                    email = "kaskr@dtu.dk")
as necessary.
Maintainer: ‘Junhui Li <junhuili@cau.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Junhui",
                    family = "Li",
                    role = c("aut", "cre"),
                    email = "junhuili@cau.edu.cn")
as necessary.
Maintainer: ‘Jian Li <rweibo@sina.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jian",
                    family = "Li",
                    role = c("aut", "cre"),
                    email = "rweibo@sina.com")
as necessary.
Maintainer: ‘Andrea Capozio <andreacapozio@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Andrea",
                    family = "Capozio",
                    role = c("aut", "cre"),
                    email = "andreacapozio@gmail.com")
as necessary.
checkRd: (-1) tv_episode_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the episode_id value found in the change entries.
       |                                                 ^
checkRd: (-1) tv_season_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the season_id value found in the change entries.
       |                                                 ^
Package required but not available: ‘SuperLearner’

Package suggested but not available for checking: ‘gam’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) pvalEffectPlot.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:94: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Stefan Theussl <Stefan.Theussl@R-project.org>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Cody Moore <Jumper9400@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Cody",
                    family = "Moore",
                    role = c("aut", "cre"),
                    email = "jumper9400@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'prettydoc', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [21s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tmt)
  - tmt 0.3.6-0 (2025-06-20)
  > 
  > test_check("tmt")
  Saving _problems/test-helperfunctions-771.R
  The following items are specified in the dataset, but not in the submitted mstdesign: ii1 
  The following items are specified in the mstdesign, but not in the dataset: i1 
  The following items are specified in the dataset, but not in the submitted mstdesign: i1 
  The following items are specified in the mstdesign, but not in the dataset: ii1 
  The following items are specified in the dataset, but not in the submitted mstdesign: ii1 
  The following items are specified in the mstdesign, but not in the dataset: i1 
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 352 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-helperfunctions.R:771:5'): test additional functions ───────────
  Error in `cbind(thres[1, , drop = FALSE], t(diff(thres)))`: number of rows of matrices must match (see arg 2)
  Backtrace:
      ▆
   1. └─tmt:::thresholds_to_probs(thres_row, opts = "", row = TRUE) at test-helperfunctions.R:771:5
   2.   └─base::cbind(thres[1, , drop = FALSE], t(diff(thres)))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 352 ]
  Error:
  ! Test failures.
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Samsiddhi Bhattacharjee <sb1@nibmg.ac.in>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Samsiddhi",
                      family = "Bhattacjarjee",
                      role = "aut",
                      email = "sb1@nibmg.ac.in"),
               person(given = "Samsiddhi",
                      family = "Bhattacharjee",
                      role = "cre",
                      email = "sb1@nibmg.ac.in"))
as necessary.
Package required but not available: ‘qgraph’

Packages suggested but not available for checking:
  'gt', 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Tore Opsahl <tore@opsahl.co.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tore",
                    family = "Opsahl",
                    role = c("aut", "cre"),
                    email = "tore@opsahl.co.uk")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [101s/106s]
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(tnl.Test)
  > 
  > test_check("tnl.Test")
  Saving _problems/test_function-65.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 64 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_function.R:65:3'): functions returns a  vector with the expected size ──
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `expect_vector(rtnl(10, 5, 10, 2), ptype = double(), size = 10)`: The package "vctrs" is required.
  Backtrace:
      ▆
   1. └─testthat::expect_vector(...) at test_function.R:65:3
   2.   └─rlang::check_installed("vctrs")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 64 ]
  Error:
  ! Test failures.
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'vcr', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(TNRS)
  > 
  > 
  > test_check("TNRS")
  Error in `source_dir()`:
  ! Failed to evaluate './setup-tnrs.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("TNRS")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(...)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at ./setup-tnrs.R:14:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<S3: packageNotFoundError>`)
   17.   └─cli::cli_abort(...)
   18.     └─rlang::abort(...)
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking:
  'apexcharter', 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ali Santacruz <amsantac@unal.edu.co>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Robert", "G."),
                      family = "Pontius",
                      role = "aut",
                      email = "rpontius@clarku.edu"),
               person(given = "Ali",
                      family = "Santacruz",
                      role = c("aut", "cre"),
                      email = "amsantac@unal.edu.co"),
               person(given = "Amin",
                      family = "Tayyebi",
                      role = "aut"),
               person(given = "Benoit",
                      family = "Parmentier",
                      role = "aut"),
               person(given = "Kangping",
                      family = "Si",
                      role = "aut"))
as necessary.
Package required but not available: ‘keyring’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Sara Algeri <salgeri@umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sara",
                    family = "Algeri",
                    role = c("aut", "cre"),
                    email = "salgeri@umn.edu")
as necessary.

The Description field contains
  <arXiv:1803.03858>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Kasper Welbers <kasperwelbers@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Kasper",
                      family = "Welbers",
                      role = c("aut", "cre"),
                      email = "kasperwelbers@gmail.com"),
               person(given = "Wouter",
                      family = "van Atteveldt",
                      role = "aut"))
as necessary.
Specified C++11: support will be removed soon
Maintainer: ‘Lincoln Mullen <lincoln@lincolnmullen.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Abedrahim Ben rebia <b.abedrahim@tomba.io>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Abedrahim", "Ben"),
                      family = "rebia",
                      role = c("ctb", "aut", "cre"),
                      email = "b.abedrahim@tomba.io"),
               person(family = "Tomba.io",
                      role = c("cph", "aut")))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Timothy Conwell <timconwell@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Timothy",
                    family = "Conwell",
                    role = c("aut", "cre"),
                    email = "timconwell@gmail.com")
as necessary.
checkRd: (-1) jsonStr.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Format data as a JSON object (like this: {"x": "120"}).}
       |                                                 ^
checkRd: (-1) jsonStr.Rd:18: Lost braces; missing escapes or markup?
    18 | Format data as a JSON object (like this: {"x": "120"}).
       |                                          ^
checkRd: (-1) fixed_width_no_modeling.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
Maintainer: ‘Mouloud Belbahri <mouloud.belbahri@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mouloud",
                      family = "Belbahri",
                      role = c("aut", "cre"),
                      email = "mouloud.belbahri@gmail.com"),
               person(given = "Olivier",
                      family = "Gandouet",
                      role = "aut"),
               person(given = "Alejandro",
                      family = "Murua",
                      role = "aut"),
               person(given = c("Vahid", "Partovi"),
                      family = "Nia",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pkgdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Gregory W. Schwartz <gsch@pennmedicine.upenn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Gregory", "W."),
                    family = "Schwartz",
                    role = c("aut", "cre"),
                    email = "gsch@pennmedicine.upenn.edu")
as necessary.
Maintainer: ‘Damian W. Betebenner <dbetebenner@nciea.org>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'Arothron', 'alphashape3d', 'morphomap', 'Morpho', 'rgl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Henrik Bengtsson <henrikb@braju.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^
checkRd: (-1) getSegsExtra.Rd:14: Lost braces
    14 | \item{data}{data.table returned from function /code{tdtr}}
       |                                                    ^
Maintainer: ‘Doug Friedman <doug.nhp@gmail.com>’

The Description field contains
  <arXiv:1206.4631v1>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'stm'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Minzhe Wang <minzhew@uchicago.edu>’

The Description field contains
  (2017) <arXiv:1704.07016>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'rJava', 'mallet', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
No examples, no tests, no vignettes
Maintainer: ‘Bastian Pfeifer <bastian.pfeifer@medunigraz.at>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Michael", "G."),
                      family = "Schimek",
                      role = "aut"),
               person(given = "Eva",
                      family = "Budinska",
                      role = "aut"),
               person(given = "Jie",
                      family = "Ding",
                      role = "aut"),
               person(given = c("Karl", "G."),
                      family = "Kugler",
                      role = "aut"),
               person(given = "Vendula",
                      family = "Svendova",
                      role = "aut"),
               person(given = "Shili",
                      family = "Lin",
                      role = "aut"),
               person(given = "Bastian",
                      family = "Pfeifer",
                      role = c("aut", "cre"),
                      email = "bastian.pfeifer@medunigraz.at"))
as necessary.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking:
  'knitr', 'RGtk2', 'gWidgets2RGtk2'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/TopKLists.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'gurobi'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Gabriele Sales <gabriele.sales@unipd.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Sofia",
                      family = "Massa",
                      role = "aut"),
               person(given = "Gabriele",
                      family = "Sales",
                      role = c("aut", "cre"),
                      email = "gabriele.sales@unipd.it"))
as necessary.
Package required but not available: ‘qpgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'Racmacs', 'rgl', 'plotly', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION 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:
    ‘dat_checks.R’ ‘setters_and_getters.R’
Maintainer: ‘Mahmoud Mosalman Yazdi <m.mosalman@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Mahmoud", "Mosalman"),
                    family = "Yazdi",
                    role = c("aut", "cre"),
                    email = "m.mosalman@gmail.com")
as necessary.
Package required but not available: ‘pins’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Gilberto Camara <gilberto.camara.inpe@gmail.com>’

The Description field contains
  (a) 'adabelief' by Zhuang et al (2020), <arXiv:2010.07468>; (b)
  'adabound' by Luo et al.(2019), <arXiv:1902.09843>; (c) 'adahessian' by
  Yao et al.(2021) <arXiv:2006.00719>; (d) 'adamw' by Loshchilov & Hutter
  (2019), <arXiv:1711.05101>; (e) 'madgrad' by Defazio and Jelassi
  (2021), <arXiv:2101.11075>; (f) 'nadam' by Dozat (2019),
  Ma and Yarats(2019), <arXiv:1810.06801>; (h) 'radam' by Liu et al.
  (2019), <arXiv:1908.03265>; (i) 'swats' by Shekar and Sochee (2018),
  <arXiv:1712.07628>; (j) 'yogi' by Zaheer et al.(2019),
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘quanteda’

Packages suggested but not available for checking:
  'toscaData', 'knitr', 'devtools', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Running examples in ‘toscutil-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: update_docstring
> ### Title: Update docstring for a Function
> ### Aliases: update_docstring
> ### Keywords: doc
> 
> ### ** Examples
> 
> uri <- system.file("testfiles/funcs.R", package = "toscutil")
> func <- "f4"
> update_docstring(uri, func)
Error in get_formals(uri, content, func) : 
  Package 'languageserver' is required for parsing formals. Please install first.
Calls: update_docstring -> get_formals
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(toscutil)
  > 
  > test_check("toscutil")
  Saving _problems/test-update_docstring-4.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 45 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-update_docstring.R:4:5'): update_docstring works ───────────────
  Error in `get_formals(uri, content, func)`: Package 'languageserver' is required for parsing formals. Please install first.
  Backtrace:
      ▆
   1. └─toscutil::update_docstring(uri, "f2") at test-update_docstring.R:4:5
   2.   └─toscutil::get_formals(uri, content, func)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 45 ]
  Error:
  ! Test failures.
  Execution halted
Package required but not available: ‘bibliometrix’

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘TOSTER-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dataTOSTone
> ### Title: TOST One Sample T-Test
> ### Aliases: dataTOSTone
> 
> ### ** Examples
> 
> library("TOSTER")
> 
> dataTOSTone(data=iris, vars="Sepal.Width", mu=3, low_eqbound=-0.3, high_eqbound=0.3,
+             alpha=0.05, desc=TRUE, plots=TRUE)
Error in loadNamespace(x) : there is no package called ‘knitr’
Calls: dataTOSTone ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
boot_log_TOST 5.281  0.139   6.722
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Guanglai Li <liguanglai@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Guanglai",
                    family = "Li",
                    role = c("aut", "cre"),
                    email = "liguanglai@gmail.com")
as necessary.
Maintainer: ‘Martin R. Smith <martin.smith@durham.ac.uk>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'plotly'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rmarkdown’

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:
    ‘response_builder.R’
Problems with news in ‘NEWS.md’:
No news entries found.
Packages required but not available: 'DT', 'leaflet'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'tcpl', 'covr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'DT', 'flextable', 'ggiraph'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Xiang Lyu <lyu17@purdue.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hanfang",
                      family = "Yang",
                      role = "aut"),
               person(given = "Kun",
                      family = "Lu",
                      role = "aut"),
               person(given = "Xiang",
                      family = "Lyu",
                      role = c("aut", "cre"),
                      email = "lyu17@purdue.edu"),
               person(given = "Feifang",
                      family = "Hu",
                      role = "aut"),
               person(given = "Yichuan",
                      family = "Zhao",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ronja Foraita <foraita@leibniz-bips.de>’

The Description field contains
  <arXiv:2108.13395> provide a guide how to use tpc to analyse cohort
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Carlos P. Carmona <perezcarmonacarlos@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Carlos", "P."),
                    family = "Carmona",
                    role = c("aut", "cre"),
                    email = "perezcarmonacarlos@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Wei Jiang <jiangwei@hrbmu.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Wei",
                    family = "Jiang",
                    role = c("aut", "cre"),
                    email = "jiangwei@hrbmu.edu.cn")
as necessary.
Package required but not available: ‘MESS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Alessio Locallo <alessio.locallo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alessio",
                      family = "Locallo",
                      role = c("aut", "cre"),
                      email = "alessio.locallo@gmail.com"),
               person(given = "Davide",
                      family = "Prandi",
                      role = "aut",
                      email = "davide.prandi@unitn.it"),
               person(given = "Francesca",
                      family = "Demichelis",
                      role = "aut",
                      email = "f.demichelis@unitn.it"))
as necessary.
Packages required but not available: 'knitr', 'xlsx'

Package suggested but not available for checking: ‘rmarkdown’

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘replace_leading_whitespace.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rgl’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/TPmsm.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jun Yan <jun.yan@uconn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jun",
                    family = "Yan",
                    role = c("aut", "cre"),
                    email = "jun.yan@uconn.edu")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Chanwoo Lee <chanwoo.lee@wisc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chanwoo",
                      family = "Lee",
                      role = c("aut", "cre"),
                      email = "chanwoo.lee@wisc.edu"),
               person(given = "Lexin",
                      family = "Li",
                      role = "aut",
                      email = "lexinli@berkeley.edu"),
               person(given = c("Hao", "Helen"),
                      family = "Zhang",
                      role = "aut",
                      email = "hzhang@math.arizona.edu"),
               person(given = "Miaoyan",
                      family = "Wang",
                      role = "aut",
                      email = "miaoyan.wang@wisc.edu"))
as necessary.

The Description field contains
  Series Representation. <arXiv:2105.01783>. The method employs the
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘keras’

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

Package suggested but not available for checking: ‘knitr’

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'shinytest2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) parse_beast_output_files.Rd:23: Lost braces
    23 |     item{\code{estimates}: parameter estimates}
       |         ^
checkRd: (-1) parse_beast_output_files.Rd:24-28: Lost braces
    24 |     item{
       |         ^
checkRd: (-1) parse_beast_output_files.Rd:29-31: Lost braces
    29 |     item{\code{operators}: the BEAST2 MCMC operator
       |         ^
checkRd: (-1) parse_beast_posterior.Rd:28: Lost braces
    28 |     item{\code{estimates}: parameter estimates}
       |         ^
checkRd: (-1) parse_beast_posterior.Rd:29-33: Lost braces
    29 |     item{
       |         ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Filipe Campelo <fcampelo@uc.pt>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Filipe",
                    family = "Campelo",
                    role = c("aut", "cre"),
                    email = "fcampelo@uc.pt")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Marjolein Bruijning <m.bruijning@uva.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Marjolein",
                      family = "Bruijning",
                      role = c("aut", "cre"),
                      email = "m.bruijning@uva.nl"),
               person(given = c("Marco", "D."),
                      family = "Visser",
                      role = "aut"),
               person(given = c("Caspar", "A."),
                      family = "Hallmann",
                      role = "aut"),
               person(given = "Eelke",
                      family = "Jongejans",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Claudio Zandonella Callegher <claudiozandonella@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘rmarkdown’

Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr', 'pagedown', 'vcr'

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

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

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

Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown', 'covr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Brian Battaile <brian.battaile@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Brian",
                    family = "Battaile",
                    role = c("aut", "cre"),
                    email = "brian.battaile@gmail.com")
as necessary.
Note: skipping ‘TrackReconstruction.Snw’ due to unavailable dependencies:
  'rgl'
Package required but not available: ‘knitr’

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'competitiontoolbox', 'rmarkdown', 'bookdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'vcr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tradestatistics)
  > 
  > test_check("tradestatistics")
  Error in `source_dir()`:
  ! Failed to evaluate './helper-tradestatistics.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("tradestatistics")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_helpers(".", env)
    7. │           └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(...)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library(vcr) at ./helper-tradestatistics.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─cli::cli_abort(...)
   18.     └─rlang::abort(...)
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Kleanthis Koupidis <koupidis.okfgr@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Kleanthis",
                      family = "Koupidis",
                      role = c("aut", "cre"),
                      email = "koupidis.okfgr@gmail.com"),
               person(given = "Aikaterini",
                      family = "Chatzopoulou",
                      role = "aut"),
               person(given = "Charalampos",
                      family = "Bratsas",
                      role = "aut"),
               person(given = "Panagiotis",
                      family = "Tzenos",
                      role = "dtc"),
               person(given = c("Josep", "Maria"),
                      family = "Salanova",
                      role = "dtc"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘adabag’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) trait_missing.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'OpenStreetMap', 'knitr', 'rgl', 'taxidata'

VignetteBuilder package required for checking but not installed: ‘knitr’
'::' or ':::' import not declared from: ‘devtools’
'library' or 'require' calls not declared from:
  ‘XML’ ‘devtools’ ‘jsonlite’ ‘ks’ ‘maps’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package suggested but not available for checking: ‘knitr’

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/RJ-2021-075.Rnw’
   ‘inst/doc/mixed-effects-additive-models.Rnw’
   ‘inst/doc/tramME-JSS.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'knitr', 'kableExtra'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/tramnet.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Rich FitzJohn <rich.fitzjohn@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Packages suggested but not available for checking:
  'knitr', 'randomForestSRC', 'rms'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/NAMI.Rnw’
   ‘inst/doc/mtram.Rnw’
   ‘inst/doc/survtram.Rnw’
   ‘inst/doc/tram.Rnw’
(Is a VignetteBuilder field missing?)

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

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/tramvs.Rnw’
(Is a VignetteBuilder field missing?)

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Babak Naderi <bnaderi9@gmail.com>’

The Description field contains
  Möller (2020) <arXiv:2004.11490>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
No examples, no tests, no vignettes
Package required but not available: ‘yaml’

Packages suggested but not available for checking:
  'covr', 'devtools', 'pkgdown', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Cristhian Paredes <craparedesca@unal.edu.co>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Cristhian",
                      family = "Paredes",
                      role = c("aut", "cre"),
                      email = "craparedesca@unal.edu.co"),
               person(given = c("Eduardo", "Rodríguez", "de", "San"),
                      family = "Miguel",
                      role = "aut"))
as necessary.
Package required but not available: ‘ggformula’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jie Zhou <zhoujie02569@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jie",
                      family = "Zhou",
                      role = c("aut", "cre"),
                      email = "zhoujie02569@gmail.com"),
               person(given = "Jiajia",
                      family = "Zhang",
                      role = "aut"),
               person(given = "Wenbin",
                      family = "Lu",
                      role = "aut"))
as necessary.
Maintainer: ‘Xavier Didelot <xavier.didelot@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Specified C++11: support will be removed soon
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Somenath Sit <somenath.bhu.2010@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Somenath",
                    family = "Sit",
                    role = c("aut", "cre"),
                    email = "somenath.bhu.2010@gmail.com")
as necessary.
Packages required but not available: 'ggtree', 'Hmisc'

Packages suggested but not available for checking:
  'prettydoc', 'knitr', 'ggtreeExtra', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ecpc', 'fwelnet', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Almut E. D. Veraart <a.veraart@imperial.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Almut", "E.", "D."),
                    family = "Veraart",
                    role = c("aut", "cre"),
                    email = "a.veraart@imperial.ac.uk")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Lam Opal Huang <opal.huang@mail.mcgill.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Lam", "Opal"),
                    family = "Huang",
                    role = c("aut", "cre"),
                    email = "opal.huang@mail.mcgill.ca")
as necessary.
Packages required but not available:
  'sunburstR', 'networkD3', 'htmlwidgets'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'usethis', 'Eunomia', 'DatabaseConnector',
  'SqlRender', 'CohortGenerator', 'ResultModelManager', 'CirceR',
  'plotly', 'PaRe'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Marshall Brown <mdbrown@fhcrc.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Marshall",
                      family = "Brown",
                      role = c("aut", "cre"),
                      email = "mdbrown@fhcrc.org"),
               person(given = "Holly",
                      family = "Janes",
                      role = "aut"))
as necessary.
checkRd: (-1) trtsel.Rd:69: Lost braces; missing escapes or markup?
    69 | numeric with two values {0,1} and gaussian(link = "identity") otherwise.
       |                         ^
Package required but not available: ‘rgl’

Package suggested but not available for checking: ‘knitr’

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:
    ‘tree_mesh.R’ ‘tree_mesh.Rd’ ‘zzz.R’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Sophie Kersting <sophie_kersting@gmx.de>’

The Description field contains
  Kersting, and L. Kühn (2023) <arXiv:2307.14537>, which provides precise
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Silvestre Garcia de Jalon <s.garciadejalon@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Silvestre", "Garcia"),
                    family = "de Jalon",
                    role = c("aut", "cre"),
                    email = "s.garciadejalon@gmail.com")
as necessary.
Maintainer: ‘Wen Tian (Wendy) Wang <wtwang@sfu.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Wen", "Tian", "Wang,Lloyd"),
                      family = "Elliott",
                      role = "aut",
                      comment = "Wendy"),
               person(given = c("Wen", "Tian"),
                      family = "Wang",
                      role = "cre",
                      email = "wtwang@sfu.ca",
                      comment = "Wendy"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'bookdown', 'kdensity', 'knitr', 'plotly', 'rmarkdown', 'rgl',
  'spelling', 'TreeDistData', 'Umatrix'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'Seurat', 'knitr', 'plotly', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘treefit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generate_n_arms_star_data
> ### Title: Generate a multi-dimensional star tree data
> ### Aliases: generate_n_arms_star_data
> 
> ### ** Examples
> 
> # Generate a 100-dimensional star tree data that contain 500 data points
> # and fit a star tree with 3 arms. The generated data are a bit noisy but
> # tree-like.
> star100.tree_like <- treefit::generate_n_arms_star_data(100, 500, 3, 0.1)
> # Reduce dimension to visualize.
> star3.tree_like = prcomp(star100.tree_like, rank.=3)$x
> plotly::plot_ly(data.frame(star3.tree_like),
+                 x=~PC1,
+                 y=~PC2,
+                 z=~PC3,
+                 type="scatter3d",
+                 mode="markers",
+                 marker=list(size=1))
Error in loadNamespace(x) : there is no package called ‘plotly’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'shinytest', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION 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:
    ‘ranger_surv.unify.Rd’
Maintainer: ‘Oskar Hagen <oskar.hagen@outlook.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Oskar",
                      family = "Hagen",
                      role = c("aut", "cre"),
                      email = "oskar.hagen@outlook.com"),
               person(given = "Tanja",
                      family = "Stadler",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tanja Stadler <tanja.stadler@bsse.ethz.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tanja",
                    family = "Stadler",
                    role = c("aut", "cre"),
                    email = "tanja.stadler@bsse.ethz.ch")
as necessary.
File ‘treesitter/libs/treesitter.so’:
  Found non-API call to R: ‘SET_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.
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'htmlwidgets', 'rgl', 'RLumShiny', 'scatterD3'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'RPANDA', 'lintr', 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'ggtree', 'knitr', 'rmarkdown', 'bookdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘treestructure-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.TreeStructure
> ### Title: Plot TreeStructure tree with cluster and partition variables
> ### Aliases: plot.TreeStructure
> 
> ### ** Examples
> 
> 
> #tree <- ape::read.tree( system.file('sim.nwk', package = 'treestructure') )
> # you can run the example below before plotting
> #struc <- trestruct( tree )
> 
> #because it can take a minute or so to run treestructure, we will load it here
> struc <- readRDS( system.file('struc_plot_example.rds', package='treestructure') )
> #plot treestructure object
> 
> suppressWarnings(plot(struc))
Error in .plot.TreeStructure.ggtree(x, ...) : 
  "ggtree" %in% utils::installed.packages()[, 1] is not TRUE
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'htmlwidgets', 'knitr', 'fidelius'

Packages suggested but not available for checking:
  'plotly', 'covr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'vcr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tremendousr)
  > 
  > test_check("tremendousr")
  Error in `source_dir()`:
  ! Failed to evaluate './setup-tremendousr.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("tremendousr")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(...)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at ./setup-tremendousr.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<S3: packageNotFoundError>`)
   17.   └─cli::cli_abort(...)
   18.     └─rlang::abort(...)
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ashkan Ertefaie <ashkan_ertefaie@urmc.rochester.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xinyao",
                      family = "Ji",
                      role = "aut"),
               person(given = "Ashkan",
                      family = "Ertefaie",
                      role = c("aut", "cre"),
                      email = "ashkan_ertefaie@urmc.rochester.edu"))
as necessary.
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘usethis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jasin Machkour <jasin.machkour@tu-darmstadt.de>’

The Description field contains
  (2022) <arXiv:2110.06048>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'WGCNA'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
No news entries found.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'DiagrammeR'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rpact’

Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'rmarkdown', 'survminer'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Vicky Qian Wu <wuqian7@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Ed", "Zhang", ";", "Vicky", "Qian", "Wu", ";", "Shein-Chung", "Chow", ";", "Harry"),
                      family = "G.Zhang",
                      role = "aut",
                      email = "ed.zhang.jr@gmail.com",
                      comment = "Quality check"),
               person(given = c("Vicky", "Qian"),
                      family = "Wu",
                      role = "cre",
                      email = "wuqian7@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Specified C++11: support will be removed soon
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'leaflet'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Os Keyes <ironholds@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Os",
                      family = "Keyes",
                      role = c("aut", "cre"),
                      email = "ironholds@gmail.com"),
               person(given = "Drew",
                      family = "Schmidt",
                      role = "aut"),
               person(given = "Yuuki",
                      family = "Takano",
                      role = "cph"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'DT', 'factoextra'

Package suggested but not available for checking: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Phil Mike Jones <philmikejones@gmail.com>’

Found the following (possibly) invalid file URI:
  URI: CODE_OF_CONDUCT.md
    From: README.md
Cannot process vignettes
Packages suggested but not available for checking:
  'bookdown', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rgl’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Timo Stöcker <timo.stoecker@hhu.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Timo",
                      family = "Stöcker",
                      role = c("aut", "cre"),
                      email = "timo.stoecker@hhu.de"),
               person(given = "Noah",
                      family = "Simon",
                      role = "aut"),
               person(given = "Jerome",
                      family = "Friedman",
                      role = "aut"),
               person(given = "Trevor",
                      family = "Hastie",
                      role = "aut"),
               person(given = "Rob",
                      family = "Tibshirani",
                      role = "aut"))
as necessary.
Maintainer: ‘Michael D. Sumner <mdsumner@gmail.com>’

The BugReports field in DESCRIPTION has
  https://github.com/Trackage/tripEstimation
which should likely be
  https://github.com/Trackage/tripEstimation/issues
instead.
Maintainer: ‘Felix Schönbrodt <felix.schoenbrodt@psy.lmu.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("F.", "D."),
                      family = "Schönbrodt",
                      role = "aut"),
               person(given = c("M.", "D."),
                      family = "Back",
                      role = "aut"),
               person(given = c("S.", "C."),
                      family = "Schmukle",
                      role = "aut"),
               person(given = "Felix",
                      family = "Schönbrodt",
                      role = "cre",
                      email = "felix.schoenbrodt@psy.lmu.de"))
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'covr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Richard Ambler <rambler@ibwya.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Richard",
                    family = "Ambler",
                    role = c("aut", "cre"),
                    email = "rambler@ibwya.net")
as necessary.
Malformed Title field: should not end in a period.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Somjit Roy <somjit.roy2001@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Somjit",
                    family = "Roy",
                    role = c("aut", "cre"),
                    email = "somjit.roy2001@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘David Hugh-Jones <davidhughjones@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "David",
                    family = "Hugh-Jones",
                    role = c("aut", "cre"),
                    email = "davidhughjones@gmail.com")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yuyao Wang <yuw079@ucsd.edu>’

The Description field contains
  dependent left truncation" <arXiv:2208.06836>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Frederick Novomestky <fnovomes@poly.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Frederick",
                      family = "Novomestky",
                      role = c("aut", "cre"),
                      email = "fn334@nyu.edu"),
               person(given = "Saralees",
                      family = "Nadarajah",
                      role = "aut",
                      email = "saralees.nadarajah@manchester.ac.uk"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michael Braun <braunm@smu.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Specified C++11: support will be removed soon
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Charles J. Geyer <charlie@stat.umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Charles", "J."),
                      family = "Geyer.",
                      role = "aut",
                      email = "charlie@stat.umn.edu"),
               person(given = c("Charles", "J."),
                      family = "Geyer",
                      role = "cre",
                      email = "charlie@stat.umn.edu"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Rainer Schlittgen <R.Schlittgen@t-online.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Rainer",
                    family = "Schlittgen",
                    role = c("aut", "cre"),
                    email = "r.schlittgen@t-online.de")
as necessary.
Maintainer: ‘Kung-Sik Chan <kungsik.chan@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Kung-Sik",
                      family = "Chan",
                      role = c("aut", "cre"),
                      email = "kungsik.chan@gmail.com"),
               person(given = "Brian",
                      family = "Ripley",
                      role = "aut"))
as necessary.
checkRd: (-1) summary.armasubsets.Rd:16: Lost braces
    16 | \item{matrix.logical}{With matrix=TRUE, the matrix is logical TRUE/FALSE or string "*"/code{" "}}
       |                                                                                            ^
Package required but not available: ‘scoringRules’

Packages suggested but not available for checking:
  'knitr', 'kableExtra', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'dygraphs', 'knitr', 'rmarkdown', 'spelling', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) tsBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:34: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘longitudinalData’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘calc_distance.R’ ‘reason_dataleaks.R’ ‘viz_dataleaks.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Javier López-de-Lacalle <javlacalle@yahoo.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Javier",
                    family = "López-de-Lacalle",
                    role = c("aut", "cre"),
                    email = "javlacalle@yahoo.es")
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘tsdecomp-package.Rd’:
    \keyword{package, ts}
Maintainer: ‘Wenchuan Guo <wguo1017@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Wenchuan",
                      family = "Guo",
                      role = c("aut", "cre"),
                      email = "wguo1017@gmail.com"),
               person(given = "Jianan",
                      family = "Hui",
                      role = "aut"),
               person(given = "Bob",
                      family = "Zhong",
                      role = "aut"))
as necessary.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jorge Vieira <jorgealexandrevieira@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jorge",
                    family = "Vieira",
                    role = c("aut", "cre"),
                    email = "jorgealexandrevieira@gmail.com")
as necessary.
Maintainer: ‘Luke Mosley <l.mosley@lancaster.ac.uk>’

The Description field contains
  <arXiv:2108.05783> for disaggregating low-frequency series in the
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Maintainer: ‘Usue Mori <usue.mori@ehu.eus>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Packages required but not available: 'longitudinalData', 'TSclust'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Vitor Cerqueira <cerqueira.vitormanuel@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Hakki Sabah <hakkisabah@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hakki",
                    family = "Sabah",
                    role = c("aut", "cre"),
                    email = "hakkisabah@hotmail.com")
as necessary.
Maintainer: ‘Antonio Fabio Di Narzo <antonio.fabio@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(family = "Antonio",
                      role = c("aut", "cre"),
                      email = "antonio.fabio@gmail.com"),
               person(given = c("Fabio", "Di"),
                      family = "Narzo",
                      role = "aut"))
as necessary.
Found the following HTML validation problems:
tseriesTARMA.html:628:1 (TARMA.fit.Rd:99): Warning: <script> anchor "MathJax-script" already defined
tseriesTARMA.html:972:1 (TARMA.fit2.Rd:91): Warning: <script> anchor "MathJax-script" already defined
tseriesTARMA.html:1240:1 (TARMA.sim.Rd:64): Warning: <script> anchor "MathJax-script" already defined
tseriesTARMA.html:2431:1 (supLMQur.Rd:26): Warning: <script> anchor "MathJax-script" already defined
Maintainer: ‘Ali Saeb <ali.saeb@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ali",
                    family = "Saeb",
                    role = c("aut", "cre"),
                    email = "ali.saeb@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Francisco Martinez <fmartin@ujaen.es>’

The BugReports field in DESCRIPTION has
  https://github.com/franciscomartinezdelrio/tsfgrnn
which should likely be
  https://github.com/franciscomartinezdelrio/tsfgrnn/issues
instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Dr. Ranjit Kumar Paul <ranjitstat@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Sandipan",
                      family = "Samanta",
                      role = "aut"),
               person(given = c("Ranjit", "Kumar"),
                      family = "Paul",
                      role = "aut"),
               person(given = "Dipankar",
                      family = "Mitra",
                      role = "aut"),
               person(given = c("Dr.", "Ranjit", "Kumar"),
                      family = "Paul",
                      role = "cre",
                      email = "ranjitstat@gmail.com"))
as necessary.
Package required but not available: ‘flextable’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'timetk', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘tsgc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FilterResults-class
> ### Title: FilterResults
> ### Aliases: FilterResults-class FilterResults
> 
> ### ** Examples
> 
> library(tsgc)
> data(gauteng,package="tsgc")
> idx.est <- zoo::index(gauteng) <= as.Date("2020-07-20")
> 
> # Specify a model
> model <- SSModelDynamicGompertz$new(Y = gauteng[idx.est], q = 0.005)
> # Estimate a specified model
> res <- model$estimate()
Warning in `dim<-.zoo`(`*tmp*`, value = length(x)) :
  setting this dimension may lead to an invalid zoo object
Warning in `dim<-.zoo`(`*tmp*`, value = c(n, p)) :
  setting this dimension may lead to an invalid zoo object
> # Print estimation results
> res$print_estimation_results()
Error in loadNamespace(x) : there is no package called ‘kableExtra’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘yaml’

Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Yao-Hwei Fang <yhfang@nhri.org.tw>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yao-Hwei",
                      family = "Fang",
                      role = c("aut", "cre"),
                      email = "yhfang@nhri.org.tw"),
               person(given = "Jie-Huei",
                      family = "Wang",
                      role = "aut"),
               person(given = c("Chao", "A."),
                      family = "Hsiung",
                      role = "aut"))
as necessary.
Maintainer: ‘Charles J. Geyer <charlie@stat.umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jun",
                      family = "Sheng",
                      role = "aut"),
               person(given = "Peihua",
                      family = "Qiu",
                      role = "aut",
                      email = "pqiu@ufl.edu"),
               person(given = c("Charles", "J."),
                      family = "Geyer",
                      role = c("aut", "cre"),
                      email = "charlie@stat.umn.edu"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

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

Packages suggested but not available for checking:
  'rmarkdown', 'tstests', 'knitr'

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

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

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

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tstests'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Eraldo B. dos Anjos Filho <ebdaf1@de.ufpe.br>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Eraldo", "B.", "dos", "Anjos"),
                      family = "Filho",
                      role = c("aut", "cre"),
                      email = "ebdaf1@de.ufpe.br"),
               person(given = c("Aldo", "William", "Medina"),
                      family = "Garay",
                      role = "aut",
                      email = "agaray@de.ufpe.br"))
as necessary.
Maintainer: ‘Roger D. Peng <roger.peng@austin.utexas.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Roger", "D."),
                      family = "Peng",
                      role = c("aut", "cre"),
                      email = "roger.peng@austin.utexas.edu"),
               person(given = c("with", "contributions", "from", "Aidan"),
                      family = "McDermott",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ergm'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Justin Donaldson <jdonaldson@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Justin",
                    family = "Donaldson",
                    role = c("aut", "cre"),
                    email = "jdonaldson@gmail.com")
as necessary.
Maintainer: ‘Javier López-de-Lacalle <javlacalle@yahoo.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Javier",
                    family = "López-de-Lacalle",
                    role = c("aut", "cre"),
                    email = "javlacalle@yahoo.es")
as necessary.
Maintainer: ‘Jouni Helske <jouni.helske@iki.fi>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jouni",
                    family = "Helske",
                    role = c("aut", "cre"),
                    email = "jouni.helske@iki.fi")
as necessary.
Maintainer: ‘Bernd Bischl <bernd_bischl@gmx.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Bernd",
                      family = "Bischl",
                      role = c("aut", "cre"),
                      email = "bernd_bischl@gmx.net"),
               person(given = "Jakob",
                      family = "Bossek",
                      role = "aut",
                      email = "jakob.bossek@tu-dortmund.de"),
               person(given = "Olaf",
                      family = "Mersmann",
                      role = "aut",
                      email = "olafm@p-value.net"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Packages required but not available: 'keras', 'tfdatasets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Higor Cotta <cotta.higor@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Higor",
                      family = "Cotta",
                      role = c("aut", "cre"),
                      email = "cotta.higor@gmail.com"),
               person(given = "Valderio",
                      family = "Reisen",
                      role = "aut"),
               person(given = "Pascal",
                      family = "Bondon",
                      role = "aut"),
               person(given = "Céline",
                      family = "Lévy-Leduc",
                      role = "aut"))
as necessary.
Maintainer: ‘Peter Laurinec <tsreprpackage@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) repr_dwt.Rd:28: Lost braces; missing escapes or markup?
    28 | The final representation has length equal to floor(n / 2^{level}), where n is a length of original time series.
       |                                                          ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michał Narajewski <michal.narajewski@uni-due.de>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Avi Blinder <aviblinder@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Avi",
                    family = "Blinder",
                    role = c("aut", "cre"),
                    email = "aviblinder@gmail.com")
as necessary.
Package required but not available: ‘dsa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Arden Burrell <arden.burrell@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Masami Saga <msaga@mtb.biglobe.ne.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("The", "Institute", "of", "Statistical"),
                      family = "Mathematics",
                      role = "aut"),
               person(given = c("based", "on", "the", "program", "by", "Genshiro"),
                      family = "Kitagawa",
                      role = "aut"),
               person(given = "Masami",
                      family = "Saga",
                      role = "cre",
                      email = "msaga@mtb.biglobe.ne.jp"))
as necessary.
Package required but not available: ‘plotly’

Packages suggested but not available for checking:
  'devtools', 'DT', 'knitr', 'rmarkdown'

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tsgarch'

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Alberto Lopez Moreno <bertolomo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Alberto", "Lopez"),
                    family = "Moreno",
                    role = c("aut", "cre"),
                    email = "bertolomo@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

Package suggested but not available for checking: ‘lintr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Marco Albrecht <marco.albrecht@posteo.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Marco",
                    family = "Albrecht",
                    role = c("aut", "cre"),
                    email = "marco.albrecht@posteo.de")
as necessary.
Package required but not available: ‘DT’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Antonio Meneses <antoniomenesesfreire@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Antonio",
                      family = "Meneses",
                      role = c("aut", "cre"),
                      email = "antoniomenesesfreire@hotmail.com"),
               person(given = "Salvador",
                      family = "Naya",
                      role = "aut",
                      email = "salva@udc.es"),
               person(given = "Javier",
                      family = "Tarrio-Saavedra",
                      role = "aut",
                      email = "jtarrio@udc.es"))
as necessary.
Maintainer: ‘Carlos A. Martinez <amartin@unal.edu.co>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Carlos", "A.", "Martinez", "based", "on", "the", "work", "of"),
                      family = "Ribeiro",
                      role = c("aut", "cre")),
               person(family = "Rosseti.",
                      comment = "2015"),
               person(given = c("Carlos", "A."),
                      family = "Martinez",
                      role = "cre",
                      email = "amartin@unal.edu.co"))
as necessary.
Package required but not available: ‘knitr’

Packages suggested but not available for checking: 'rmarkdown', 'table1'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Thorn Thaler <thorn.thaler@thothal.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thorn",
                    family = "Thaler",
                    role = c("aut", "cre"),
                    email = "thorn.thaler@thothal.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'lintr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'lintr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'knitr', 'rmarkdown'

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Michael C Sachs <sachsmc@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Michael", "C"),
                    family = "Sachs",
                    role = c("aut", "cre"),
                    email = "sachsmc@gmail.com")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Packages required but not available: 'rmarkdown', 'knitr'

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

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

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

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/ExamplesTukeytrendtest.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Yuqing Pan <yuqing.pan@stat.fsu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yuqing",
                      family = "Pan",
                      role = c("aut", "cre"),
                      email = "yuqing.pan@stat.fsu.edu"),
               person(given = "Qing",
                      family = "Mai",
                      role = "aut",
                      email = "mai@stat.fsu.edu"),
               person(given = "Xin",
                      family = "Zhang",
                      role = "aut",
                      email = "henry@stat.fsu.edu"))
as necessary.

The Description field contains
  (2019) <arXiv:1904.03469>. Functions are included for covariate
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Julia Wilkerson <jmwilkers@outlook.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Julia",
                    family = "Wilkerson",
                    role = c("aut", "cre"),
                    email = "jmwilkers@outlook.com")
as necessary.
Maintainer: ‘Hans Kestler <hans.kestler@uni-ulm.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Christoph",
                      family = "Müssel",
                      role = "aut"),
               person(given = "Ludwig",
                      family = "Lausser",
                      role = "aut"),
               person(given = "Hans",
                      family = "Kestler",
                      role = c("aut", "cre"),
                      email = "hans.kestler@uni-ulm.de"))
as necessary.
Maintainer: ‘Emmanuel Lazaridis <emmanuel@lazaridis.eu>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘duplicate.Rd’:
    \keyword{duplicate,}
    \keyword{duplicated,}
    \keyword{repeat,}
  File ‘not-in.Rd’:
    \keyword{time,}
  File ‘orphan.Rd’:
    \keyword{orphan,}
  File ‘triplicate.Rd’:
    \keyword{repeat,}
    \keyword{triplicate,}
    \keyword{triplicated,}
  File ‘triplicated.Rd’:
    \keyword{repeat,}
    \keyword{triplicate,}
    \keyword{triplicated,}
  File ‘tuplicate.Rd’:
    \keyword{n-replicate,}
    \keyword{n-replicated,}
    \keyword{repeat,}
    \keyword{repeated,}
  File ‘tuplicated.Rd’:
    \keyword{n-replicate,}
    \keyword{n-replicated,}
    \keyword{repeat,}
    \keyword{repeated,}
Package suggested but not available for checking: ‘knitr’

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/turner_introduction.Rnw’
(Is a VignetteBuilder field missing?)

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

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/TurtleGraphics.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Feifei ZHANG<tushare_pro@163.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Feifei",
                    family = "ZHANG",
                    role = c("aut", "cre"),
                    email = "tushare_pro@163.com")
as necessary.
Package required but not available: ‘tidyverse’

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

Packages suggested but not available for checking:
  'knitr', 'quarto', 'roxygen2', 'tidyverse'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘fGarch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Vincent Landau <vincent@csp-inc.org>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Juan Manuel Truppia <jmtruppia@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Juan", "Manuel"),
                    family = "Truppia",
                    role = c("aut", "cre"),
                    email = "jmtruppia@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Lane Burgette <burgette@rand.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Matthew",
                      family = "Cefalu",
                      role = "aut"),
               person(given = "Greg",
                      family = "Ridgeway",
                      role = "aut"),
               person(given = "Dan",
                      family = "McCaffrey",
                      role = "aut"),
               person(given = "Andrew",
                      family = "Morral",
                      role = "aut"),
               person(given = c("Beth", "Ann"),
                      family = "Griffin",
                      role = "aut"),
               person(given = "Lane",
                      family = "Burgette",
                      role = c("aut", "cre"),
                      email = "burgette@rand.org"))
as necessary.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
ps.fast: warning in xgboost(data = sparse.data, label = data[,
  treat.var], params = params, tree_method = tree_method, feval =
  pred.xgboost, nrounds = n.trees, verbose = verbose, weight = sampW,
  callbacks = callback.list): partial argument match of 'weight' to
  'weights'
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'lintr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Peter K. Dunn <pdunn2@usc.edu.au>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) tweedie-internal.Rd:74: Lost braces
    74 |         doi{10.1093/biomet/74.2.221}
       |            ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Specified C++11: support will be removed soon
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Michael Swanson <dms866@mail.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Michael",
                    family = "Swanson",
                    role = c("aut", "cre"),
                    email = "dms866@mail.harvard.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Connor Dowd <cd@codowd.com>’

The Description field contains
  that of Anderson-Darling. See the companion paper at <arXiv:2007.01360>
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) twosigmag.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘tmle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |     ^
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |                                  ^
Package required but not available: ‘knitr’

Package suggested but not available for checking: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

Package which this enhances but not available for checking: ‘sl3’

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |  ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |               ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |                                ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rlist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Sebastien Thonnard <sebastien.thonnard@icloud.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sebastien",
                    family = "Thonnard",
                    role = c("aut", "cre"),
                    email = "sebastien.thonnard@icloud.com")
as necessary.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) cambodia.Rd:47: Lost braces
    47 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
checkRd: (-1) microdata.Rd:33: Lost braces
    33 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
checkRd: (-1) u5mr_cohort.Rd:111: Lost braces
   111 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Problems with news in ‘NEWS.md’:
No news entries found.
Packages required but not available: 'link2GI', 'rlist'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'mapview', 'htmlwidgets'

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

Packages suggested but not available for checking:
  'DT', 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Christophe Zemmour <christophe.zemmour@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Benjamin", "Esterni", "with", "contribution", "from", "Baboukar"),
                      family = "Mane",
                      role = "aut"),
               person(given = "Christophe",
                      family = "Zemmour",
                      role = "cre",
                      email = "christophe.zemmour@gmail.com"))
as necessary.
Packages required but not available:
  'flextable', 'knitr', 'onbrand', 'rmarkdown', 'rhandsontable'

Package suggested but not available for checking: ‘babelmixr2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Mikaela Koutrouli <mikaela.koutrouli@cpr.ku.dk>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Gabriela Cybis <gcybis@gmail.com>’

The Description field contains
  Valk and Gabriela B. Cybis (2021) <arXiv:2106.09115>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'DT', 'knitr', 'plotly', 'rmarkdown', 'survminer'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'prettydoc', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Luc Duchateau <Luc.Duchateau@ugent.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hans",
                      family = "Laevens",
                      role = "aut"),
               person(given = "Luc",
                      family = "Duchateau",
                      role = c("aut", "cre"),
                      email = "luc.duchateau@ugent.be"),
               person(given = "Klara",
                      family = "Goethals",
                      role = "aut"),
               person(given = "Ewoud",
                      family = "De Troyer",
                      role = "aut"),
               person(given = "Paul",
                      family = "Janssen",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer field differs from that derived from Authors@R
  Maintainer: ‘ORPHANED’
  Authors@R:  ‘James Hiebert <hiebert@uvic.ca>’
Packages required but not available: 'FactoMineR', 'factoextra'

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

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘Paul TERNYNCK <ternynck@lisic.univ-littoral.fr>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘MarelCarnot.Rd’:
    http://doi.org/10.17882/39754
Package required but not available: ‘FactoMineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Minna Genbaeck <minna.genback@umu.se>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Minna",
                      family = "Genbaeck,",
                      role = c("aut", "cre")),
               person(given = "Minna",
                      family = "Genbaeck",
                      role = "cre",
                      email = "minna.genback@umu.se"))
as necessary.
Packages required but not available: 'rmarkdown', 'xaringan'

Package suggested but not available for checking: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'spelling', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'leaflet'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘quanteda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Kaniav Kamary <kamary@ceremade.dauphine.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Kaniav",
                      family = "Kamary",
                      role = c("aut", "cre"),
                      email = "kamary@ceremade.dauphine.fr"),
               person(given = "Kate",
                      family = "Lee",
                      role = "aut"))
as necessary.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘readtextgrid.R’
Maintainer: ‘Tomasz Konopka <tokonopka@gmail.com>’

The Description field contains
  (2018) in <arXiv:1802.03426>. This package provides an interface for
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘AdaptGauss’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Linus Seelinger <mail@linusseelinger.de>’

The BugReports field in DESCRIPTION has
  https://github.com/um-bridge
which should likely be
  https://github.com/um-bridge/issues
instead.
Packages required but not available: 'DT', 'plotly'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘Charles J. Geyer <charlie@stat.umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Charles", "J."),
                      family = "Geyer",
                      role = c("aut", "cre"),
                      email = "charlie@stat.umn.edu"),
               person(given = c("Glen", "D."),
                      family = "Meeden",
                      role = "aut",
                      email = "glen@stat.umn.edu"))
as necessary.
Packages required but not available: 'DiagrammeR', 'kableExtra', 'knitr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'dygraphs', 'echarts4r', 'gt', 'gtExtras', 'highcharter',
  'htmlwidgets', 'leaflet', 'leaflet.extras', 'plotly', 'sunburstR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Piotr Fryzlewicz <p.fryzlewicz@lse.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Piotr",
                    family = "Fryzlewicz",
                    role = c("aut", "cre"),
                    email = "p.fryzlewicz@lse.ac.uk")
as necessary.
Maintainer: ‘Hugo Gasca-Aragon <hugo_gasca_aragon@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hugo",
                    family = "Gasca-Aragon",
                    role = c("aut", "cre"),
                    email = "hugo_gasca_aragon@hotmail.com")
as necessary.
Packages required but not available: 'devtools', 'usethis'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'officedown', 'pagedown', 'rmarkdown', 'xaringan'

Package suggested but not available for checking: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'tidyverse', 'ggstream'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘annotate_mf.R’ ‘annotate_mf_all.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yunro Chung <yunro.chung@asu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yunro",
                    family = "Chung",
                    role = c("aut", "cre"),
                    email = "yunro.chung@asu.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘config’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/unifDAG-vignette.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Oscar Alberto Quijano Xacur <oscar.quijano@use.startmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Oscar", "Alberto", "Quijano"),
                    family = "Xacur",
                    role = c("aut", "cre"),
                    email = "oscar.quijano@use.startmail.com")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Chia-Wei Hsu <Chia-Wei.Hsu@stjude.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chia-Wei",
                      family = "Hsu",
                      role = c("aut", "cre"),
                      email = "chia-wei.hsu@stjude.org"),
               person(given = "Haitao",
                      family = "Pan",
                      role = "aut"),
               person(given = "Rongji",
                      family = "Mu",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'lintr', 'pkgdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Stéphane Laurent <laurent_step@outlook.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Stéphane",
                    family = "Laurent",
                    role = c("aut", "cre"),
                    email = "laurent_step@outlook.fr")
as necessary.
Package required but not available: ‘rgl’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Zhipeng Xu <xzhipeng@umich.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhipeng",
                      family = "Xu",
                      role = c("aut", "cre"),
                      email = "xzhipeng@umich.edu"),
               person(given = "Chenkai",
                      family = "Sun",
                      role = "aut",
                      email = "sunchenk@umich.edu"),
               person(given = "Aman",
                      family = "Karunakaran",
                      role = "aut",
                      email = "akarunak@umich.edu"),
               person(given = "Quentin",
                      family = "Stout",
                      role = "aut",
                      email = "qstout@umich.edu"))
as necessary.
checkRd: (-1) reg_1d.Rd:42: Lost braces; missing escapes or markup?
    42 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
checkRd: (-1) reg_2d.Rd:33: Lost braces; missing escapes or markup?
    33 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Specified C++11: support will be removed soon
Packages required but not available:
  'tidyverse', 'networkD3', 'htmlwidgets', 'alakazam', 'gprofiler2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Claudia Koellmann <koellmann@statistik.tu-dortmund.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Claudia",
                    family = "Koellmann",
                    role = c("aut", "cre"),
                    email = "koellmann@statistik.tu-dortmund.de")
as necessary.
Maintainer: ‘Takeshi Emura <takeshiemura@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Takeshi",
                      family = "Emura",
                      role = c("aut", "cre"),
                      email = "takeshiemura@gmail.com"),
               person(given = "Wei-Chern",
                      family = "Hsu",
                      role = "aut"))
as necessary.
Maintainer: ‘Jonathan Berrisch <Jonathan@Berrisch.biz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jonathan",
                    family = "Berrisch",
                    role = c("aut", "cre"),
                    email = "jonathan@berrisch.biz")
as necessary.
Package suggested but not available for checking: ‘knitr’

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/unitedR.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘David Navarro-Gonzalez <david.navarro@urv.cat>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Pere", "Joan"),
                      family = "Ferrando",
                      role = "aut"),
               person(given = "David",
                      family = "Navarro-Gonzalez",
                      role = c("aut", "cre"),
                      email = "david.navarro@urv.cat"),
               person(given = "Urbano",
                      family = "Lorenzo-Seva",
                      role = "aut"))
as necessary.
Package required but not available: ‘fGarch’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Marcello D'Orazio <mdo.statmatch@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Marcello",
                    family = "D'Orazio",
                    role = c("aut", "cre"),
                    email = "mdo.statmatch@gmail.com")
as necessary.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ran Gao <rgao8@uic.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hakan",
                      family = "Demirtas",
                      role = "aut"),
               person(given = "Rawan",
                      family = "Allozi",
                      role = "aut"),
               person(given = "Ran",
                      family = "Gao",
                      role = c("aut", "cre"),
                      email = "rgao8@uic.edu"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘runm.Rd’ ‘unm_summary.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Erika S. Helgeson <helge@umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Erika", "S."),
                      family = "Helgeson",
                      role = c("aut", "cre"),
                      email = "helge@umn.edu"),
               person(given = "David",
                      family = "Vock",
                      role = "aut"),
               person(given = "Eric",
                      family = "Bair",
                      role = "aut"))
as necessary.
checkRd: (-1) UNPaC_Copula.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}
       |                                  ^
checkRd: (-1) UNPaC_Copula.Rd:60: Lost braces; missing escapes or markup?
    60 | \item{\code{sim_CI}}: {vector containing the cluster indices for each generated unimodal reference distribution}
       |                       ^
checkRd: (-1) UNPaC_Copula.Rd:61-62: Lost braces
    61 | \item{\code{pvalue_emp}}: {the empirical p-value:  the proportion of times the cluster index from the reference
       |                           ^
checkRd: (-1) UNPaC_Copula.Rd:63: Lost braces; missing escapes or markup?
    63 | \item{\code{pvalue_norm}}: {the normalized p-value: the simulated p-value based on comparison to a standard normal distribution }
       |                            ^
checkRd: (-1) UNPaC_num_clust.Rd:58-62: Lost braces
    58 | \item{\code{BestK}}: {A matrix with 1 row and 4 columns named: "Max_CI","Max_CI_wi_1SE","Max_scaled_CI" and "Max_logWCSS_wi_1SE".
       |                      ^
checkRd: (-1) UNPaC_num_clust.Rd:63-65: Lost braces
    63 | \item{\code{full_process}}: {A matrix containing the number of clusters, K, evaluated, the CI from the data, the average CI from the null
       |                             ^
checkRd: (-1) UNPaC_num_clust.Rd:66: Lost braces; missing escapes or markup?
    66 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}}
       |                                  ^
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'DT', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'bookdown', 'covr', 'kableExtra', 'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'devtools', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘tidyverse’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ 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:
    ‘available_version.R’
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'VariantAnnotation'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘mixtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'lintr', 'pkgdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package suggested but not available for checking: ‘knitr’

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/ExtendedAppendix.Rnw’
   ‘inst/doc/Manuscript.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'rmarkdown', 'covr', 'lintr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'EviewsR', 'knitr'

Package suggested but not available for checking: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Irucka Embry <iembry@ecoccs.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Irucka",
                    family = "Embry",
                    role = c("aut", "cre"),
                    email = "iembry@ecoccs.com")
as necessary.
Maintainer: ‘Frederick Liu <sliu85@u.rochester.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Frederick",
                    family = "Liu",
                    role = c("aut", "cre"),
                    email = "sliu85@u.rochester.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION 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:
    ‘county_complete.Rd’ ‘fatal_police_shootings.Rd’ ‘gerrymander.Rd’
    ‘pierce_county_house_sales.Rd’ ‘pop_age_2019.Rd’ ‘pop_race_2019.Rd’
    ‘state_stats.Rd’ ‘us_temp.Rd’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Babak Naimi <naimi.b@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Babak",
                    family = "Naimi",
                    role = c("aut", "cre"),
                    email = "naimi.b@gmail.com")
as necessary.
Packages required but not available: 'kableExtra', 'knitr'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'spelling'

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

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:
    ‘intersection_powerset.R’ ‘powerset_icounts.Rd’ ‘pr.R’ ‘pr.boot.Rd’
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
No examples, no tests, no vignettes
Package required but not available: ‘yaml’

Packages suggested but not available for checking:
  'covr', 'knitr', 'quarto', 'rmarkdown', 'roxygen2', 'spelling'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'plotly'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘usgas.Rd’
Running examples in ‘USgas-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: usgas
> ### Title: US Monthly Consumption of Natural Gas by End Use
> ### Aliases: usgas
> ### Keywords: datasets gas natural state timeseries us
> 
> ### ** Examples
> 
> 
> library(plotly)
Error in library(plotly) : there is no package called ‘plotly’
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Running examples in ‘USgrid-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Cal_elec
> ### Title: Demand for California Independent System Operator (CISO)
> ### Aliases: Cal_elec
> ### Keywords: datasets time-series
> 
> ### ** Examples
> 
> 
> data(Cal_elec)
> 
> library(plotly)
Error in library(plotly) : there is no package called ‘plotly’
Execution halted
Maintainer: ‘Sinead E. Morris <sinead.morris@columbia.edu>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘John Verzani <verzani@math.csi.cuny.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "John",
                    family = "Verzani",
                    role = c("aut", "cre"),
                    email = "verzani@math.csi.cuny.edu")
as necessary.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Paula M. Murray <paula.murray@math.mcmaster.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Paula", "M."),
                      family = "Murray",
                      role = c("aut", "cre"),
                      email = "paula.murray@math.mcmaster.ca"),
               person(given = c("Ryan", "P."),
                      family = "Browne",
                      role = "aut"),
               person(given = c("Paul", "D."),
                      family = "McNicholas",
                      role = "aut"))
as necessary.
Package suggested but not available for checking: ‘knitr’

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/usl.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Thomas B. Berrett <tom.berrett@warwick.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Thomas", "B."),
                      family = "Berrett",
                      role = c("aut", "cre"),
                      email = "tom.berrett@warwick.ac.uk"),
               person(given = "Ioannis",
                      family = "Kontoyiannis",
                      role = "aut",
                      email = "yiannis@maths.cam.ac.uk"),
               person(given = c("Richard", "J."),
                      family = "Samworth",
                      role = "aut",
                      email = "r.samworth@statslab.cam.ac.uk"))
as necessary.

The Description field contains
  <arXiv:2001.05513>, and shown to be minimax rate optimal in a wide
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Snigdhansu Chatterjee <chatt019@umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Snigdhansu",
                    family = "Chatterjee",
                    role = c("aut", "cre"),
                    email = "chatt019@umn.edu")
as necessary.
Maintainer: ‘Matt Barry <mrb@softisms.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Matt",
                    family = "Barry",
                    role = c("aut", "cre"),
                    email = "mrb@softisms.com")
as necessary.
Malformed Title field: should not end in a period.
Maintainer: ‘Antonio J. Segura <segura.antonioj@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Antonio", "J."),
                    family = "Segura",
                    role = c("aut", "cre"),
                    email = "segura.antonioj@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION 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:
    ‘build_model.coxph.Rd’ ‘build_table.coxph.Rd’ ‘build_table.lm.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:
    ‘cusum_failure.Rd’ ‘cusum_loglike.Rd’ ‘cusum_ome.Rd’ ‘cusum_sprt.Rd’
    ‘paste.R’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ben Derrick <ben.derrick@uwe.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ben",
                    family = "Derrick",
                    role = c("aut", "cre"),
                    email = "ben.derrick@uwe.ac.uk")
as necessary.
Maintainer: ‘Zhiqiang Tan <ztan@stat.rutgers.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhiqiang",
                      family = "Tan",
                      role = c("aut", "cre"),
                      email = "ztan@stat.rutgers.edu"),
               person(given = "Emilio",
                      family = "Gallicchio",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘benchmark_event.R’ ‘benchmark_event.Rd’ ‘benchmark_score.R’
    ‘benchmark_score.Rd’ ‘benchmark_time.R’
    ‘compare_means_between_groups.R’ ‘compare_means_between_groups.Rd’
    ‘compare_means_within_groups.R’ ‘compare_rates_between_groups.R’
    ‘compare_rates_between_groups.Rd’ ‘compare_rates_within_groups.R’
    ‘get_concordant_discordant_pairs.R’
    ‘get_confidence_intervals_within_groups.R’
    ‘table_observed_expected.R’ ‘test_chisq_one.R’ ‘test_chisq_one.Rd’
    ‘test_chisq_two.Rd’ ‘test_fisher.Rd’ ‘test_mcnemar.R’
    ‘test_n_1_prop.R’ ‘test_n_1_prop.Rd’ ‘test_t.R’ ‘test_t_paired.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'SuperLearner', 'survML', 'gam'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'learnr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ron Sielinski <sielinski@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ron",
                    family = "Sielinski",
                    role = c("aut", "cre"),
                    email = "sielinski@hotmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Problems with news in ‘NEWS.md’:
No news entries found.
Maintainer: ‘Irucka Embry <iembry@ecoccs.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Irucka",
                    family = "Embry",
                    role = c("aut", "cre"),
                    email = "iembry@ecoccs.com")
as necessary.

Found the following (possibly) invalid file URI:
  URI: info@vaers.org
    From: README.md
Maintainer: ‘Irucka Embry <iembry@ecoccs.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Irucka",
                    family = "Embry",
                    role = c("aut", "cre"),
                    email = "iembry@ecoccs.com")
as necessary.

Found the following (possibly) invalid file URI:
  URI: info@vaers.org
    From: README.md
Maintainer: ‘Bruna Wundervald <brunadaviesw@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Bruna",
                    family = "Wundervald",
                    role = c("aut", "cre"),
                    email = "brunadaviesw@gmail.com")
as necessary.
Maintainer: ‘Han Lin Shang <hanlin.shang@anu.edu.au>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Missing dependency on R >= 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_surv.Rd’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘keyring’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Sean Wen <sean.wenwx@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sean",
                    family = "Wen",
                    role = c("aut", "cre"),
                    email = "sean.wenwx@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Christopher Belanger <christopher.a.belanger@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Christopher",
                    family = "Belanger",
                    role = c("aut", "cre"),
                    email = "christopher.a.belanger@gmail.com")
as necessary.
Package required but not available: ‘leaflet’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Greer B. Humphrey <greer.humphrey@student.adelaide.edu.au>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘ar9.Rd’:
    http://dx.doi.org/10.1016/S0022-1694(00)00346-2
  File ‘validann.Rd’:
    http://dx.doi.org/10.1016/j.envsoft.2006.06.008
    http://dx.doi.org/10.1016/j.ecolmodel.2004.03.013
    http://dx.doi.org/10.1016/S0304-3800(02)00257-0
    http://dx.doi.org/10.1109/ijcnn.2006.247166
    http://dx.doi.org/10.5194/hess-17-2827-2013
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
Packages required but not available:
  'listviewer', 'framecleaner', 'badger', 'rlist'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) sendTasks.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sendTasks.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘yaml’

Packages suggested but not available for checking:
  'knitr', 'bookdown', 'rmarkdown'

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Benjamin Hivert <benjamin.hivert@u-bordeaux.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Benjamin",
                    family = "Hivert",
                    role = c("aut", "cre"),
                    email = "benjamin.hivert@u-bordeaux.fr")
as necessary.

The Description field contains
  practical considerations", <arXiv:2210.13172>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Packages required but not available: 'plotly', 'rmarkdown', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'roxygen2', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Clay Ford <joe.clayton.ford@gmail.com>’

The Description field contains
  were downloaded from https://www.valottery.com/.
Please enclose URLs in angle brackets (<...>).
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'devtools', 'DT', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'leaflet', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘H. Robert Frost <rob.frost@dartmouth.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("H.", "Robert"),
                    family = "Frost",
                    role = c("aut", "cre"),
                    email = "rob.frost@dartmouth.edu")
as necessary.
Maintainer: ‘Jens von Bergmann <jens@mountainmath.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jens",
                    family = "von Bergmann",
                    role = c("aut", "cre"),
                    email = "jens@mountainmath.ca")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘datasets.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Guo Yu <gy63@cornell.edu>’

The Description field contains
  Bien (2016) and is available at <https://arxiv.org/abs/1604.07451>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) sample_gen.Rd:18: Lost braces; missing escapes or markup?
    18 | Generate \code{n} random samples from multivariate Gaussian distribution N(0, (L^TL)^{-1})
       |                                                                                      ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Daniel Safai <danielsafai@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Daniel",
                    family = "Safai",
                    role = c("aut", "cre"),
                    email = "danielsafai@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'qtl', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Piotr Sobczyk <pj.sobczyk@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Piotr",
                      family = "Sobczyk",
                      role = c("aut", "cre"),
                      email = "pj.sobczyk@gmail.com"),
               person(given = "Stanislaw",
                      family = "Wilczynski",
                      role = "aut"),
               person(given = "Julie",
                      family = "Josse",
                      role = "aut"),
               person(given = "Malgorzata",
                      family = "Bogdan",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Edzer Pebesma <edzer.pebesma@uni-muenster.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ernst",
                      family = "Glatzer",
                      role = "aut",
                      email = "ernst.glatzer@wu-wien.ac.at"),
               person(given = "Edzer",
                      family = "Pebesma",
                      role = "cre",
                      email = "edzer.pebesma@uni-muenster.de"))
as necessary.
Maintainer: ‘Martins Liberts <martins.liberts@csb.gov.lv>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘lingini2.Rd’:
    http://dx.doi.org/10.1007/BF03263549
  File ‘varpoord.Rd’:
    http://dx.doi.org/10.1007/BF03263549
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) vardannual.Rd:97: Lost braces
    97 | \item{ID_level2}{Optional}{variable for unit ID codes. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                           ^
checkRd: (-1) vardannual.Rd:99: Lost braces
    99 | \item{dataset}{Optional}{survey data object convertible to \code{data.table}.}
       |                         ^
checkRd: (-1) vardcrospoor.Rd:122: Lost braces
   122 | \item{ind_gr}{Optional}{variable by which divided independently X matrix of the auxiliary variables for the calibration. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                        ^
checkRd: (-1) vardcrospoor.Rd:124: Lost braces
   124 | \item{use.estVar}{Logical}{value. If value is \code{TRUE}, then \code{R} function \code{estVar} is used for the  estimation of covariance matrix of the residuals. If value is \code{FALSE}, then \code{R} function \code{estVar} is not used for the estimation of covariance matrix of the residuals.}
       |                           ^
checkRd: (-1) vardom_othstr.Rd:69: Lost braces
    69 | \item{percentratio}{Positive}{numeric value. All linearized variables are multiplied with \code{percentratio} value, by default - 1.}
       |                              ^
checkRd: (-1) varpoord.Rd:121: Lost braces
   121 | \item{month_at_work}{Variable}{for total number of month at work (sum of the number of months spent at full-time work as employee, number of months spent at part-time work as employee, number of months spent at full-time work as self-employed (including family worker), number of months spent at part-time work as self-employed (including family worker)).  One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                               ^
Maintainer: ‘Wenlin Dai <wenlin.dai@kaust.edu.sa>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Wenlin",
                      family = "Dai",
                      role = c("aut", "cre"),
                      email = "wenlin.dai@kaust.edu.sa"),
               person(given = "Tiejun",
                      family = "Tong.",
                      role = "aut",
                      email = "tongt@hkbu.edu.sa"))
as necessary.
checkRd: (-1) betaburr.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Burr distribution due to Parana\'{i}ba et al. (2011) given by
       |                                                                                                                        ^
checkRd: (-1) betafrechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Fr\'{e}chet distribution due to Barreto-Souza et al. (2011) given by
       |                                                                                           ^
checkRd: (-1) frechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                      ^
checkRd: (-1) frechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                                                      ^
checkRd: (-1) kumburr7.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Kumaraswamy Burr XII distribution due to Parana\'{i}ba et al. (2013) given by
       |                                                                                                                                   ^
Maintainer: ‘Sayanti Guha Majumdar <sayanti23gm@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Sayanti", "Guha"),
                      family = "Majumdar",
                      role = c("aut", "cre"),
                      email = "sayanti23gm@gmail.com"),
               person(given = "Anil",
                      family = "Rai",
                      role = "aut"),
               person(given = c("Dwijesh", "Chandra"),
                      family = "Mishra",
                      role = "aut"))
as necessary.
Maintainer: ‘Jae H. Kim <jaekim8080@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Jae.", "H."),
                      family = "Kim",
                      role = "aut"),
               person(given = c("Jae", "H."),
                      family = "Kim",
                      role = "cre",
                      email = "jaekim8080@gmail.com"))
as necessary.
checkRd: (-1) simulateDCSIS.Rd:40: Lost braces
    40 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + exp(2*X22)*e
       |                                ^
checkRd: (-1) simulateDCSIS.Rd:42: Lost braces
    42 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + 6*X22 + e
       |                                ^
Maintainer: ‘David Scott <d.scott@auckland.ac.nz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "David",
                      family = "Scott",
                      role = c("aut", "cre"),
                      email = "d.scott@auckland.ac.nz"),
               person(given = c("Christine", "Yang"),
                      family = "Dong",
                      role = "aut",
                      email = "c.dong@auckland.ac.nz"))
as necessary.
Maintainer: ‘Joshua F. Wiley <josh@elkhartgroup.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Joshua", "F."),
                      family = "Wiley",
                      role = c("aut", "cre"),
                      email = "josh@elkhartgroup.com"),
               person(given = c("Elkhart", "Group"),
                      family = "Limited",
                      role = "cph"))
as necessary.
Package required but not available: ‘sparklyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Craig Wang <craig.wang@math.uzh.ch>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘yaml’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michele Dalponte <michele.dalponte@fmach.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Michele",
                      family = "Dalponte",
                      role = c("aut", "cre"),
                      email = "michele.dalponte@fmach.it"),
               person(given = c("Hans", "Ole"),
                      family = "Oerka",
                      role = "aut"))
as necessary.
Maintainer: ‘Ramon Diaz-Uriarte <rdiaz02@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ramon",
                    family = "Diaz-Uriarte",
                    role = c("aut", "cre"),
                    email = "rdiaz02@gmail.com")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rticles', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) Acoef_sh.Rd:23: Lost braces; missing escapes or markup?
    23 | The function returns the K-by-K matrices {A_1, ..., A_p} as a list object.
       |                                          ^
checkRd: (-1) VARshrink.Rd:58: Lost braces; missing escapes or markup?
    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                    ^
checkRd: (-1) VARshrink.Rd:58: Lost braces; missing escapes or markup?
    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                                        ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘WenSui Liu <liuwensui@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "WenSui",
                    family = "Liu",
                    role = c("aut", "cre"),
                    email = "liuwensui@gmail.com")
as necessary.
Problems with news in ‘NEWS.md’:
No news entries found.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jiehuan Sun <jiehuan.sun@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jiehuan",
                    family = "Sun",
                    role = c("aut", "cre"),
                    email = "jiehuan.sun@gmail.com")
as necessary.
Maintainer: ‘Michael Salter-Townshend <mike.saltertownshend@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Michael",
                    family = "Salter-Townshend",
                    role = c("aut", "cre"),
                    email = "mike.saltertownshend@gmail.com")
as necessary.
Package required but not available: ‘ergm’

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

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Bo (Yu-Chien) Ning <bo.ning@upmc.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Bo",
                      family = "Ning",
                      role = "aut",
                      comment = "Yu-Chien"),
               person(given = "Bo",
                      family = "Ning",
                      role = "cre",
                      email = "bo.ning@upmc.fr",
                      comment = "Yu-Chien"))
as necessary.

The Description field contains
  proposed by Ning (2020) <arXiv:2102.00305>. There are two algorithms:
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) decomposition.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |      ^
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |          ^
checkRd: (-1) moving.estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Package suggested but not available for checking: ‘quarto’

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'rgl', 'Hmisc', 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Michael Chirico <MichaelChirico4@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Michael",
                    family = "Chirico",
                    role = c("aut", "cre"),
                    email = "michaelchirico4@gmail.com")
as necessary.
Package required but not available: ‘rlist’

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'pkgdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
File ‘vctrs/libs/vctrs.so’:
  Found non-API calls to R: ‘BODY’, ‘CLOENV’, ‘ENCLOS’, ‘EXTPTR_PROT’,
    ‘EXTPTR_TAG’, ‘FORMALS’, ‘FRAME’, ‘HASHTAB’, ‘IS_S4_OBJECT’,
    ‘LEVELS’, ‘OBJECT’, ‘PRENV’, ‘PRVALUE’, ‘R_PromiseExpr’,
    ‘Rf_allocSExp’, ‘Rf_findVarInFrame3’, ‘SETLENGTH’, ‘SET_BODY’,
    ‘SET_CLOENV’, ‘SET_ENCLOS’, ‘SET_FORMALS’, ‘SET_GROWABLE_BIT’,
    ‘SET_OBJECT’, ‘SET_S4_OBJECT’, ‘SET_TRUELENGTH’, ‘STDVEC_DATAPTR’,
    ‘STRING_PTR’, ‘TRUELENGTH’, ‘UNSET_S4_OBJECT’
These entry points may be removed soon:
‘SET_ENCLOS’, ‘STDVEC_DATAPTR’, ‘SET_S4_OBJECT’, ‘UNSET_S4_OBJECT’, ‘EXTPTR_PROT’, ‘EXTPTR_TAG’, ‘FRAME’, ‘HASHTAB’, ‘IS_S4_OBJECT’, ‘BODY’, ‘FORMALS’, ‘CLOENV’, ‘ENCLOS’, ‘OBJECT’, ‘SET_FORMALS’, ‘SET_BODY’, ‘SET_CLOENV’, ‘STRING_PTR’, ‘LEVELS’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Anne Le Maitre <anne.le.maitre@univie.ac.at>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘Tropheus.IK.coord.Rd’:
    https://doi.org/10.1038/hdy.2013.78
    https://doi.org/10.5061/dryad.fc02f
  File ‘Tropheus.Rd’:
    https://doi.org/10.5061/dryad.fc02f
    https://doi.org/10.1038/hdy.2013.78
  File ‘relative.eigen.Rd’:
    https://doi.org/10.1007/s11692-013-9260-5
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'geomorph'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Cody Moore <Jumper9400@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Cody",
                    family = "Moore",
                    role = c("aut", "cre"),
                    email = "jumper9400@gmail.com")
as necessary.
Maintainer: ‘Solveig Pospiech <s.pospiech@hzdr.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Solveig",
                    family = "Pospiech",
                    role = c("aut", "cre"),
                    email = "s.pospiech@hzdr.de")
as necessary.
Specified C++11: support will be removed soon
Maintainer: ‘Alexander Yermanos <ayermanos@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alexander",
                    family = "Yermanos",
                    role = c("aut", "cre"),
                    email = "ayermanos@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Lu Tian <lutian@stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ramon",
                      family = "Durazo-Arvizu",
                      role = "aut"),
               person(given = "Chris",
                      family = "Sempos",
                      role = "aut"),
               person(given = "Lu",
                      family = "Tian",
                      role = c("aut", "cre"),
                      email = "lutian@stanford.edu"))
as necessary.
Package required but not available: ‘qgraph’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'mclogit', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘tidyverse’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Tunc Oygur <info@tuncoygur.com.tr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Tunc",
                      family = "Oygur",
                      role = c("aut", "cre"),
                      email = "info@tuncoygur.com.tr"),
               person(given = "Gazanfer",
                      family = "Unal",
                      role = "aut"),
               person(given = c("Tarik", "C."),
                      family = "Gouhier",
                      role = "ctb"),
               person(given = "Aslak",
                      family = "Grinsted",
                      role = "ctb"),
               person(given = "Viliam",
                      family = "Simko",
                      role = "ctb"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘fdasrvf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Bob Rudis <bob@rudis.net>’

Found the following (possibly) invalid file URI:
  URI: CONDUCT.md
    From: README.md
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown', 'listviewer', 'yaml', 'usethis',
  'learnr', 'rsconnect'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/vegdata.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Robert Nuske <robert.nuske@mailbox.org>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘taxlist’

Packages suggested but not available for checking:
  'biblio', 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Andrew A Zaffos <azaffos@email.arizona.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Andrew", "A."),
                      family = "Zaffos",
                      role = "aut"),
               person(given = c("Andrew", "A"),
                      family = "Zaffos",
                      role = "cre",
                      email = "azaffos@email.arizona.edu"))
as necessary.
checkRd: (-1) additiveBeta.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:33: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'usethis'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Paul Boutros <pboutros@mednet.ucla.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hanbo",
                      family = "Chen",
                      role = "aut"),
               person(given = "Paul",
                      family = "Boutros",
                      role = "cre",
                      email = "pboutros@mednet.ucla.edu"))
as necessary.
Maintainer: ‘Simon Urbanek <simon.urbanek@r-project.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Lee",
                      family = "Wilkinson",
                      role = "aut",
                      email = "leland.wilkinson@gmail.com"),
               person(given = "Simon",
                      family = "Urbanek",
                      role = "cre",
                      email = "simon.urbanek@r-project.org"))
as necessary.
Package required but not available: ‘rJava’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Conor Neilson <condwanaland@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Conor",
                    family = "Neilson",
                    role = c("aut", "cre"),
                    email = "condwanaland@gmail.com")
as necessary.
Package required but not available: ‘yaml’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Nick Golding <nick.golding.research@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Nick",
                    family = "Golding",
                    role = c("aut", "cre"),
                    email = "nick.golding.research@gmail.com")
as necessary.
Maintainer: ‘Rishabh Singh<rishabhsinghrsg@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Rishabh",
                    family = "Singh",
                    role = c("aut", "cre"),
                    email = "rishabhsinghrsg@gmail.com")
as necessary.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Javier Leiva Cuadrado <jleivacuadrado@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Javier", "Leiva"),
                    family = "Cuadrado",
                    role = c("aut", "cre"),
                    email = "jleivacuadrado@gmail.com")
as necessary.
Package required but not available: ‘pins’

Packages suggested but not available for checking:
  'covr', 'flexdashboard', 'keras', 'knitr', 'plotly', 'rmarkdown',
  'rsconnect', 'tensorflow'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex125.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Dian Li <lidian@zju.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Tobias",
                      family = "Elze",
                      role = "aut"),
               person(given = "Dian",
                      family = "Li",
                      role = c("aut", "cre"),
                      email = "lidian@zju.edu.cn",
                      comment = "documentation"),
               person(given = c("Eun", "Young"),
                      family = "Choi",
                      role = "aut",
                      comment = "QC"))
as necessary.
Maintainer: ‘Sarah Goslee <Sarah.Goslee@ars.usda.gov>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Adam T. Kocsis <adam.t.kocsis@gmail.com>’

The BugReports field in DESCRIPTION has
  https://github.com/adamkocsis/via
which should likely be
  https://github.com/adamkocsis/via/issues
instead.
checkRd: (-1) VirtualArray-single-bracket-method.Rd:6: Lost braces
     6 | \title{Indexing to extract subsets of a 'code{\link[via:XArray-class]{VirtualArray}}'-class object}
       |                                              ^
checkRd: (-1) subset.Rd:20: Lost braces
    20 | \item{drop}{\code{logical} in case the result of subsetting is a single element, should the \\code{\link[via:XArray-class]{VirtualArray}} wrapper be dropped?}
       |                                                                                                   ^
Packages required but not available: 'golem', 'knitr'

Packages suggested but not available for checking:
  'spelling', 'bayesrules', 'htmlwidgets', 'INLA', 'plotly',
  'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) vic_param.Rd:311: Lost braces
   311 | albedo must be supplied in code{forcing_veg}. Default = 1.}
       |                                ^
checkRd: (-1) vic_param.Rd:323: Lost braces
   323 | supplied in code{forcing_veg}. Default = 1.}
       |                 ^
checkRd: (-1) vic_param.Rd:341: Lost braces
   341 | be supplied in code{forcing_veg} Default = 0.}
       |                    ^
Package required but not available: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'shinytest2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) vietnamcode.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:16: Lost braces in \itemize; meant \describe ?
Packages required but not available:
  'config', 'golem', 'JBrowseR', 'DT', 'plotly'

Package suggested but not available for checking: ‘shinytest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Joseph de Vilmarest <joseph.de-vilmarest@vikingconseil.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Joseph",
                    family = "de Vilmarest",
                    role = c("aut", "cre"),
                    email = "joseph.de-vilmarest@vikingconseil.fr",
                    comment = c(ORCID = "0000-0002-0634-8484"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'leaflet', 'plotly', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Zhicheng Du <dgdzc@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Zhicheng",
                    family = "Du",
                    role = c("aut", "cre"),
                    email = "dgdzc@hotmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘SuperLearner’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'gam', 'covr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'reactable', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘VIM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tableMiss
> ### Title: create table with highlighted missings/imputations
> ### Aliases: tableMiss
> 
> ### ** Examples
> 
> data(tao)
> x_IMPUTED <- kNN(tao[, c("Air.Temp", "Humidity")])
Humidity Humidity 
    71.6     94.8 
Air.Temp Air.Temp 
   21.42    28.50 
> tableMiss(x_IMPUTED[105:114, ])
Error in loadNamespace(x) : there is no package called ‘reactable’
Calls: tableMiss ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jefferson Paril <jeffersonparil@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jefferson",
                    family = "Paril",
                    role = c("aut", "cre"),
                    email = "jeffersonparil@gmail.com")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Scott Sherrill-Mix <ssm@msu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Scott",
                      family = "Sherrill-Mix",
                      role = c("aut", "cre"),
                      email = "ssm@msu.edu"),
               person(given = "Erik",
                      family = "Clarke",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'bookdown', 'DT', 'covr', 'knitr', 'rmarkdown'

Packages which this enhances but not available for checking:
  'mixOmics', 'sparklyr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘matlib’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) viridis.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:24-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:31-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:45: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'covr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'kableExtra', 'survminer', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘gt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'lintr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: visa.est
> ### Title: Valid Improved Sparsity A-Learning for Optimal Treatment
> ###   Decision
> ### Aliases: visa.est
> 
> ### ** Examples
> 
> data(visa_SimuData)
> y = visa_SimuData$y
> a = visa_SimuData$a
> x = visa_SimuData$x
> # estimation
> result <- visa.est(y, x, a, IC = "BIC", lambda.list = c(0.1, 0.5))
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized),  :
  Passed unrecognized parameters: verbose. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'data' has been renamed to 'x'. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized),  :
  Passed unrecognized parameters: verbose. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'data' has been renamed to 'x'. This warning will become an error in a future version.
Warning in parallel::mclapply(seq(no_rep), wt_calc) :
  all scheduled cores encountered errors in user code
Error in FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...) : 
  non-numeric argument to binary operator
Calls: visa.est -> visa.weight -> sweep
Execution halted
Packages required but not available: 'ggpmisc', 'plotly'

Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'ggExtra', 'Hmisc', 'qgraph'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'plotly', 'knitr', 'rmarkdown', 'spelling', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'plotly'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) ViSiElse.Rd:101-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:105-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:108-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:114-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:116: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:128-134: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:135-147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:148-157: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:152-153: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:154-155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dim-ViSibook-methods.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dim-ViSibook-methods.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary-ViSigrid-methods.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary-ViSigrid-methods.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'usethis', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'colourpicker', 'sparkline'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

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

Packages suggested but not available for checking:
  'covr', 'DT', 'flextable', 'gt', 'knitr', 'plotly', 'reactable',
  'rmarkdown', 'sortable'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rgl', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

Packages suggested but not available for checking:
  'prettydoc', 'knitr', 'rmarkdown', 'covr', 'highcharter'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'Hmisc', 'DT', 'htmlTable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Marcelo Ponce <m.ponce@utoronto.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Marcelo",
                    family = "Ponce",
                    role = c("aut", "cre"),
                    email = "m.ponce@utoronto.ca")
as necessary.
Packages required but not available: 'plotly', 'htmlwidgets'

Packages suggested but not available for checking:
  'knitr', 'devtools', 'roxygen2', 'rmarkdown'

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

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

Packages suggested but not available for checking:
  'knitr', 'quarto', 'rmarkdown'

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

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

Package suggested but not available for checking: ‘knitr’

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

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

Package suggested but not available for checking: ‘shinytest2’

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

Package suggested but not available for checking: ‘covr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘David J. Sharrow <dsharrow@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gregor",
                      family = "Passolt",
                      role = "aut"),
               person(given = c("James", "J."),
                      family = "Anderson",
                      role = "aut"),
               person(given = "Ting",
                      family = "Li",
                      role = "aut"),
               person(given = c("David", "H."),
                      family = "Salinger",
                      role = "aut"),
               person(given = c("David", "J."),
                      family = "Sharrow",
                      role = c("aut", "cre"),
                      email = "dsharrow@uw.edu"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'demography', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'networkD3', 'rmarkdown', 'wpa'

Package suggested but not available for checking: ‘flexdashboard’

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

Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VLMC.Rcheck/00install.out’ for details.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘oeli’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) getTurnType.Rd:38: Lost braces; missing escapes or markup?
    38 | Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
       |               ^
Package required but not available: ‘wrassp’

Packages suggested but not available for checking: 'knitr', 'tidyverse'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'BCEA', 'INLA', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'plotly', 'htmlwidgets'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'kableExtra', 'usethis', 'easylabel'

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

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

Package suggested but not available for checking: ‘safetyGraphics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'skimr', 'knitr', 'kableExtra', 'rmarkdown', 'heplots'

Packages suggested but not available for checking: 'tidyverse', 'usethis'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'covr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'htmlwidgets', 'DT'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Maintainer: ‘Carlo Pacioni <C.Pacioni@Murdoch.edu.au>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘campbell.Rd’:
    https://dx.doi.org/10.1080/14486563.2015.1028486
  File ‘pac.clas.Nadults.Rd’:
    https://doi.org/10.1071/PC17002
  File ‘pac.clas.Ne.Rd’:
    https://doi.org/10.1071/PC17002
  File ‘pac.clas.Rd’:
    https://doi.org/10.1071/PC17002
  File ‘pac.clas.lookup.Rd’:
    https://doi.org/10.1071/PC17002
  File ‘pac.clas.pairw.Rd’:
    https://doi.org/10.1071/PC17002
  File ‘pac.lhs.Rd’:
    https://doi.org/10.1071/PC17002
  File ‘pac.run.lhs.Rd’:
    https://doi.org/10.1071/PC17002
  File ‘pac.yr.Rd’:
    https://doi.org/10.1071/PC17002
  File ‘pacioni.Rd’:
    https://doi.org/10.1071/PC17002
  File ‘sta.evy5.Rd’:
    https://dx.doi.org/10.1080/14486563.2015.1028486
  File ‘sta.evy5.b11.Rd’:
    https://dx.doi.org/10.1080/14486563.2015.1028486
  File ‘sta.main.Rd’:
    https://dx.doi.org/10.1080/14486563.2015.1028486
  File ‘vortexRdata.Rd’:
    https://dx.doi.org/10.1080/14486563.2015.1028486
    https://doi.org/10.1071/PC17002
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
Maintainer: ‘Bryan Gertzel <bryan.gertzel@anu.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Bryan",
                      family = "Gertzel",
                      role = c("aut", "cre"),
                      email = "bryan.gertzel@anu.edu.au"),
               person(given = "Robert",
                      family = "Ackland",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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DESCRIPTION file?
Maintainer: ‘Pavel V. Moskalev <moskalefff@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Pavel", "V."),
                    family = "Moskalev",
                    role = c("aut", "cre"),
                    email = "moskalefff@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'formattable', 'knitr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling', 'vcr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(votesmart)
  > 
  > abrams_id <- 67385
  > aoc_id <- 180416
  > pelosi_id <- 26732
  > obama_id <- 9490
  > pete_id <- 127151
  > warren_id <- 141272
  > 
  > test_check("votesmart")
  Error in `source_dir()`:
  ! Failed to evaluate './helper-vcr.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("votesmart")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_helpers(".", env)
    7. │           └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(...)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at ./helper-vcr.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─cli::cli_abort(...)
   18.     └─rlang::abort(...)
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michael Gampmayer <michael.gampmayer@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Michael",
                    family = "Gampmayer",
                    role = c("aut", "cre"),
                    email = "michael.gampmayer@gmail.com")
as necessary.
Maintainer: ‘Tyler Kendall <tsk@uoregon.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Tyler",
                      family = "Kendall",
                      role = c("aut", "cre"),
                      email = "tsk@uoregon.edu"),
               person(given = c("Erik", "R."),
                      family = "Thomas",
                      role = "aut"))
as necessary.
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ron Keizer <ronkeizer@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ron",
                    family = "Keizer",
                    role = c("aut", "cre"),
                    email = "ronkeizer@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
File ‘vroom/libs/vroom.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.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jae H. Kim <jaekim8080@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Jae", "H."),
                    family = "Kim",
                    role = c("aut", "cre"),
                    email = "jaekim8080@gmail.com")
as necessary.
Maintainer: ‘Philippe Regnault <philipperegnault@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Justine",
                      family = "Lequesne",
                      role = "aut"),
               person(given = "Philippe",
                      family = "Regnault",
                      role = c("aut", "cre"),
                      email = "philipperegnault@hotmail.com"))
as necessary.
Package suggested but not available for checking: ‘knitr’

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/vsgoftest_tutorial.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'rmdformats'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Karolina Klockmann <karolina.klockmann@gmx.de>’

The Description field contains
  (Klockmann, Krivobokova; 2023), <arXiv:2303.10018>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) Data-Examples.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data-Examples.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data-Examples.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aquaporin.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vsts_create_release.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vsts_create_release.Rd:34: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'kableExtra', 'knitr'

Package suggested but not available for checking: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Packages required but not available: 'DiagrammeR', 'htmlwidgets'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Kartikeya Bolar <kartikeya.bolar@tapmi.edu.in>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kartikeya",
                    family = "Bolar",
                    role = c("aut", "cre"),
                    email = "kartikeya.bolar@tapmi.edu.in")
as necessary.
Package required but not available: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Andreas Schulz <ades-s@web.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Andreas",
                      family = "Schulz",
                      role = "cre",
                      email = "ades-s@web.de"),
               person(family = "PhD",
                      role = c("aut", "cre")))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
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Maintainer: ‘Csaba Farago <farago@inf.u-szeged.hu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Csaba",
                    family = "Farago",
                    role = c("aut", "cre"),
                    email = "farago@inf.u-szeged.hu")
as necessary.
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Specified C++11: support will be removed soon
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'datamods', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'itsadug'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'quarto', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'DT', 'knitr', 'pkgdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ronan Trépos <ronan.trepos@inrae.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Denis",
                      family = "Allard",
                      role = c("aut", "cre")),
               person(given = "Ronan",
                      family = "Trépos",
                      role = c("aut", "cre"),
                      email = "ronan.trepos@inrae.fr"))
as necessary.
checkRd: (-1) WACS.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACSreadAgroclim.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) WACSreadAgroclim.Rd:16-17: Lost braces in \itemize; \value handles \item{}{} directly
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'packer', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tyler Rinker <tyler.rinker@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘John Whalen <whalenjf@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "John",
                    family = "Whalen",
                    role = c("aut", "cre"),
                    email = "whalenjf@gmail.com")
as necessary.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘walkscore.R’
Packages required but not available:
  'leaflet', 'DT', 'ecospat', 'ENMeval', 'leafem', 'leaflet.extras',
  'rJava', 'rmarkdown', 'spocc', 'spThin'

Packages suggested but not available for checking:
  'knitr', 'mapview', 'occCite', 'rangeModelMetadata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Paul F. Blanche <paulfblanche@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Paul", "F"),
                      family = "Blanche",
                      role = "aut",
                      email = "paulfblanche@gmail.com"),
               person(given = c("Thomas", "A."),
                      family = "Gerds",
                      role = "aut",
                      email = "tag@biostat.ku.dk"),
               person(given = c("Paul", "F."),
                      family = "Blanche",
                      role = "cre",
                      email = "paulfblanche@gmail.com"))
as necessary.
Package required but not available: ‘riskRegression’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jonathon Love <jon@thon.cc>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jonathon",
                      family = "Love",
                      role = c("aut", "cre"),
                      email = "jon@thon.cc"),
               person(given = "Patrick",
                      family = "Mair",
                      role = "aut"))
as necessary.
Maintainer: ‘Harvinder Singh <harvindermaan4@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Harvinder",
                    family = "Singh",
                    role = c("aut", "cre"),
                    email = "harvindermaan4@gmail.com")
as necessary.
Package required but not available: ‘flextable’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

Packages suggested but not available for checking:
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VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Lu Mao <lmao@biostat.wisc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Lu",
                    family = "Mao",
                    role = c("aut", "cre"),
                    email = "lmao@biostat.wisc.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'kableExtra', 'survminer'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Emilie Devijver <emilie.devijver@kuleuven.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Emilie",
                      family = "Devijver",
                      role = c("aut", "cre"),
                      email = "emilie.devijver@kuleuven.be"),
               person(given = "Gerda",
                      family = "Claeskens",
                      role = "aut"),
               person(given = "Irene",
                      family = "Gijbels",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Andrea Venturini <andrea.venturini@bancaditalia.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Andrea",
                    family = "Venturini",
                    role = c("aut", "cre"),
                    email = "andrea.venturini@bancaditalia.it")
as necessary.
Package required but not available: ‘flextable’

Package suggested but not available for checking: ‘covr’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'bookdown', 'rmarkdown', 'kableExtra', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
'::' or ':::' import not declared from: ‘NPRED’
'library' or 'require' call not declared from: ‘NPRED’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Hugh Parsonage <hugh.parsonage+waterfall@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hugh",
                    family = "Parsonage",
                    role = c("aut", "cre"),
                    email = "hugh.parsonage+waterfall@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'tmap'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michael Stewart <michael.stewart@sydney.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Marc",
                      family = "Raimondo",
                      role = "aut",
                      email = "marcr@maths.usyd.edu.au"),
               person(given = "Michael",
                      family = "Stewart",
                      role = c("aut", "cre"),
                      email = "michael.stewart@sydney.edu.au"))
as necessary.
Maintainer: ‘Dr. Ranjit Kumar Paul <ranjitstat@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Dr.", "Ranjit", "Kumar"),
                      family = "Paul",
                      role = c("aut", "cre"),
                      email = "ranjitstat@gmail.com"),
               person(given = "Sandipan",
                      family = "Samanta",
                      role = "aut"),
               person(given = "Ankit",
                      family = "Tanwar",
                      role = "aut"))
as necessary.
Package required but not available: ‘TSLSTM’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Eric Aldrich <ealdrich@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Eric",
                    family = "Aldrich",
                    role = c("aut", "cre"),
                    email = "ealdrich@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'Hmisc', 'rlist', 'DecomposeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Olivia Cheronet <cheronetolivia@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Olivia",
                      family = "Cheronet",
                      role = c("aut", "cre"),
                      email = "cheronetolivia@gmail.com"),
               person(given = c("John", "A."),
                      family = "Finarelli",
                      role = "aut"))
as necessary.
Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
Maintainer: ‘Brandon Whitcher <bwhitcher@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Brandon",
                    family = "Whitcher",
                    role = c("aut", "cre"),
                    email = "bwhitcher@gmail.com")
as necessary.
Package required but not available: ‘spectacles’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Vicente J. Bolos <vicente.bolos@uv.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Vicente", "J."),
                      family = "Bolos",
                      role = c("aut", "cre"),
                      email = "vicente.bolos@uv.es"),
               person(given = "Rafael",
                      family = "Benitez",
                      role = "aut"))
as necessary.
Maintainer: ‘Pablo Rodríguez-Sánchez <pablo.rodriguez.sanchez@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Pablo",
                    family = "Rodríguez-Sánchez",
                    role = c("aut", "cre"),
                    email = "pablo.rodriguez.sanchez@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Package suggested but not available for checking: ‘quarto’

VignetteBuilder package required for checking but not installed: ‘quarto’
Running ‘testthat.R’ [8s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(wbids)
  > 
  > test_check("wbids")
  Reading in file.
  Processing file.
  Downloading file to: /tmp/Rtmpaq4aLK/fileb688d6df8595c.xlsx
  Processing file.
  Downloading file to: /tmp/Rtmpaq4aLK/fileb688d7767e78c.xlsx
  Reading in file.
  Downloading file to: /tmp/Rtmpaq4aLK/fileb688d3477c105.xlsx
  Saving _problems/test-ids_get-474.R
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 153 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (6): 'test-ids_bulk.R:161:3', 'test-ids_bulk.R:215:3',
    'test-ids_bulk.R:248:3', 'test-ids_bulk.R:301:3', 'test-ids_bulk.R:368:3',
    'test-ids_get_ed.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-ids_get.R:472:3'): ids_get filters post-observed-year NAs correctly ──
  Expected `all(result$year <= as.numeric(format(Sys.Date(), "%Y")) | !is.na(result$value))` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 153 ]
  Error:
  ! Test failures.
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘David Preinerstorfer <david.preinerstorfer@ulb.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "David",
                    family = "Preinerstorfer",
                    role = c("aut", "cre"),
                    email = "david.preinerstorfer@ulb.be")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

The Description field contains
  Heteroskedasticity Robust Tests?" <arXiv:2005.04089>. This diagnostic
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'vcr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Karolos Korkas <kkorkas@yahoo.co.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Karolos",
                      family = "Korkas",
                      role = c("aut", "cre"),
                      email = "kkorkas@yahoo.co.uk"),
               person(given = "Piotr",
                      family = "Fryzlewicz",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown', 'tidyverse', 'lemon'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘wcde-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: edu_group_sum
> ### Title: Education group sums
> ### Aliases: edu_group_sum
> 
> ### ** Examples
> 
> library(tidyverse)
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ujjwal Singh <ujjwalrsmt@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Ujjwal", "Singh", "Prashant", "K", "Srivastava", "<prashant.just@gmail.com)>", "Dharmendra", "Kumar", "Pandey", "<Dkp@sac.isro.gov.in>", "Sumit", "Kumar", "Chaudhary", "<sumit.mathe@gmail.com>", "Dileep", "Kumar", "Gupta"),
                      family = "<dileepgupta85@gmail.com>",
                      role = "aut",
                      email = "dileepgupta85@gmail.com"),
               person(given = "Ujjwal",
                      family = "Singh",
                      role = "cre",
                      email = "ujjwalrsmt@gmail.com"))
as necessary.
Maintainer: ‘Lu Mao <lmao@biostat.wisc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Lu",
                    family = "Mao",
                    role = c("aut", "cre"),
                    email = "lmao@biostat.wisc.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
No examples, no tests, no vignettes
Packages required but not available: 'binman', 'yaml'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'roxygen2', 'rmarkdown', 'prepr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘RHRV’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Brooke Anderson <brooke.anderson@colostate.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'apsimx', 'knitr'

Packages suggested but not available for checking:
  'covr', 'mailR', 'rmarkdown', 'roxyglobals', 'spelling', 'usethis',
  'vcr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'rcdk', 'covr', 'knitr', 'rmarkdown', 'usethis', 'vcr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Timothy Conwell <timconwell@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Timothy",
                    family = "Conwell",
                    role = c("aut", "cre"),
                    email = "timconwell@gmail.com")
as necessary.
Maintainer: ‘Gábor Csárdi <csardi.gabor@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ariya",
                      family = "Hidayat",
                      role = "aut"),
               person(given = "Gábor",
                      family = "Csárdi",
                      role = c("aut", "cre"),
                      email = "csardi.gabor@gmail.com"),
               person(given = "Gabor",
                      family = "Torok",
                      role = "aut"),
               person(given = "Ivan",
                      family = "De Marino",
                      role = "aut"),
               person(given = "Robert",
                      family = "Gieseke",
                      role = "aut"),
               person(given = "Steven",
                      family = "Masala",
                      role = "aut"),
               person(given = "Winston",
                      family = "Chang",
                      role = "aut"),
               person(given = "Zack",
                      family = "Weinberg",
                      role = "aut"))
as necessary.
checkRd: (-1) Session.Rd:146: Lost braces
   146 | sQuote{page load} timeout specifies a time to wait for the page loading
       |       ^
Packages required but not available: 'knitr', 'yaml', 'rmarkdown'

Packages suggested but not available for checking: 'bookdown', 'quarto'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Richard Barnes <rijard.barnes@gmail.com>’

The BugReports field in DESCRIPTION has
  https://github.com/r-barnes/webglobe/
which should likely be
  https://github.com/r-barnes/webglobe/issues
instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'htmlwidgets', 'leaflet'

Packages suggested but not available for checking:
  'covr', 'knitr', 'pkgdown', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Oliver Keyes <ironholds@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Oliver",
                    family = "Keyes",
                    role = c("aut", "cre"),
                    email = "ironholds@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'iptools', 'rgeolocate', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'flextable', 'rrtable', 'ztable'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Author field differs from that derived from Authors@R
  Author:    ‘Winston Chang [aut, cre], Barret Schloerke [ctb] (<https://orcid.org/0000-0001-9986-114X>), Posit Software, PBC [cph, fnd] (03wc8by49)’
  Authors@R: ‘Winston Chang [aut, cre], Barret Schloerke [ctb] (ORCID: <https://orcid.org/0000-0001-9986-114X>), Posit Software, PBC [cph, fnd] (ROR: <https://ror.org/03wc8by49>)’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jodi Beggs <jodi@alum.mit.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Rense Nieuwenhuis <rense.nieuwenhuis@sofi.su.se>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rense",
                      family = "Nieuwenhuis",
                      role = c("aut", "cre"),
                      email = "rense.nieuwenhuis@sofi.su.se"),
               person(given = c("Manfred", "te"),
                      family = "Grotenhuis",
                      role = "aut"),
               person(given = "Ben",
                      family = "Pelzer",
                      role = "aut"),
               person(given = "Alexander",
                      family = "Schmidt",
                      role = "aut"),
               person(given = "Ruben",
                      family = "Konig",
                      role = "aut"),
               person(given = "Rob",
                      family = "Eisinga",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘usethis’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) busTrace.Rd:15: Lost braces
    15 | /href{https://crawdad.org/coppe-ufrj/RioBuses/20180319/}
       |      ^
Package required but not available: ‘plotly’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/WeightedCluster.Rnw’
   ‘inst/doc/WeightedClusterFR.Rnw’
   ‘inst/doc/WeightedClusterPreview.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Abbas Parchami <parchami@uk.ac.ir>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Abbas",
                    family = "Parchami",
                    role = c("aut", "cre"),
                    email = "parchami@uk.ac.ir",
                    comment = "Department of Statistics, Faculty of Mathematics and Computer, Shahid Bahonar University of Kerman, Kerman, Iran")
as necessary.
Maintainer: ‘Cyrill Scheidegger <cyrill.scheidegger@stat.math.ethz.ch>’

The Description field contains
  Measure" <arXiv:2111.04361>. The test is a generalisation of the
  Testing and the Generalised Covariance Measure" <arXiv:1804.07203>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
train.xgboost1: no visible global function definition for
  ‘cb.evaluation.log’
Undefined global functions or variables:
  cb.evaluation.log
Maintainer: ‘Toby Dylan Hocking <toby.hocking@r-project.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Toby", "Dylan"),
                    family = "Hocking",
                    role = c("aut", "cre"),
                    email = "toby.hocking@r-project.org")
as necessary.
checkRd: (-1) WeightedROC.Rd:10: Lost braces; missing escapes or markup?
    10 | integer/numeric with values all in {0=negative,1=positive} or
       |                                    ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       | ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       |                            ^
Maintainer: ‘Aristidis K. Nikoloulopoulos <a.nikoloulopoulos@uea.ac.uk>’

The Description field contains
  <arXiv:1510.07376>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) CLIC.Rd:149: Lost braces
   149 | Composite likelihood {E}{M} algorithm with applications to
       |                         ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'SuperLearner', 'mclogit', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Viviane Philipps <Viviane.Philipps@u-bordeaux.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Viviane",
                    family = "Philipps",
                    role = c("aut", "cre"),
                    email = "viviane.philipps@u-bordeaux.fr")
as necessary.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘William Asquith <william.asquith@ttu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "William",
                    family = "Asquith",
                    role = c("aut", "cre"),
                    email = "william.asquith@ttu.edu")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Pablo J. Villacorta <pjvi@decsai.ugr.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Pablo", "J."),
                    family = "Villacorta",
                    role = c("aut", "cre"),
                    email = "pjvi@decsai.ugr.es")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Marco Colombo <mar.colombo13@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Han Yu <hyu9@buffalo.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Han",
                      family = "Yu",
                      role = c("aut", "cre"),
                      email = "hyu9@buffalo.edu"),
               person(given = c("Rachael", "Hageman"),
                      family = "Blair",
                      role = "aut"))
as necessary.
Package required but not available: ‘qtl’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Zihuai He <zihuai@stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Zihuai",
                    family = "He",
                    role = c("aut", "cre"),
                    email = "zihuai@stanford.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘bandit’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Soubhik Barari <soubhikbarari@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Heather",
                      family = "Stoll",
                      role = "aut",
                      email = "hstoll@polsci.ucsb.edu"),
               person(given = "Gary",
                      family = "King",
                      role = "aut",
                      email = "king@harvard.edu"),
               person(given = "Langche",
                      family = "Zeng",
                      role = "aut",
                      email = "zeng@ucsd.edu"),
               person(given = "Christopher",
                      family = "Gandrud",
                      role = "aut",
                      email = "zelig.zee@gmail.com"),
               person(given = "Ben",
                      family = "Sabath",
                      role = "aut"),
               person(given = "Soubhik",
                      family = "Barari",
                      role = "cre",
                      email = "soubhikbarari@gmail.com"))
as necessary.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
Packages required but not available: 'qdap', 'visNetwork', 'leaflet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘coords_from_words.R’ ‘get_available_languages.R’
    ‘words_from_coords.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘xlsx’

Packages suggested but not available for checking:
  'DiagrammeR', 'knitr', 'rmarkdown'

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

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

Packages suggested but not available for checking:
  'knitr', 'pointblank', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'kableExtra', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'kableExtra', 'knitr', 'quarto', 'yaml'

Package suggested but not available for checking: ‘usethis’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Edwin de Jonge <edwindjonge@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Edwin",
                    family = "de Jonge",
                    role = c("aut", "cre"),
                    email = "edwindjonge@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Korbinian Strimmer <strimmerlab@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Korbinian",
                      family = "Strimmer",
                      role = c("aut", "cre"),
                      email = "strimmerlab@gmail.com"),
               person(given = "Takoua",
                      family = "Jendoubi",
                      role = "aut"),
               person(given = "Agnan",
                      family = "Kessy",
                      role = "aut"),
               person(given = "Alex",
                      family = "Lewin",
                      role = "aut"))
as necessary.
Maintainer: ‘Jorge Lopez Perez <jorge@loperez.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘usethis’

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'knitr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Bhaskar Karambelkar <bhaskarvk@gmail.com>’

Found the following (possibly) invalid file URIs:
  URI: rmarkdown.rstudio.com
    From: inst/doc/Using_widgetframe.html
  URI: yihui.name/knitr/
    From: inst/doc/Using_widgetframe.html
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Joerg grosse Schlarmann (aka Produnis) <schlarmann@produnis.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Joerg", "grosse"),
                    family = "Schlarmann",
                    role = c("aut", "cre"),
                    email = "schlarmann@produnis.de",
                    comment = "aka Produnis")
as necessary.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking:
  'tidyverse', 'knitr', 'pageviews'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) milakes.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:22: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Os Keyes <ironholds@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Os",
                      family = "Keyes",
                      role = c("aut", "cre"),
                      email = "ironholds@gmail.com"),
               person(given = "Brock",
                      family = "Tilbert",
                      role = "ctb"),
               person(given = "Clemens",
                      family = "Schmid",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'WikidataR', 'pageviews'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘WikidataR’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'vcr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Bradley Shanrock-Solberg <greblosb@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Bradley",
                    family = "Shanrock-Solberg",
                    role = c("aut", "cre"),
                    email = "greblosb@gmail.com")
as necessary.
Packages required but not available:
  'plotly', 'DT', 'colourpicker', 'FactoMineR', 'factoextra',
  'heatmaply'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) secondDerivative.Rd:14: Lost braces
    14 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
checkRd: (-1) windAC.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) windAC.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) windAC.Rd:33: Lost braces in \itemize; meant \describe ?
Maintainer: ‘Neeraj Bokde <neerajdhanraj@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Neeraj",
                      family = "Bokde",
                      role = c("aut", "cre"),
                      email = "neerajdhanraj@gmail.com"),
               person(given = "Andres",
                      family = "Feijoo",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Novica Nakov <nnovica@gmail.com>’

The BugReports field in DESCRIPTION has
  https://github.com/windsor-ai/windsoraiR/
which should likely be
  https://github.com/windsor-ai/windsoraiR/issues
instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Kevin Duarte <k.duarte@chru-nancy.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Kevin",
                      family = "Duarte",
                      role = c("aut", "cre"),
                      email = "k.duarte@chru-nancy.fr"),
               person(given = c("Joao", "Pedro"),
                      family = "Ferreira",
                      role = "aut"))
as necessary.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘WinRatio-package.Rd’:
    https://doi.org/10.1093/eurheartj/ehr352
    https://doi.org/10.1093/biostatistics/kxv032
Package required but not available: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Robert W. Cort <rcorty@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Robert", "W."),
                    family = "Cort",
                    role = c("aut", "cre"),
                    email = "rcorty@gmail.com")
as necessary.
Package required but not available: ‘roxygen2’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'config', 'knitr'

Packages suggested but not available for checking: 'rmarkdown', 'yaml'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ian Cook <ianmcook@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("TIBCO", "Software"),
                      family = "Inc.",
                      role = "aut"),
               person(given = "Ian",
                      family = "Cook",
                      role = "cre",
                      email = "ianmcook@gmail.com"))
as necessary.
Maintainer: ‘Wencan Zhu <wencan.zhu@yahoo.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Wencan",
                    family = "Zhu",
                    role = c("aut", "cre"),
                    email = "wencan.zhu@yahoo.com")
as necessary.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ilana Trumble <ilana.trumble@cuanschutz.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ilana",
                      family = "Trumble",
                      role = c("aut", "cre"),
                      email = "ilana.trumble@cuanschutz.edu"),
               person(given = "Orlando",
                      family = "Ferrer",
                      role = "aut"),
               person(given = "Camden",
                      family = "Bay",
                      role = "aut"),
               person(given = "Katie",
                      family = "Mollan",
                      role = "aut"))
as necessary.

The Description field contains
  <doi:10.1080/10543406.2020.1730866> <arXiv:1901.04597>, (Mann and
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Shahla Faisal <shahla_ramzan@yahoo.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Shahla",
                    family = "Faisal",
                    role = c("aut", "cre"),
                    email = "shahla_ramzan@yahoo.com")
as necessary.
Maintainer: ‘Jeffrey B. Lewis <jblewis@ucla.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Keith",
                      family = "Poole",
                      role = "aut",
                      email = "ktpoole@uga.edu"),
               person(given = "Jeffrey",
                      family = "Lewis",
                      role = "aut",
                      email = "jblewis@ucla.edu"),
               person(given = "James",
                      family = "Lo",
                      role = "aut",
                      email = "lojames@usc.edu"),
               person(given = "Royce",
                      family = "Carroll",
                      role = "aut",
                      email = "rcarroll@rice.edu"),
               person(given = c("Jeffrey", "B."),
                      family = "Lewis",
                      role = "cre",
                      email = "jblewis@ucla.edu"))
as necessary.
Maintainer: ‘Thilo Eichenberg <te.r@gmx.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thilo",
                    family = "Eichenberg",
                    role = c("aut", "cre"),
                    email = "te.r@gmx.net")
as necessary.
Maintainer: ‘Sudarson Mothilal Thoppay <sudarson@outlook.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Sudarson", "Mothilal"),
                    family = "Thoppay",
                    role = c("aut", "cre"),
                    email = "sudarson@outlook.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'lintr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'rmarkdown', 'prereg', 'yaml', 'rticles', 'usethis'

Packages suggested but not available for checking:
  'papaja', 'targets', 'tarchetypes', 'knitr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Neda Daneshgar<ne_da978@stu-mail.um.ac.ir>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Neda",
                      family = "Daneshagr",
                      role = "aut"),
               person(given = "Majid",
                      family = "Sarmad.",
                      role = "aut"),
               person(given = "Neda",
                      family = "Daneshgar",
                      role = "cre",
                      email = "ne_da978@stu-mail.um.ac.ir"))
as necessary.
Maintainer: ‘Dawei Lang <chiffonlang@icloud.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dawei",
                      family = "Lang",
                      role = c("aut", "cre"),
                      email = "chiffonlang@icloud.com"),
               person(given = "Guan-tin",
                      family = "Chien",
                      role = "aut"))
as necessary.
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ian Fellows <ian@fellstat.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ian",
                    family = "Fellows",
                    role = c("aut", "cre"),
                    email = "ian@fellstat.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘quanteda’

Package suggested but not available for checking: ‘spelling’

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

Package suggested but not available for checking: ‘wordnetDicts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jonathan Bratt <jonathan.bratt@macmillan.com>’

The Description field contains
  Apply 'Wordpiece' (<arXiv:1609.08144>) tokenization to input text,
  given an appropriate vocabulary. The 'BERT' (<arXiv:1810.04805>)
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) wordpiece_cache_dir.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) wordpiece_cache_dir.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) wordpiece_cache_dir.Rd:20-21: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION 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:
    ‘TWP.Rd’
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
'library' or 'require' call not declared from: ‘shiny’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tomas Hovorka <tomashovorka@seznam.cz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tomas",
                    family = "Hovorka",
                    role = c("aut", "cre"),
                    email = "tomashovorka@seznam.cz")
as necessary.
Package required but not available: ‘flextable’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘quanteda’

Package suggested but not available for checking: ‘spelling’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘yaml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘leaflet’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'rmarkdown', 'vcr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘test-all.R’ [1s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("worrms")
  Loading required package: worrms
  Error in `source_dir()`:
  ! Failed to evaluate './helper-worrms.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("worrms")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_helpers(".", env)
    7. │           └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(...)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at ./helper-worrms.R:2:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─cli::cli_abort(...)
   18.     └─rlang::abort(...)
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘yaml’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'rmarkdown', 'networkD3', 'DT'

Packages suggested but not available for checking: 'knitr', 'flexdashboard'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Neil A. Weiss <neil.a.weiss@asu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Neil", "A."),
                    family = "Weiss",
                    role = c("aut", "cre"),
                    email = "neil.a.weiss@asu.edu")
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘wPerm-package.Rd’:
    \keyword{ package, datasets, graphs }
Cannot process vignettes
Packages suggested but not available for checking:
  'kinship2', 'knitr', 'leaflet', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Hana Sevcikova <hanas@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hana",
                      family = "Sevcikova",
                      role = c("aut", "cre"),
                      email = "hanas@uw.edu"),
               person(given = "Patrick",
                      family = "Gerland",
                      role = "aut",
                      email = "gerland@un.org"))
as necessary.
Malformed Description field: should contain one or more complete sentences.
Maintainer: ‘Hana Sevcikova <hanas@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hana",
                      family = "Sevcikova",
                      role = c("aut", "cre"),
                      email = "hanas@uw.edu"),
               person(given = "Patrick",
                      family = "Gerland",
                      role = "aut",
                      email = "gerland@un.org"))
as necessary.
Malformed Description field: should contain one or more complete sentences.
Maintainer: ‘Hana Sevcikova <hanas@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hana",
                      family = "Sevcikova",
                      role = c("aut", "cre"),
                      email = "hanas@uw.edu",
                      comment = "hanas@uw.edu"),
               person(given = "Patrick",
                      family = "Gerland",
                      role = "aut",
                      comment = "gerland@un.org"),
               person(given = "Kirill",
                      family = "Andreev",
                      role = "aut",
                      comment = "andreev@un.org"),
               person(given = "Nan",
                      family = "Li",
                      role = "aut",
                      comment = "li32@un.org"),
               person(given = "Danan",
                      family = "Gu",
                      role = "aut",
                      comment = "gud@un.org"),
               person(given = "Thomas",
                      family = "Spoorenberg",
                      role = "aut",
                      comment = "spoorenberg@un.org"))
as necessary.
Malformed Description field: should contain one or more complete sentences.
Maintainer: ‘Hana Sevcikova <hanas@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("United", "Nations", "Population"),
                      family = "Division",
                      role = "aut"),
               person(given = "Hana",
                      family = "Sevcikova",
                      role = "cre",
                      email = "hanas@uw.edu"))
as necessary.
Maintainer: ‘Hana Sevcikova <hanas@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("United", "Nations", "Population"),
                      family = "Division",
                      role = "aut"),
               person(given = "Hana",
                      family = "Sevcikova",
                      role = "cre",
                      email = "hanas@uw.edu"))
as necessary.
Maintainer: ‘Hana Sevcikova <hanas@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hana",
                    family = "Sevcikova",
                    role = c("aut", "cre"),
                    email = "hanas@uw.edu")
as necessary.
Packages required but not available: 'Hmisc', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'wmtsa', 'knitr', 'rmarkdown', 'bookdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘gWQS’

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

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

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

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Tim Bergsma <bergsmat@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tim",
                    family = "Bergsma",
                    role = c("aut", "cre"),
                    email = "bergsmat@gmail.com")
as necessary.
Packages required but not available:
  'knitr', 'kableExtra', 'rlist', 'flextable'

Package suggested but not available for checking: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wrassp.Rcheck/00install.out’ for details.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'factoextra', 'FactoMineR', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'fdapace', 'fdadensity', 'modeest'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [16s/16s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

Packages suggested but not available for checking:
  'kableExtra', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Lu Mao <lmao@biostat.wisc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Lu",
                      family = "Mao",
                      role = c("aut", "cre"),
                      email = "lmao@biostat.wisc.edu"),
               person(given = "Tuo",
                      family = "Wang",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages suggested but not available for checking: 'knitr', 'mediation'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/WRS2.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Rezgar Arabzadeh <rezgararabzadeh@ut.ac.ir>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Rezgar", "Arabzadeh;", "Parisa", "Aberi;", "Kaveh", "Panaghi;", "Shahab", "Araghinejad;", "Majid"),
                      family = "Montaseri",
                      role = "aut"),
               person(given = "Rezgar",
                      family = "Arabzadeh",
                      role = "cre",
                      email = "rezgararabzadeh@ut.ac.ir"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'plotly', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘wrProteo’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Specified C++11: support will be removed soon
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Rui Sun <rsunzju@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rui",
                      family = "Sun",
                      role = c("aut", "cre"),
                      email = "rsunzju@gmail.com"),
               person(given = c("Maggie", "Haitian"),
                      family = "Wang",
                      role = "aut"))
as necessary.
checkRd: (-1) wtest.Rd:61-64: Lost braces
    61 | {When \code{w.order} =2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
checkRd: (-1) wtest.high.Rd:61-64: Lost braces
    61 | {When \code{w.order} > 2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
Maintainer: ‘Deisy Morselli Gysi <deisy.ccnr@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Deisy", "Morselli"),
                      family = "Gysi",
                      role = c("aut", "cre"),
                      email = "deisy.ccnr@gmail.com"),
               person(given = "Andre",
                      family = "Voigt",
                      role = "aut"),
               person(given = c("Tiago", "Miranda"),
                      family = "Fragoso",
                      role = "aut"),
               person(given = "Eivind",
                      family = "Almaas",
                      role = "aut"),
               person(given = "Katja",
                      family = "Nowick.",
                      role = "aut"))
as necessary.
Package required but not available: ‘visNetwork’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'plotly'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Shu Chen <chenshu@umich.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Shu",
                      family = "Chen",
                      role = c("aut", "cre"),
                      email = "chenshu@umich.edu"),
               person(given = "Andrzej",
                      family = "Galecki",
                      role = "aut",
                      email = "agalecki@umich.edu"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘ftsa’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'mapview', 'lfstat'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Fabien Gelineau <neonira@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Fabien",
                    family = "Gelineau",
                    role = c("aut", "cre"),
                    email = "neonira@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) exploreSignatures.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:67-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateData.Rd:47: Lost braces
    47 | \bold{code{data}} \tab the generated data \cr
       |           ^
checkRd: (-1) generateData.Rd:53: Lost braces
    53 | Refer to \bold{\emph{code{\link{retrieveDataFactory}}}} and to
       |                          ^
checkRd: (-1) qualifyFunctionArguments.Rd:14: Lost braces
    14 | A emph{\code{list}} with following names
       |       ^
checkRd: (-1) qualifyFunctionArguments.Rd:26: Lost braces
    26 | \item{code{arguments}}{a \code{pairList} of argument names and values.
       |           ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Fabien Gelineau <neonira@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Fabien",
                    family = "Gelineau",
                    role = c("aut", "cre"),
                    email = "neonira@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Fabien Gelineau <neonira@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Fabien",
                    family = "Gelineau",
                    role = c("aut", "cre"),
                    email = "neonira@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) completeManualPage.Rd:12: Lost braces
    12 | See \emph{\bold{code{\link{ProcessingContext}}}}. Only
       |                     ^
checkRd: (-1) produceAllManualPagesFromObject.Rd:14: Lost braces
    14 | See \emph{\bold{\\code{\link{ProcessingContext}}}}.}
       |                       ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Fabien Gelineau <neonira@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Fabien",
                    family = "Gelineau",
                    role = c("aut", "cre"),
                    email = "neonira@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'rgl', 'yaml'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘knitr’

Packages suggested but not available for checking: 'rmarkdown', 'xaringan'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'xaringan'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Philip Leifeld <philip.leifeld@essex.ac.uk>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘chemnet.Rd’:
    http://dx.doi.org/10.1111/j.1540-5907.2011.00580.x
    http://dx.doi.org/10.1007%2F978-3-531-91883-9_6
  File ‘knecht.Rd’:
    http://dx.doi.org/10.1111/j.1467-9507.2009.00564.x
    http://dx.doi.org/10.1016/j.socnet.2009.02.004
Package required but not available: ‘ergm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
No examples, no tests, no vignettes
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'DiagrammeR', 'htmlwidgets'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘xgboost-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xgb.plot.multi.trees
> ### Title: Project all trees on one tree
> ### Aliases: xgb.plot.multi.trees
> 
> ### ** Examples
> 
> 
> data(agaricus.train, package = "xgboost")
> 
> ## Keep the number of threads to 2 for examples
> nthread <- 2
> data.table::setDTthreads(nthread)
> 
> model <- xgboost(
+   agaricus.train$data, factor(agaricus.train$label),
+   nrounds = 30,
+   verbosity = 0L,
+   nthreads = nthread,
+   max_depth = 15,
+   learning_rate = 1,
+   min_child_weight = 50
+ )
> 
> p <- xgb.plot.multi.trees(model, features_keep = 3)
Error in xgb.plot.multi.trees(model, features_keep = 3) : 
  DiagrammeR is required for xgb.plot.multi.trees
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking:
  'knitr', 'pkgdown', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Juste Goungounga <juste.goungounga@ehesp.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Juste",
                      family = "Goungounga",
                      role = c("aut", "cre"),
                      email = "juste.goungounga@ehesp.fr",
                      comment = c(ORCID = "0000-0002-9039-2639")),
               person(given = "Hadrien",
                      family = "Charvat",
                      role = "aut",
                      comment = c(ORCID = "0000-0003-3624-1394")),
               person(given = "Darlin",
                      family = "Mba",
                      role = "aut",
                      comment = c(ORCID = "0000-0001-9768-0230")),
               person(given = "Nathalie",
                      family = "Graffeo",
                      role = "aut",
                      comment = c(ORCID = "0000-0001-7227-7525")),
               person(given = "Roch",
                      family = "Giorgi",
                      role = "aut",
                      comment = c(ORCID = "0000-0001-6135-3078")))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Susan Holmes <sp.holmes@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Susan",
                      family = "Holmes",
                      role = c("aut", "cre"),
                      email = "sp.holmes@gmail.com"),
               person(given = "Sourav",
                      family = "Chatterjee",
                      role = "aut"))
as necessary.

The Description field contains
  Chatterjee, Sourav (2020) <arXiv:1909.10140> This package includes the
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Thomas Lumley <t.lumley@auckland.ac.nz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Thomas",
                      family = "Lumley",
                      role = c("aut", "cre"),
                      email = "t.lumley@auckland.ac.nz"),
               person(given = c("using", "data", "from", "Randall"),
                      family = "Munroe",
                      role = "aut"),
               person(given = c("about", "2.2e5", "survey"),
                      family = "participants",
                      role = "aut"))
as necessary.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pkgdown'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Emeline Perthame <emeline.perthame@pasteur.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Emeline",
                      family = "Perthame",
                      role = c("aut", "cre"),
                      email = "emeline.perthame@pasteur.fr",
                      comment = "emeline.perthame@inria.fr"),
               person(given = "Florence",
                      family = "Forbes",
                      role = "aut",
                      comment = "florence.forbes@inria.fr"),
               person(given = "Antoine",
                      family = "Deleforge",
                      role = "aut",
                      comment = "antoine.deleforge@inria.fr"),
               person(given = "Emilie",
                      family = "Devijver",
                      role = "aut",
                      comment = "emilie.devijver@kuleuven.be"),
               person(given = "Melina",
                      family = "Gallopin",
                      role = "aut",
                      comment = "melina.gallopin@u-psud.fr"))
as necessary.

The Description field contains
  al (2017) <arXiv:1701.07899>) which is an extension of GLLiM with a
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘mixOmics’

Package suggested but not available for checking: ‘shock’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rJava’

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

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) xml_to_df.Rd:144: Lost braces; missing escapes or markup?
   144 | Default {NULL} means the workbook will not be protected with a password}
       |         ^
Maintainer: ‘Gábor Csárdi <csardi.gabor@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Gábor",
                    family = "Csárdi",
                    role = c("aut", "cre"),
                    email = "csardi.gabor@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION 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:
    ‘add_frag.R’ ‘data_frag.R’ ‘elem.Rd’ ‘list_as_xml_document.R’
    ‘read_fragment.R’ ‘tag.R’ ‘write_xml.R’ ‘xml_fragment.R’
    ‘xmlbuilder.R’ ‘xmlbuilder.Rd’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Joris Meys <Joris.Meys@UGent.be>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘drugTargetInteraction.Rd’:
    https://doi.org/10.1093/bioinformatics/btn162
  File ‘loo.Rd’:
    http://doi.org/10.1093/bib/bby095
  File ‘proteinInteraction.Rd’:
    https://doi.org/10.1093/bioinformatics/bth910
  File ‘xnet-package.Rd’:
    http://doi.org/10.1093/bib/bby095
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ChemmineR', 'covr', 'fmcsR'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘qtl’

Packages suggested but not available for checking: 'devtools', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'FactoMineR', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'DT', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'Hmisc', 'gam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nlmixr2est’

Package suggested but not available for checking: ‘nlmixr2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'plotly'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'DiagrammeR', 'knitr', 'nlmixr2', 'nlmixr2est', 'rmarkdown',
  'spelling', 'xpose.nlmixr2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Found the following significant warnings:
  Warning: namespace ‘nlmixr2est’ is not available and has been replaced
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/xpose.xtras.Rcheck/00install.out’ for details.
Running examples in ‘xpose.xtras-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: backfill_nlmixr2_props
> ### Title: Populate some properties from nlmixr2 fit
> ### Aliases: backfill_nlmixr2_props
> 
> ### ** Examples
> 
> 
> xpdb_nlmixr2 %>%
+   set_prop(condn = "not implemented") %>%
+   get_prop("condn")
[1] "not implemented"
> 
> xpdb_nlmixr2 %>%
+   set_prop(condn = "not implemented") %>%
+   backfill_nlmixr2_props() %>%
+   get_prop("condn")
Error in `backfill_nlmixr2_props()`:
! Incompatible nlmixr2/rxode2 fit object detected
ℹ This object was created with rxode2 < 5.0 and cannot be used with rxode2 >= 5.0
✖ The internal rxUi structure is incompatible between versions
! Please regenerate the fit object using current versions of nlmixr2est and rxode2
Backtrace:
    ▆
 1. ├─... %>% get_prop("condn")
 2. ├─xpose.xtras::get_prop(., "condn")
 3. │ └─xpose::get_summary(xpdb)
 4. │   └─xpose::check_xpdb(xpdb, check = "summary")
 5. │     └─xpose::is.xpdb(xpdb)
 6. └─xpose.xtras::backfill_nlmixr2_props(.)
 7.   └─rlang::abort(...)
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘John Chambers <jmc@r-project.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("John", "M."),
                      family = "Chambers",
                      role = "aut"),
               person(given = "John",
                      family = "Chambers",
                      role = "cre",
                      email = "jmc@r-project.org"))
as necessary.
Maintainer: ‘John Chambers <jmc@r-project.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("John", "M."),
                      family = "Chambers",
                      role = "aut"),
               person(given = "John",
                      family = "Chambers",
                      role = "cre",
                      email = "jmc@r-project.org"))
as necessary.
Maintainer: ‘Hitoshi Iuchi <hiuchi@sfc.keio.ac.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hitoshi",
                      family = "Iuchi",
                      role = c("aut", "cre"),
                      email = "hiuchi@sfc.keio.ac.jp"),
               person(given = c("Rikuhiro", "G."),
                      family = "Yamada",
                      role = "aut"))
as necessary.
Package suggested but not available for checking: ‘knitr’

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/OtherPackagesGallery.Rnw’
   ‘inst/doc/listOfTablesGallery.Rnw’
   ‘inst/doc/margintable.Rnw’
   ‘inst/doc/xtableGallery.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Joao Claudio Macosso <joaoclaudiomacosso@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Joao", "Claudio"),
                    family = "Macosso",
                    role = c("aut", "cre"),
                    email = "joaoclaudiomacosso@gmail.com")
as necessary.
Packages required but not available: 'knitr', 'kableExtra'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘plotly’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) xwfGridsearch.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{iter}{Number of levels in the adaptive grid search. The resolution in b obtained is 2^{-1-iter}.}
       |                                                                                             ^
checkRd: (-1) cat_sim.Rd:110: Lost braces; missing escapes or markup?
   110 | \code{min} and {max} are mandatory for setting limits on the test length. User-defined
       |                ^
Packages required but not available:
  'Seurat', 'clusterProfiler', 'ReactomePA'

Packages suggested but not available for checking:
  'DT', 'knitr', 'kableExtra', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Carter T. Butts <buttsc@uci.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Carter", "T."),
                    family = "Butts",
                    role = c("aut", "cre"),
                    email = "buttsc@uci.edu")
as necessary.
Maintainer: ‘WenSui Liu <liuwensui@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "WenSui",
                    family = "Liu",
                    role = c("aut", "cre"),
                    email = "liuwensui@gmail.com")
as necessary.
Maintainer: ‘John W. Emerson <john.emerson@yale.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("John", "W."),
                      family = "Emerson",
                      role = c("aut", "cre"),
                      email = "john.emerson@yale.edu"),
               person(given = c("Walton", "A."),
                      family = "Green",
                      role = "aut"))
as necessary.
Packages required but not available: 'yaml', 'spork', 'knitr'

Packages suggested but not available for checking:
  'table1', 'rmarkdown', 'tablet', 'kableExtra'

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

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

Package suggested but not available for checking: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/yaml.Rcheck/00install.out’ for details.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Somjit Roy <somjit.roy2001@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Somjit",
                    family = "Roy",
                    role = c("aut", "cre"),
                    email = "somjit.roy2001@gmail.com")
as necessary.
Package required but not available: ‘usethis’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Greg Lamp <greg@yhathq.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Greg",
                      family = "Lamp",
                      role = c("aut", "cre"),
                      email = "greg@yhathq.com"),
               person(given = "Stevie",
                      family = "Smith",
                      role = "aut",
                      email = "dev@yhathq.com"),
               person(given = "Ross",
                      family = "Kippenbrock",
                      role = "aut",
                      email = "ross@yhathq.com"))
as necessary.
'library' or 'require' calls not declared from:
  ‘plyr’ ‘randomForest’
Maintainer: ‘Sergio Salvino Guirreri <sergioguirreri@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Sergio", "Salvino"),
                    family = "Guirreri",
                    role = c("aut", "cre"),
                    email = "sergioguirreri@gmail.com")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Packages required but not available: 'rmarkdown', 'usethis', 'yaml'

Packages suggested but not available for checking:
  'blogdown', 'bookdown', 'covr', 'knitr', 'pkgdown', 'prettydoc',
  'roxygen2', 'spelling', 'xaringan'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Tinniam V Ganesh <tvganesh.85@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Tinniam", "V"),
                    family = "Ganesh",
                    role = c("aut", "cre"),
                    email = "tvganesh.85@gmail.com")
as necessary.
Package required but not available: ‘yaml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Matías Castillo Aguilar <matcasti@umag.cl>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Fabio Demarqui <fndemarqui@est.ufmg.br>’

The Description field contains
  et al. (2019) <arXiv:1910.04475>. Model fitting can be carried out via
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Daewoo Pak <heavyrain.pak@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Daewoo",
                      family = "Pak",
                      role = c("aut", "cre"),
                      email = "heavyrain.pak@gmail.com"),
               person(given = "Song",
                      family = "Yang",
                      role = "aut"))
as necessary.
Maintainer: ‘Junlong Sun <junlong.sun@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Junlong",
                      family = "Sun",
                      role = c("aut", "cre"),
                      email = "junlong.sun@gmail.com"),
               person(given = "Song",
                      family = "Yang",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Fabio Demarqui <fndemarqui@est.ufmg.br>’

The Description field contains
  Mayrink (2019) <arXiv:1910.02406>. Model fitting carried out via
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'usethis'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘spelling’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Xuanhua (Peter) Yin <peteryin.sju@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Manuel",
                      family = "Russon",
                      role = "aut",
                      email = "RUSSONM@stjohns.edu"),
               person(given = "Xuanhua",
                      family = "Yin",
                      role = "aut",
                      email = "peteryin.sju@hotmail.com",
                      comment = "Peter"),
               person(given = "Xuanhua",
                      family = "Yin",
                      role = "cre",
                      email = "peteryin.sju@hotmail.com",
                      comment = "Peter"))
as necessary.
Maintainer: ‘Emanuele Guidotti <emanuele.guidotti@hotmail.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("YUIMA", "Project"),
                      family = "Team",
                      role = "aut"),
               person(given = "Emanuele",
                      family = "Guidotti",
                      role = "cre",
                      email = "emanuele.guidotti@hotmail.it"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Packages required but not available: 'DT', 'plotly'

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

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Robert Lee <rhlee@colorado.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Robert",
                    family = "Lee",
                    role = c("aut", "cre"),
                    email = "rhlee@colorado.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'sinew', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Clare Horscroft <chorscroft@aol.co.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Clare",
                    family = "Horscroft",
                    role = c("aut", "cre"),
                    email = "chorscroft@aol.co.uk")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'mapview'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘zcta.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Francois Brun <francois.brun@acta.asso.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Francois",
                      family = "Brun",
                      role = c("aut", "cre"),
                      email = "francois.brun@acta.asso.fr",
                      comment = "ACTA"),
               person(given = "David",
                      family = "Makowski",
                      role = "aut",
                      comment = "INRA"),
               person(given = "Daniel",
                      family = "Wallach",
                      role = "aut",
                      comment = "INRA"),
               person(given = c("James", "W."),
                      family = "Jones.",
                      role = "aut",
                      comment = "U.of Florida"))
as necessary.
'library' or 'require' calls not declared from:
  ‘coda’ ‘dlm’ ‘maps’ ‘mgcv’ ‘mnormt’ ‘mvtnorm’ ‘randomForest’ ‘rpart’
  ‘rpart.plot’ ‘sensitivity’ ‘sp’ ‘spatial’ ‘tseries’
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools', 'usethis'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘lomb’

Packages suggested but not available for checking: 'covr', 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'atom4R'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Tanya Cashorali <tanyacash@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tanya",
                    family = "Cashorali",
                    role = c("aut", "cre"),
                    email = "tanyacash@gmail.com")
as necessary.
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:
    ‘cache_report.R’ ‘list_deposit.R’
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'scagnostics'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘polite’

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Magnus Thor Torfason <m@zulutime.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Magnus", "Thor"),
                    family = "Torfason",
                    role = c("aut", "cre"),
                    email = "m@zulutime.net")
as necessary.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘external_fitters.Rd’ ‘zfunction.Rd’ ‘zlm.Rd’ ‘zprint.Rd’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Markus Jochmann <markus.jochmann@ncl.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Markus",
                    family = "Jochmann",
                    role = c("aut", "cre"),
                    email = "markus.jochmann@ncl.ac.uk")
as necessary.
Package required but not available: ‘knitr’

Package suggested but not available for checking: ‘rmarkdown’

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:
    ‘convert-jyear-legacy.R’
Maintainer: ‘Gavin Rozzi <gr@gavinrozzi.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tianchen Xu <tx2155@columbia.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Tianchen",
                      family = "Xu",
                      role = c("aut", "cre"),
                      email = "tx2155@columbia.edu",
                      comment = c(ORCID = "0000-0002-0102-7630")),
               person(given = c("Ryan", "T."),
                      family = "Demmer",
                      role = "aut"),
               person(given = "Gen",
                      family = "Li",
                      role = "aut"))
as necessary.
Maintainer: ‘Ariel Duarte-López <aduarte@ac.upc.edu>’

The Description field contains
  (2013) <arXiv:1304.4540>, the Zipf-Poisson Extreme (Zipf-PE), the
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘tolerance’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Stefan Evert <stefan.evert@fau.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Stefan",
                      family = "Evert",
                      role = c("aut", "cre"),
                      email = "stefan.evert@fau.de"),
               person(given = "Marco",
                      family = "Baroni",
                      role = "aut",
                      email = "marco.baroni@unitn.it"))
as necessary.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘productivity_measures.Rd’:
    http://dx.doi.org/10.18419/opus-2556
  File ‘zipfR_package.Rd’:
    http://dx.doi.org/10.18419/opus-2556
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Melina Ribaud <melina.ribaud@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Melina",
                    family = "Ribaud",
                    role = c("aut", "cre"),
                    email = "melina.ribaud@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Magnus Thor Torfason <m@zulutime.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Magnus", "Thor"),
                    family = "Torfason",
                    role = c("aut", "cre"),
                    email = "m@zulutime.net")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘notate.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tmap', 'leaflet', 'covr', 'bookdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rgl’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

Package suggested but not available for checking: ‘rJava’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jose M Pozo <josmpozo@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) in.zoom.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:13: Lost braces in \itemize; meant \describe ?
Maintainer: ‘David Beiner <zra.r.package@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "David",
                    family = "Beiner",
                    role = c("aut", "cre"),
                    email = "zra.r.package@gmail.com")
as necessary.
Package required but not available: ‘dygraphs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ernest Guevarra <ernestgmd@gmail.com>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘anthro4.Rd’:
    https://doi.org/10.1136/bmj.j3423
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘flextable’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Oliver Kirchkamp <oliver@kirchkamp.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Oliver",
                    family = "Kirchkamp",
                    role = c("aut", "cre"),
                    email = "oliver@kirchkamp.de")
as necessary.
Maintainer: ‘Vincent Guyader <vincent@thinkr.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Vincent",
                    family = "Guyader",
                    role = c("aut", "cre"),
                    email = "vincent@thinkr.fr")
as necessary.
Maintainer: ‘Frederik Kok Hansen <frederik_kok@icloud.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Frederik", "Kok"),
                    family = "Hansen",
                    role = c("aut", "cre"),
                    email = "frederik_kok@icloud.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  /data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
See ‘/data/gannet/ripley/R/packages/tests-clang/abn.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 21.1.6’
* used C++ compiler: ‘clang version 21.1.6’
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
checkRd: (-1) bind_tweets.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bind_tweets.Rd:22: Lost braces in \itemize; meant \describe ?
File ‘acc/libs/acc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘acep_load_base.Rd’ ‘acep_rst.Rd’ ‘acep_token_plot.R’
    ‘acep_token_table.R’
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be 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:
    ‘acoRn.R’ ‘clean_input.R’ ‘create_mock_dataset.R’
    ‘exclude_duplicates.R’ ‘find_parents.R’ ‘identify_duplicates.R’
Namespace in Imports field not imported from: ‘hunspell’
  All declared Imports should be used.
checkRd: (-1) Ehrenfest.Rd:19: Lost braces
    19 | In this experiment there are i balls in Urn I, and remaining 2n-i balls in Urn II. Then at any instance, the probability of selecting a ball from Urn I and placing it in Urn II is i/2n, and the other way of placing a ball from Urn II to Urn I is (2n-i)/2n. At each instant we let the number i of balls in the Urn I to be the state of the system. Thus, the state space is S = { 0, 1, 2, \ldots, 2n }. Then we can pass from state i only to either of the states i-1 or i+1.
       |                                                                                                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) Ehrenfest.Rd:20: Lost braces
    20 | Here, S = {0, 1, \ldots, 2n}. 
       |           ^
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘compute_accumulation_metrics.R’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppProgress’
  All declared Imports should be used.
Found the following files/directories:
  ‘Example.jpeg’
checkRd: (-1) est_S_Plus_Plus_MethodA.Rd:31: Lost braces; missing escapes or markup?
    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
checkRd: (-1) est_S_Plus_Plus_MethodB.Rd:31: Lost braces; missing escapes or markup?
    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method B}
       |                                                          ^
checkRd: (-1) est_S_Star_Plus_MethodA.Rd:29: Lost braces; missing escapes or markup?
    29 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
checkRd: (-1) est_S_Star_Plus_MethodB.Rd:29: Lost braces; missing escapes or markup?
    29 |   \item{trt_diff}{Estimate of treatment difference for S_{*+} using Method B}
       |                                                          ^
Specified C++11: support will be removed soon
checkRd: (-1) adana.Rd:25: Lost braces; missing escapes or markup?
    25 |   \item{gatype}{Type of GA. \itemize{\item{"gga": generational GA}  \item{"ssga": steady state GA} } {Default value is "gga"}}
       |                                                                                                      ^
checkRd: (-1) adana.Rd:26: Lost braces; missing escapes or markup?
    26 |   \item{objective}{Type of optimization. \itemize{\item{"min": minimization}  \item{"max": maximization} } {Default value is "max"}}
       |                                                                                                            ^
checkRd: (-1) adana.Rd:34: Lost braces; missing escapes or markup?
    34 |                  {Default value is "initbin"}}
       |                  ^
checkRd: (-1) adana.Rd:56: Lost braces; missing escapes or markup?
    56 |                \itemize{\item{"integer"}  \item{"real"} } {Default value is "real"}}
       |                                                           ^
checkRd: (-1) adana.Rd:185: Lost braces; missing escapes or markup?
   185 |     {Default value is "w"}
       |     ^
Namespaces in Imports field not imported from:
  ‘lefko3’ ‘rlang’
  All declared Imports should be used.
checkRd: (-1) adapt.Rd:46: Lost braces
    46 | \item{qvals}{a vector of values in [0, 1]U{Inf}. Q-values. See Details}
       |                                           ^
checkRd: (-1) corr_lfdr.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ctgm_lfdr.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ctgm_lfdr.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot_2d.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{plot_2d_lfdr} gives the contour plot of local FDR estimates when all p-values are equal to \code{targetp}. It is recommended to run \code{plot_2d_lfdr} for multiple \code{targetp}'s ranging from {0.001, 0.005, 0.01, 0.05}.
       |                                                                                                                                                                                                          ^
checkRd: (-1) SVMDECON.Rd:23: Lost braces; missing escapes or markup?
    23 | and the best result from three values of v = {0.25, 0.5, 0.75}
       |                                              ^
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be 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:
    ‘IntervalEstimator-class.Rd’ ‘PValue-class.Rd’
    ‘PointEstimator-class.Rd’ ‘analyze.R’ ‘estimators.R’
    ‘evaluate_estimator.R’ ‘fisher_information.R’
    ‘integrate_over_sample_space.R’ ‘mle_distribution.R’ ‘n2c2_helpers.R’
    ‘plot.R’ ‘print.R’ ‘reference_implementation.R’
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) med.groups.Rd:20: Lost braces; missing escapes or markup?
    20 | medication groups using the construction \emph{"{NAME}"}.
       |                                                 ^
checkRd: (-1) med.groups.Rd:26: Lost braces; missing escapes or markup?
    26 | Another example is "NotVita" defined as "(!{Vitamines})", which selects all
       |                                            ^
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be 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:
    ‘cm_formula.R’ ‘tag_add.R’
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
Found the following significant warnings:
  /data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:35:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
See ‘/data/gannet/ripley/R/packages/tests-clang/ads.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 21.1.6’
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘Hmisc’ ‘WRS2’ ‘boot’ ‘car’ ‘dplyr’ ‘effects’
  ‘effsize’ ‘forcats’ ‘ggplot2’ ‘lm.beta’ ‘nlme’ ‘readr’ ‘robust’
  ‘sandwich’ ‘sjstats’ ‘tidyr’
  All declared Imports should be used.
checkRd: (-1) count_cases.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitaep.Rd:14: Lost braces
    14 | \item A sequence of goodness-of-fit measures consist of Akaike Information Criterion (\code{AIC}), Consistent Akaike Information Criterion (\code{CAIC}), Bayesian Information Criterion (\code{BIC}), Hannan-Quinn information criterion (\code{HQIC}), Anderson-Darling (\code{AD}), Cram\'{e}er-von Misses (\code{CVM}), Kolmogorov-Smirnov (\code{KS}), and log-likelihood (\code{log-likelihood}) statistics.
       |                                                                                                                                                                                                                                                                                              ^
Found the following files/directories:
  ‘table_AeRobiology’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘report_basic.R’ ‘report_cum_plots.R’ ‘report_log_mass.R’
    ‘report_plots.R’ ‘set_params_2.R’
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be 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:
    ‘colour_table.R’ ‘save_govuk.Rd’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) estimate.affinity.matrix.Rd:31: Lost braces; missing escapes or markup?
    31 | than \code{Y}, then those variables that appear in \code{X} but no in {Y}
       |                                                                       ^
checkRd: (-1) estimate.affinity.matrix.lowrank.Rd:36: Lost braces; missing escapes or markup?
    36 | \code{Y}, then those variables that appear in \code{X} but no in {Y} should
       |                                                                  ^
checkRd: (-1) show.correlations.Rd:47: Lost braces
    47 | code{ndims} dimensions. Defaults to all dimensions unless the latter are
       |     ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘am_data.Rd’
Namespaces in Imports field not imported from:
  ‘mFilter’ ‘regclass’ ‘writexl’
  All declared Imports should be 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:
    ‘generate_workbook.Rd’
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘docstring’
  All declared Imports should be used.
Specified C++11: support will be removed soon
File ‘ahaz/libs/ahaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: support will be removed soon
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
checkRd: (-1) AEHMLE.Rd:42-45: Lost braces
    42 | \item{basehaz}{: {baseline hazard structure including baseline
       |                  ^
checkRd: (-1) AHMLE.Rd:41-43: Lost braces
    41 | \item{basehaz}{: {baseline hazard structure including baseline
       |                  ^
checkRd: (-1) aimPlot.Rd:39: Lost braces; missing escapes or markup?
    39 |  \item \code{Variable} {1st column: The various aims to be completed}
       |                        ^
checkRd: (-1) aimPlot.Rd:40: Lost braces; missing escapes or markup?
    40 |  \item \code{Percentage} {2nd column: The percentage of completeness}
       |                          ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘plot.GRiwrm.R’
checkRd: (-1) RunModel_GR2M.Rd:62: height/width attributes should be in pixels
checkRd: (-1) RunModel_GR4J.Rd:71: height/width attributes should be in pixels
checkRd: (-1) RunModel_GR5H.Rd:77: height/width attributes should be in pixels
checkRd: (-1) RunModel_GR5J.Rd:72: height/width attributes should be in pixels
checkRd: (-1) RunModel_GR6J.Rd:75: height/width attributes should be in pixels
checkRd: (-1) get_airnow_area.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{parameters}{Parameter(s) to return data for. Choices are PM_{2.5}
       |                                                                   ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘airship.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘calc_plan_stats.R’
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) APEXMS.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) APEXMS.Rd:15: Lost braces in \enumerate; meant \describe ?
File ‘AlgDesign/libs/AlgDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘lambda_functions.R’ ‘likelihood-space.R’ ‘snc.R’
checkRd: (-1) allestimates.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allestimates.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allestimates.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allestimates.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_cohorts.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_cohorts.Rd:36: Lost braces in \itemize; meant \describe ?
File ‘alphabetr/libs/alphabetr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
checkRd: (-1) altopt.ic.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
checkRd: (-1) convertCoord.Rd:32: Lost braces
    32 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) convertCoord.individual.Rd:33: Lost braces
    33 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) getCoord.Rd:39: Lost braces
    39 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) getCoord.individual.Rd:39: Lost braces
    39 | here{https://lbs.amap.com/faq/account/key/72}}
       |     ^
checkRd: (-1) getLocation.Rd:60: Lost braces; missing escapes or markup?
    60 | {https://lbs.amap.com/faq/account/key/72}}
       | ^
checkRd: (-1) getLocation.individual.Rd:60: Lost braces
    60 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
Package required but not available: ‘tidyjson’

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

Quitting from data_import.Rmd:215-222 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Failed to connect to ftp.fluxdata.org port 21 after 270476 ms: Could not connect to server
---
Backtrace:
    ▆
 1. ├─amerifluxr::amf_var_info()
 2. │ └─RCurl::getURL(amf_server("var_info"), ftp.use.epsv = FALSE, dirlistonly = TRUE)
 3. │   └─RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
 4. └─RCurl (local) `<fn>`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'data_import.Rmd' failed with diagnostics:
Failed to connect to ftp.fluxdata.org port 21 after 270476 ms: Could not connect to server
--- failed re-building ‘data_import.Rmd’

--- re-building ‘site_selection.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘site_selection.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following HTML validation problems:
ammistability.html:307:1 (ASI.AMMI.Rd:37): Warning: <script> anchor "MathJax-script" already defined
ammistability.html:445:52 (ASTAB.AMMI.Rd:42): Warning: <script> anchor "MathJax-script" already defined
ammistability.html:591:52 (AVAMGE.AMMI.Rd:43): Warning: <script> anchor "MathJax-script" already defined
ammistability.html:742:39 (DA.AMMI.Rd:45): Warning: <script> anchor "MathJax-script" already defined
ammistability.html:891:26 (DZ.AMMI.Rd:46): Warning: <script> anchor "MathJax-script" already defined
ammistability.html:1034:63 (EV.AMMI.Rd:42): Warning: <script> anchor "MathJax-script" already defined
ammistability.html:1178:52 (FA.AMMI.Rd:42): Warning: <script> anchor "MathJax-script" already defined
ammistability.html:1346:52 (MASI.AMMI.Rd:45): Warning: <script> anchor "MathJax-script" already defined
ammistability.html:1507:39 (MASV.AMMI.Rd:45): Warning: <script> anchor "MathJax-script" already defined
ammistability.html:1690:63 (SIPC.AMMI.Rd:42): Warning: <script> anchor "MathJax-script" already defined
ammistability.html:1842:1 (SSI.Rd:35): Warning: <script> anchor "MathJax-script" already defined
ammistability.html:2020:26 (ZA.AMMI.Rd:44): Warning: <script> anchor "MathJax-script" already defined
Namespaces in Imports field not imported from:
  ‘devtools’ ‘dplyr’ ‘gridExtra’
  All declared Imports should be used.
checkRd: (-1) aMNLFA.prune.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
checkRd: (-1) AmpliconDuo-package.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:40-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:43-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:53-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:56-58: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘RtmpvoGSN6\amCluster_QWPG7J54.htm’
  ‘RtmpvoGSN6\amPairwise_IKA9UCQW.htm’
  ‘RtmpvoGSN6\amUnique_8VNI324D.htm’
Specified C++11: support will be removed soon
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: 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.R’
checkRd: (-1) animate.Rd:625-627: Lost braces
   625 | group = function(...) {
       |                       ^
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ANOFA-contrastFrequencies.R’ ‘ANOFA-emFrequencies.R’
Namespace in Imports field not imported from: ‘class’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
checkRd: (-1) orsf.Rd:336: height/width attributes should be in pixels
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
Specified C++11: support will be removed soon
checkRd: (-1) predict_adjust.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iconplot.Rd:172: Lost braces
   172 |     the height of the area containing the panels and a margin of size code{100 * 0.1} 
       |                                                                           ^
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Found the following files/directories:
  ‘APBinary_PPV.csv’ ‘APBinary_TPF.csv’
  ‘APBinary_ap_summary(method=perturbation,B=1500).csv’
  ‘APBinary_auc_summary(method=perturbation,B=1500).csv’
  ‘APSurv_PPV.csv’ ‘APSurv_TPF.csv’
  ‘APSurv_ap_summary(method=bootstrap,B=500).csv’
  ‘APSurv_auc_summary(method=bootstrap,B=500).csv’
  ‘CompareAP_Binary_dap_summary(method=none).csv’
  ‘CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv’
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                              ^
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                                            ^
Namespaces in Imports field not imported from:
  ‘bannerCommenter’ ‘config’ ‘feather’ ‘here’ ‘knitr’ ‘log4r’ ‘ps’
  ‘rmarkdown’ ‘skimr’ ‘snakecase’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
Specified C++11: support will be removed soon
checkRd: (-1) estimate_t0.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_t0.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_t0.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:75: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
checkRd: (-1) arcpullr-package.Rd:12: height/width attributes should be in pixels
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       | ^
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       |                                 ^
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       |                                                ^
checkRd: (-1) uecm.Rd:76: Lost braces; missing escapes or markup?
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |   ^
checkRd: (-1) uecm.Rd:76: Lost braces; missing escapes or markup?
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                  ^
checkRd: (-1) uecm.Rd:76-77: Lost braces
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                                             ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘adb_archive.R’ ‘adb_backup.R’ ‘adb_querry.R’ ‘helpers.R’
    ‘normGeometry.R’
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
File ‘ash/libs/ash.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) plot.AssetPricing.Rd:199-200: Lost braces
   199 |   yakka. (Note that \code{flap} stands for dQuote{function list
       |                                                  ^
Namespaces in Imports field not imported from:
  ‘DHARMa’ ‘DT’ ‘MASS’ ‘MVN’ ‘bestNormalize’ ‘brglm2’ ‘broom’
  ‘broom.mixed’ ‘bslib’ ‘car’ ‘coin’ ‘compositions’ ‘correlation’
  ‘dplyr’ ‘effectsize’ ‘fontawesome’ ‘ggpubr’ ‘glmmTMB’ ‘htmltools’
  ‘kableExtra’ ‘knitr’ ‘lme4’ ‘lmerTest’ ‘modelbased’ ‘nnet’
  ‘patchwork’ ‘performance’ ‘rstatix’ ‘see’ ‘shinyBS’ ‘shinyjs’
  ‘shinyscreenshot’ ‘sjPlot’ ‘tidyverse’
  All declared Imports should be used.
checkRd: (-1) ataCoKriging.Rd:52: Lost braces; missing escapes or markup?
    52 | only one contrained condition for all points and all variables, \\sum_{i=1}^n\\lambda_i +\\sum_{j=1}^m\\beta_j =1, assuming expected means of variables known and constant with the study area.
       |                                                                       ^
checkRd: (-1) ataCoKriging.Rd:52: Lost braces; missing escapes or markup?
    52 | only one contrained condition for all points and all variables, \\sum_{i=1}^n\\lambda_i +\\sum_{j=1}^m\\beta_j =1, assuming expected means of variables known and constant with the study area.
       |                                                                                                ^
checkRd: (-1) simulation_dgp.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{x_discrete}{TRUE if the distribution of the covariate is uniform on {-3.0, -2.9, ..., 3.0} and
       |                                                                           ^
checkRd: (-1) simulation_dgp.Rd:23: Lost braces
    23 | \item{att_oracle}{the sample analog of E[D{Y(1) - Y(0)}|D=1]}
       |                                           ^
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R.rsp’
  All declared Imports should be 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:
    ‘atpol_grids.R’ ‘miscRscript.r’ ‘plot_points_on_atpol.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘catchment_sim.R’ ‘elementary_pop.R’
Namespaces in Imports field not imported from:
  ‘dlnm’ ‘ggplot2’ ‘mvmeta’ ‘pbs’ ‘tsModel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Missing dependency on R >= 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_freiburg.Rd’
checkRd: (-1) audioSample.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) audioSample.Rd:21: Lost braces in \itemize; meant \describe ?
File ‘audio/libs/audio.so’:
  Found non-API calls to R: ‘EXTPTR_PTR’, ‘R_checkActivity’
This entry point may be removed soon:
‘EXTPTR_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:
    ‘bind_lr.Rd’ ‘lex_density.Rd’
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
checkRd: (-1) get_candidate_covariates.Rd:50: Lost braces
    50 | \item \code{covars_data}   {The \code{data.frame} that is filtered out of \code{df} with only the selected \code{covars}}. The values of the
       |                            ^
checkRd: (-1) get_candidate_covariates.Rd:53: Lost braces
    53 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
checkRd: (-1) get_prioritised_covariates.Rd:40: Lost braces
    40 | \item \code{multiplicative_bias}{The absolute log of the multiplicative bias term for each of the auto-selected prioritised covariates}
       |                                 ^
checkRd: (-1) get_recurrence_covariates.Rd:34: Lost braces
    34 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
Specified C++11: support will be removed soon
checkRd: (-1) Autoplotprotein-package.Rd:27: Lost braces
    27 | code{\link{help}}
       |     ^
checkRd: (-1) Autoplotprotein.Rd:25: Lost braces
    25 | code{\link{help}}
       |     ^
checkRd: (-1) data.Rd:22: Lost braces
    22 | code{\link{help}}
       |     ^
checkRd: (-1) domain_data.Rd:29: Lost braces
    29 | code{\link{help}}
       |     ^
checkRd: (-1) length_data.Rd:32: Lost braces
    32 | code{\link{help}}
       |     ^
checkRd: (-1) plotdomain.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotmutagensis.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotsite.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) site_data.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) noauto_scorecard.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{fit}{See glm {stats}.}
       |                    ^
checkRd: (-1) noauto_scorecard2.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{fit}{See glm {stats}.}
       |                    ^
Namespaces in Imports field not imported from:
  ‘Ckmeans.1d.dp’ ‘broom.mixed’ ‘igraph’
  All declared Imports should be used.
Running examples in ‘autostats-Ex.R’ failed
The error most likely occurred in:

> ### Name: auto_variable_contributions
> ### Title: Plot Variable Contributions
> ### Aliases: auto_variable_contributions
> 
> ### ** Examples
> 
> 
> iris %>%
+ framecleaner::create_dummies() %>%
+ auto_variable_contributions(
+  tidy_formula(., target = Petal.Width)
+  )
1 column(s) have become 3 dummy columns
Error in if (validate & xgb_obj != "multi:softprob") { : 
  argument is of length zero
Calls: %>% -> auto_variable_contributions
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘autostats.Rmd’ using rmarkdown

Quitting from autostats.Rmd:40-43 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (validate & xgb_obj != "multi:softprob") ...`:
! argument is of length zero
---
Backtrace:
    ▆
 1. ├─iris %>% auto_variable_contributions(species_formula)
 2. ├─autostats::auto_variable_contributions(., species_formula)
 3. │ ├─base::suppressWarnings(...)
 4. │ │ └─base::withCallingHandlers(...)
 5. │ └─data %>% tidy_xgboost(formula, validate = FALSE)
 6. └─autostats::tidy_xgboost(., formula, validate = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'autostats.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘autostats.Rmd’

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

Quitting from tidyXgboost.Rmd:78-89 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `xgb$feature_names <- nms`:
! ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost]
---
Backtrace:
    ▆
 1. ├─xgb_tuned_fit_grid %>% visualize_model()
 2. ├─autostats::visualize_model(.)
 3. └─autostats:::visualize_model.xgb.Booster(.)
 4.   └─autostats:::plot_varimp_xgboost(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'tidyXgboost.Rmd' failed with diagnostics:
ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost]
--- failed re-building ‘tidyXgboost.Rmd’

SUMMARY: processing the following files failed:
  ‘autostats.Rmd’ ‘tidyXgboost.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinycssloaders’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
checkRd: (-1) avar_mo_cpp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_mo_cpp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_mo_cpp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
Namespaces in Imports field not imported from:
  ‘readxl’ ‘reshape2’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘rclipboard’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
checkRd: (-1) cosmos_mongo.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{host}{For \code{cosmos_mongo_endpoint}, the URL of the Cosmos DB MongoDB endpoint. Usually of the form "https://{account-name}.mongo.cosmos.azure.com:443/".}
       |                                                                                                                       ^
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jose’ ‘openssl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httr’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘round_rect.r’ ‘waffle.r’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘get_cyclone.R’
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘crosstalk’ ‘plotly’
  All declared Imports should be used.
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘dexpfit.R’ ‘expfit.R’ ‘icarfit.R’ ‘logisticfit.R’
checkRd: (-1) barcoding.spe.identify2.Rd:27: Lost braces; missing escapes or markup?
    27 | read.dna() from package {ape} was used to obtain DNAbin object for unaligned non-coding barcodes.
       |                         ^
File ‘Barnard/libs/Barnard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘base64enc/libs/base64enc.so’:
  Found non-API call to R: ‘SETLENGTH’
File ‘base64enc/libs/base64enc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘chadwick_installation.R’
Namespace in Imports field not imported from: ‘splines’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
File ‘BAS/libs/BAS.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.
Namespace in Imports field not imported from: ‘vtable’
  All declared Imports should be used.
File ‘batman/libs/batman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) simdata.Rd:50: height/width attributes should be in pixels
checkRd: (-1) simdata.Rd:66: height/width attributes should be in pixels
checkRd: (-1) simdata.Rd:78: height/width attributes should be in pixels
checkRd: (-1) simdata.Rd:89: height/width attributes should be in pixels
checkRd: (-1) simdata.Rd:103: height/width attributes should be in pixels
checkRd: (-1) simdata.Rd:113: height/width attributes should be in pixels
checkRd: (-1) simdata.Rd:119: height/width attributes should be in pixels
checkRd: (-1) coupledMetropolis.Rd:83-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:86-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:89-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:92-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:95-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:98-100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:101-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:104-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:110-112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:113-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:116-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:119-121: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:122-124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:125-127: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: support will be removed soon
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) bayesDccGarch.Rd:91: Lost braces; missing escapes or markup?
    91 | \item{$H_n1 }{ Bayesian prediction of volatilities and co-volatilities for y_{n+1}.}
       |                                                                              ^
checkRd: (-1) bayesDccGarch.Rd:92: Lost braces; missing escapes or markup?
    92 | \item{$R_n1 }{ Bayesian prediction of coditional correlation for y_{n+1}.}
       |                                                                    ^
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) GroupSingleVoxelFETS.Rd:53: Lost braces
    53 | online trajectories related to the state parameter, the simulated BOLD responses, \mjseqn{\hat{Y}}{ascii}.
       |                                                                                                   ^
Found the following HTML validation problems:
BayesDLMfMRI.html:1161:1 (GroupSingleVoxelFFBS.Rd:54): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:1287:1 (GroupSingleVoxelFSTS.Rd:54): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:1413:1 (SingleVoxelFETS.Rd:62): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:1554:1 (SingleVoxelFFBS.Rd:59): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:1690:1 (SingleVoxelFSTS.Rd:59): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:1853:1 (ffdEvidenceFETS.Rd:62): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:1994:1 (ffdEvidenceFFBS.Rd:58): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:2128:1 (ffdEvidenceFSTS.Rd:58): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:2262:1 (ffdGroupEvidenceFETS.Rd:60): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:2401:1 (ffdGroupEvidenceFFBS.Rd:56): Warning: <script> anchor "MathJax-script" already defined
BayesDLMfMRI.html:2534:1 (ffdGroupEvidenceFSTS.Rd:56): Warning: <script> anchor "MathJax-script" already defined
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
checkRd: (-1) gMLE.bb.Rd:18: Lost braces
    18 |   \item{optim.method}{optimization method in \code{optim()}{stats}.}
       |                                                            ^
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Specified C++11: support will be removed soon
File ‘bayesianETAS/libs/bayesianETAS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘loo’ ‘stringr’ ‘xlsx’
  All declared Imports should be used.
checkRd: (-1) bma.bx.cy.Rd:69: Lost braces
    69 | the initial values for parameters in models. For example, inits<-function(){list(alpha=0,beta=0,c=0,var1=0.5,r=1,lamda=0.01)}.
       |                                                                            ^
checkRd: (-1) DE.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DE.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DE.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DE.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:61: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘FastGP’
  All declared Imports should be 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:
    ‘helper_functions.R’
checkRd: (-1) bayesplot-package.Rd:28: height/width attributes should be in pixels
checkRd: (-1) bayesplot-package.Rd:29: height/width attributes should be in pixels
checkRd: (-1) bayesplot-package.Rd:30: height/width attributes should be in pixels
Namespaces in Imports field not imported from:
  ‘HDInterval’ ‘carData’ ‘rjags’
  All declared Imports should be used.
Specified C++11: support will be removed soon
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘matrixcalc’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
checkRd: (-1) BayesTreePrior.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:41: Lost braces in \itemize; meant \describe ?
File ‘BayesTree/libs/BayesTree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) runUI.Rd:11: Lost braces
    11 | Runs a \bold{Shiny} application. This function normally does not return; interrupt bold{R} to stop the application (usually by pressing Ctrl+C or Esc).
       |                                                                                        ^
checkRd: (-1) getOperatingSystem.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:30: Lost braces in \itemize; meant \describe ?
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘boot_bw.R’ ‘boot_bw_estimate.R’ ‘post_strat_estimation.R’
File ‘BCBCSF/libs/BCBCSF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData’
checkRd: (-1) goftype1.Rd:4: Lost braces
     4 | \description{The goodness-of-fit (GOF) measures consist of Anderson-Darling (\code{AD}) and Cram\'{e}er-von Misses (\code{CVM}) statistics for progressive type-I interval censoring scheme are given, respectively, by
       |                                                                                                   ^
Found the following files/directories:
  ‘fabiabreast.txt’
Namespaces in Imports field not imported from:
  ‘coda’ ‘knitr’ ‘plyr’
  All declared Imports should be used.
Specified C++11: support will be removed soon
checkRd: (-1) WindowSweep.Rd:32: Lost braces
    32 | `code{\link{GetVT}}`.   Otherwise, any column (e.g. \code{"Depth"}) in the 
       |      ^
checkRd: (-1) WindowSweep.Rd:36: Lost braces
    36 | \code{T.mid}  from the output of the `code{\link{GetVT}}`.}
       |                                           ^
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’
  All declared Imports should be used.
Specified C++11: support will be removed soon
checkRd: (-1) gene_s.Rd:17: Lost braces; missing escapes or markup?
    17 | giving the virus access to the cell and thus facilitating the COVID-19 disease. The gene sequence is mapped to the alphabet {0,1,2,3} via the obvious map A->0, C->1, G->2, T->3.
       |                                                                                                                             ^
checkRd: (-1) sars_cov_2.Rd:16: Lost braces; missing escapes or markup?
    16 | It consists of n = 29903 base pairs. The gene sequence is mapped to the alphabet {0,1,2,3} via the obvious map A->0, C->1, G->2, T->3.
       |                                                                                  ^
checkRd: (-1) bde.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:56: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘dump.txt’
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Missing $ inserted.
<inserted text> 
                $
l.170 }{}
         
! Missing $ inserted.
<inserted text> 
                $
l.170 }{}
         
! Missing $ inserted.
<inserted text> 
                $
l.187 \end{array} }{}
                     
! Missing $ inserted.
<inserted text> 
                $
l.187 \end{array} }{}
Found the following files/directories:
  ‘beanz-manual.tex’
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
Found the following files/directories:
  ‘beast_plot_toy.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:
    ‘apply_contrast.R’ ‘apply_contrast.Rd’ ‘average_predictions.Rd’
    ‘estimate_varcov.R’ ‘estimate_varcov.Rd’ ‘get_marginal_effect.R’
    ‘get_marginal_effect.Rd’ ‘predict_counterfactuals.R’
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘fitting.R’
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
File ‘BenfordTests/libs/BenfordTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) sockeye.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sockeye.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:14: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘BiDAG’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
Specified C++11: support will be removed soon
checkRd: (-1) gen.data.Rd:42: Lost braces
    42 | code{cortype = 2} denotes the constant structure, where the \eqn{(i,j)} entry of covariance
       |     ^
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘ggplot2’ ‘readxl’ ‘rlist’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
checkRd: (-1) BETSsearch.Rd:56: Lost braces
    56 |        \item{To exclude whole expressions from the search, surround them with code{' '} and insert a \code{~} before each of them.
       |                                                                                   ^
checkRd: (-1) dummy.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{date}{a \code{list}. The periods for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                               ^
checkRd: (-1) dummy.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{from}{An \code{integer vector} The starting period of a sequence of perids for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                                                                         ^
checkRd: (-1) dummy.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{to}{The ending period of a sequence of perids for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                                            ^
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) sp_bgsmtr.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{c.star}{The threshold for computing posterior tail probabilities p_{ij} for Bayesian FDR as defined in Section 3.2 of  Song, Ge et al.(2019). If not specified the default is to set this threshold as the minimum posterior standard deviation, where the minimum is taken over all regression coefficients in the model.}
       |                                                                          ^
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
File ‘BiasedUrn/libs/BiasedUrn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: support will be removed soon
Namespaces in Imports field not imported from:
  ‘DAAG’ ‘datasets’ ‘expm’ ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RBGL’
  All declared Imports should be used.
checkRd: (-1) BiDimRegression.Rd:29: Lost braces; missing escapes or markup?
    29 | \item \code{euclidean.df1, affine.df1} -  degrees of freedom of the nominator used for the F-statistics propagated by Nakaya (1997); df1 = p-2, with p is the number of elements  needed to calculate the referring model: p=4 for the Euclidean and p=6 for the affine geometry {Nakaya, 1997, Table 1}.
       |                                                                                                                                                                                                                                                                                  ^
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Found the following calls to data() loading into the global environment:
File ‘biglm/R/bigglm.R’:
  data(reset = TRUE)
  data(reset = FALSE)
See section ‘Good practice’ in ‘?data’.
Specified C++14: support will be removed soon
checkRd: (-1) bdm.ptsne.Rd:47: Lost braces; missing escapes or markup?
    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                         ^
checkRd: (-1) bdm.ptsne.Rd:47: Lost braces; missing escapes or markup?
    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                                                                                   ^
checkRd: (-1) pQF.Rd:30: Lost braces; missing escapes or markup?
    30 | When \code{M} is not square, a randomised estimator for the trace of \code{crossprod(M)^2} is used. This is the sample size. When \code{M} is of \code{"matrixfree"} and does not include the trace of {crossprod(M)} as a component, this sample size will also be used to compute that. See Hutchinson reference. }
       |                                                                                                                                                                                                        ^
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Specified C++11: support will be removed soon
Found the following files/directories:
  ‘ccf_ccf_ID31_ID32_res.jpg’ ‘ccf_ccf_ID31_ID32_res.pdf’
  ‘output_ENSO_NHSST.tmp’ ‘plot_plot_ts_RAW_BIN_enso_sst.pdf’
  ‘plot_plot_ts_RAW_BIN_enso_sst01.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst02.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst03.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst04.png’ ‘plot_ts_ACER_ABRUPT.pdf’
  ‘plot_ts_ACER_ABRUPT01.png’ ‘plot_ts_ACER_ABRUPT02.png’
  ‘plot_ts_ACER_ABRUPT03.png’ ‘plot_ts_ACER_ABRUPT04.png’
  ‘salida_ACER_ABRUPT.tmp’ ‘scaterplot_scatterplot_ENSO_SST.jpg’
  ‘scaterplot_scatterplot_ENSO_SST.pdf’
checkRd: (-1) binom.confint.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:32-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:45: Lost braces in \itemize; meant \describe ?
File ‘binom/libs/binom.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘bbassets.R’
Specified C++11: support will be removed soon
checkRd: (-1) calc_ed.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_pi.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_si.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) cluster_reg_exp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mmds.2D.multi.Rd:118: Lost braces
   118 |   a numeric value in inches indicating the height of graph outfile. Default differs by outfile.type. The resolution for tiff and png figures is 150 dpi. See \code{pdf}, code{tiff}, \code{png}, \code{postscript}.
       |                                                                                                                                                                              ^
checkRd: (-1) mmds.2D.plot.Rd:134: Lost braces
   134 |   a numeric value in inches indicating the height of graph outfile. Default differs by outfile.type. The resolution for tiff and png figures is 150 dpi. See \code{pdf}, code{tiff}, \code{png}, \code{postscript}.
       |                                                                                                                                                                              ^
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
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:
    ‘PCAbiplot_Helper.R’ ‘TDAbiplot.R’ ‘TDAbiplot.Rd’
    ‘TDAbiplot_helper.R’ ‘insertAxDeets.R’ ‘insertDataTable.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘AoD.Rd’ ‘AoD.biplot.Rd’ ‘CA.Rd’ ‘CA.biplot.Rd’ ‘CLPs.Rd’ ‘CVA.Rd’
    ‘CVA.biplot.Rd’ ‘PCA.Rd’ ‘PCA.biplot.Rd’ ‘PCO.Rd’ ‘PCO.biplot.Rd’
    ‘alpha.bags.Rd’ ‘axes.Rd’ ‘axes_coordinates.Rd’ ‘biplot.R’
    ‘biplot.Rd’ ‘classification.Rd’ ‘classify.Rd’ ‘density1D.Rd’
    ‘density2D.Rd’ ‘ellipses.Rd’ ‘fit.measures.Rd’ ‘interpolate.Rd’
    ‘legend.type.Rd’ ‘means.Rd’ ‘newaxes.Rd’ ‘newsamples.Rd’
    ‘plot.biplot.Rd’ ‘prediction.Rd’ ‘print.biplot.Rd’ ‘reflect.Rd’
    ‘regress.Rd’ ‘regress.biplot.Rd’ ‘rotate.Rd’ ‘samples.Rd’
    ‘summary.biplot.Rd’ ‘translate_axes.R’ ‘translate_axes.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:
    ‘bits_to_raw.Rd’ ‘bitstream-ints.R’ ‘bitstream-uints-exp-golomb.R’
Namespaces in Imports field not imported from:
  ‘knitr’ ‘markdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) RLdata500.Rd:8: Lost braces
     8 | A data frame with five variables: \code{fname_c1},\code{lname_c1},  \code{by}, code{bm}, \code{bd}.
       |                                                                                    ^
checkRd: (-1) identity.RLdata500.Rd:15: Lost braces
    15 | format A vector that contains the code{id}
       |                                       ^
checkRd: (-1) durban.Rd:16: Lost braces; missing escapes or markup?
    16 | This data set was obtained from the durban.rowcol {agridat} example in package 'agridat' 
       |                                                   ^
checkRd: (-1) fraction.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fraction.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fraction.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘assg2xBalance.R’
checkRd: (-1) estimate_density.Rd:25: Lost braces; missing escapes or markup?
    25 | evenly spaced points between \code{min} and {max}.
       |                                             ^
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
checkRd: (-1) bluebike.Rd:17: Lost braces
    17 | \item{\code{import_month_data}}\cr {Takes in numeric year/month values and imports data from \href{https://www.bluebikes.com/system-data}{Blue Bikes System Data} for the specified time}
       |                                    ^
checkRd: (-1) bluebike.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{\code{station_distance}}\cr {Returns stations with distance in ascending order given the user's current location}
       |                                   ^
checkRd: (-1) bluebike.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{\code{station_radius}}\cr {Plots the position of the stations within walking distance (500 m), and present the basic information about the stations via leaflet}
       |                                 ^
checkRd: (-1) bluebike.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{\code{trip_distance}}\cr {Computes the geographical distance between the start and end stations}
       |                                ^
checkRd: (-1) bluebike.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{\code{trip_history_sample}} \cr {A sample of 1000 trip data entries from February 2022}
       |                                       ^
checkRd: (-1) bluebike.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{\code{station_data}} \cr {A dataset that includes identification, position, and other basic information about bluebike stations}
       |                                ^
Specified C++11: support will be removed soon
checkRd: (-1) dot-pred_array_to_df.Rd:20: Lost braces; missing escapes or markup?
    20 | Helper function for as.data.frame.{fitted, forecast}. Converts predictive array to data.frame.
       |                                   ^
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) BMSC_pareto_k_table.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:57-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:60-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:64-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:67-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘bnns.R’
Namespaces in Imports field not imported from:
  ‘BH’ ‘RcppEigen’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘fastDummies’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’
  All declared Imports should be used.
checkRd: (-1) strength.viewer.Rd:148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:152: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |               ^
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |                                             ^
checkRd: (-1) refAnnots.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) refAnnots.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:19: Lost braces in \itemize; meant \describe ?
Found the following significant warnings:
  Warning: replacing previous import ‘mclust::count’ by ‘plyr::count’ when loading ‘bootcluster’
See ‘/data/gannet/ripley/R/packages/tests-clang/bootcluster.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘HSAUR3’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
File ‘bootruin/libs/bootruin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: support will be removed soon
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘sim_dat_one_trial_exp_covar.R’ ‘sim_dat_one_trial_exp_nocovar.R’
Found the following significant warnings:
  /data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
See ‘/data/gannet/ripley/R/packages/tests-clang/bqtl.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 21.1.6’
* used Fortran compiler: ‘flang version 21.1.6’
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be 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:
    ‘BranchGLM.R’ ‘BranchGLMTable.R’ ‘VariableImportance.R’
    ‘VariableImportance.boot.R’ ‘summaryBranchGLMVS.R’
File ‘Branching/libs/Branching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be 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:
    ‘brm_archetype_average_cells.Rd’ ‘brm_archetype_average_effects.Rd’
    ‘brm_archetype_cells.Rd’ ‘brm_archetype_effects.Rd’
    ‘brm_archetype_successive_cells.Rd’
    ‘brm_archetype_successive_effects.Rd’ ‘brm_formula.Rd’
    ‘brm_prior_archetype.Rd’ ‘brm_prior_label.Rd’ ‘brm_prior_template.Rd’
    ‘brm_recenter_nuisance.Rd’ ‘summary.brms_mmrm_archetype.Rd’
    ‘utils_archetype.R’
Found the following significant warnings:
  /data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
See ‘/data/gannet/ripley/R/packages/tests-clang/broman.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 21.1.6’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘glmm_tidiers.R’ ‘rstanarm_tidiers.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:
    ‘census2021.Rd’
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
checkRd: (-1) bscontrol.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{opt.solver}{a character string in the set {'enum', 'enum_c', 'gurobi', 'cplex', 'lpSolve', 'greedy'} indicating the optimization solver to be used in the program. The choice of 'cplex' requires the package \code{cplexAPI}, 'gurobi' requires the package \code{gurobi}, and 'lpSolve' requires the package \code{lpSolve}. These solver options are only available in the full version at \url{https://github.com/profyliu/bsnsing/}. The default (and the best) is 'enum_c'.}
       |                                                 ^
checkRd: (-1) bscontrol.Rd:45: Lost braces; missing escapes or markup?
    45 | \item{opt.model}{a character string in the set {'gini','error'} indicating the optimization model to solve in the program. The default is 'gini'. The 'error' option is not available in the current version.}
       |                                                ^
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘grDevices’ ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘RcppParallel’ ‘purrr’ ‘rstantools’ ‘scales’ ‘vizdraws’
  All declared Imports should be used.
checkRd: (-1) bubbleHMLegends.Rd:42: Lost braces; missing escapes or markup?
    42 | function. If {sizeBreaks} vector is supplied then this will be ignored and
       |              ^
checkRd: (-1) bubbleHeatmap.Rd:96: Lost braces; missing escapes or markup?
    96 | function. If {sizeBreaks} vector is supplied then this will be ignored and
       |              ^
checkRd: (-1) multiPlotInput.Rd:117: Lost braces; missing escapes or markup?
   117 | \code{unitBase}. This will be supplied to pretty function. If {sizeBreaks} is
       |                                                               ^
Specified C++11: support will be removed soon
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘magrittr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
Running examples in ‘bundle-Ex.R’ failed
The error most likely occurred in:

> ### Name: bundle.model_fit
> ### Title: Bundle a parsnip 'model_fit' object
> ### Aliases: bundle.model_fit bundle_model_fit
> 
> ### ** Examples
> 
> ## Don't show: 
> if (rlang::is_installed("parsnip") && rlang::is_installed("xgboost")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ # fit model and bundle ------------------------------------------------
+ library(parsnip)
+ library(xgboost)
+ 
+ set.seed(1)
+ 
+ mod <-
+   boost_tree(trees = 5, mtry = 3) %>%
+   set_mode("regression") %>%
+   set_engine("xgboost") %>%
+   fit(mpg ~ ., data = mtcars)
+ 
+ mod_bundle <- bundle(mod)
+ 
+ # then, after saveRDS + readRDS or passing to a new session ----------
+ mod_unbundled <- unbundle(mod_bundle)
+ 
+ mod_unbundled_preds <- predict(mod_unbundled, new_data = mtcars)
+ ## Don't show: 
+ }) # examplesIf
> library(parsnip)
> library(xgboost)
> set.seed(1)
> mod <- boost_tree(trees = 5, mtry = 3) %>% set_mode("regression") %>% 
+     set_engine("xgboost") %>% fit(mpg ~ ., data = mtcars)
> mod_bundle <- bundle(mod)
> mod_unbundled <- unbundle(mod_bundle)
Error in xgboost::xgb.load.raw(object, as_booster = TRUE) : 
  unused argument (as_booster = TRUE)
Calls: <Anonymous> ... <Anonymous> -> unbundle -> unbundle.bundle -> <Anonymous>
Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘get_data_from_bursa.R’ ‘list_data_names.R’
checkRd: (-1) depreciation-class.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) depreciation-class.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) depreciation-class.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) depreciation-class.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loan-class.Rd:46-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loan-class.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loan-class.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model2df-methods.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model2df-methods.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model2df-methods.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model2df-methods.Rd:38-39: Lost braces in \itemize; meant \describe ?
Running examples in ‘butcher-Ex.R’ failed
The error most likely occurred in:

> ### Name: axe-flexsurvreg
> ### Title: Axing an flexsurvreg.
> ### Aliases: axe-flexsurvreg axe_call.flexsurvreg axe_env.flexsurvreg
> 
> ### ** Examples
> 
> ## Don't show: 
> if (rlang::is_installed("flexsurv")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ # Load libraries
+ library(parsnip)
+ library(flexsurv)
+ 
+ # Create model and fit
+ flexsurvreg_fit <- surv_reg(mode = "regression", dist = "gengamma") %>%
+   set_engine("flexsurv") %>%
+   fit(Surv(Tstart, Tstop, status) ~ trans, data = bosms3)
+ 
+ out <- butcher(flexsurvreg_fit, verbose = TRUE)
+ 
+ # Another flexsurvreg model object
+ wrapped_flexsurvreg <- function() {
+   some_junk_in_environment <- runif(1e6)
+   fit <- flexsurvreg(Surv(futime, fustat) ~ 1,
+                      data = ovarian, dist = "weibull")
+   return(fit)
+ }
+ 
+ out <- butcher(wrapped_flexsurvreg(), verbose = TRUE)
+ ## Don't show: 
+ }) # examplesIf
> library(parsnip)
> library(flexsurv)
Loading required package: survival
> flexsurvreg_fit <- surv_reg(mode = "regression", dist = "gengamma") %>% 
+     set_engine("flexsurv") %>% fit(Surv(Tstart, Tstop, status) ~ trans, data = bosms3)
Error:
! `surv_reg()` was deprecated in parsnip 1.4.0 and is now defunct.
ℹ Please use `survival_reg()` instead.
Backtrace:
     ▆
  1. ├─(if (getRversion() >= "3.4") withAutoprint else force)(...)
  2. │ └─base::source(...)
  3. │   ├─base::withVisible(eval(ei, envir))
  4. │   └─base::eval(ei, envir)
  5. │     └─base::eval(ei, envir)
  6. ├─... %>% ...
  7. ├─generics::fit(., Surv(Tstart, Tstop, status) ~ trans, data = bosms3)
  8. ├─parsnip::set_engine(., "flexsurv")
  9. └─parsnip::surv_reg(mode = "regression", dist = "gengamma")
 10.   └─lifecycle::deprecate_stop("1.4.0", "surv_reg()", "survival_reg()")
 11.     └─lifecycle:::deprecate_stop0(msg)
 12.       └─rlang::cnd_signal(...)
Execution halted
File ‘bvarsv/libs/bvarsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
File ‘bvls/libs/bvls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: support will be removed soon
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
checkRd: (-1) calcUnique.Rd:24: Lost braces
    24 | functions, and often the /code{cut()} function are relatively slow when working with tens of millions of rows or more.
       |                               ^
checkRd: (-1) calibration_bands.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{y}{response variable (in {0,1}).}
       |                                ^
checkRd: (-1) Recording.Rd:112: Lost braces; missing escapes or markup?
   112 | Stop recording images with {camcorder}.
       |                            ^
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Found the following files/directories:
  ‘MDA231_tree.pdf’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘do_la.Rd’ ‘linalg.Rd’ ‘scale_matrix.Rd’ ‘solve.caracas_symbol.Rd’
    ‘solve_lin.Rd’
checkRd: (-1) plot.ca.rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ca.rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ca.rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ca.rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) fitweibull.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitweibull.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitweibull.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
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:
    ‘cosinor-constructor.R’
checkRd: (-1) build_for_cran.Rd:13: Lost braces
    13 | The exit status code{R CMD build}, invisibly.
       |                     ^
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
File ‘cartographer/libs/cartographer.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.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be 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:
    ‘CBRBase.R’ ‘RFModel.R’ ‘RegressionModel.R’ ‘distance.R’
    ‘generate_grid.R’ ‘utils.R’
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘persistent_player_profiles.Rmd’ using rmarkdown

Quitting from persistent_player_profiles.Rmd:23-34 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'persistent_player_profiles.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error:
! Can't coerce from a number to a string.
--- failed re-building ‘persistent_player_profiles.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: support will be removed soon
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘broom’ ‘epitools’
  All declared Imports should be used.
checkRd: (-1) catmapdata.Rd:9-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:20-21: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
Namespaces in Imports field not imported from:
  ‘epitools’ ‘forcats’ ‘purrr’
  All declared Imports should be used.
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) as.mbsts.Rd:71: Lost braces; missing escapes or markup?
    71 |   \item{states.samples}{(\code{niter}- \code{burn}) draws from p(alpha_t | Y_{1:T}).}
       |                                                                              ^
checkRd: (-1) mcmc.Rd:61: Lost braces; missing escapes or markup?
    61 |   \item{states.samples}{(\code{niter}- \code{burn}) draws from p(alpha_t | Y_{1:T}).}
       |                                                                              ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘causal-model.R’ ‘check-linearity.R’ ‘deprecated.R’
    ‘translation-modules.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:
    ‘cotOOP.R’ ‘utils.R’
Found the following HTML validation problems:
causalOT.html:1690:1 (Measure_-class.Rd:60): Warning: <a> anchor "method-Measure-detach" already defined
causalOT.html:1706:1 (Measure_-class.Rd:70): Warning: <a> anchor "method-Measure-get_weight_parameters" already defined
causalOT.html:1803:1 (Measure_-class.Rd:137): Warning: <a> anchor "method-Measure-clone" already defined
causalOT.html:2452:1 (OTProblem_-class.Rd:50): Warning: <a> anchor "method-OTProblem-add" already defined
causalOT.html:2481:1 (OTProblem_-class.Rd:67): Warning: <a> anchor "method-OTProblem-subtract" already defined
causalOT.html:2510:1 (OTProblem_-class.Rd:84): Warning: <a> anchor "method-OTProblem-multiply" already defined
causalOT.html:2539:1 (OTProblem_-class.Rd:101): Warning: <a> anchor "method-OTProblem-divide" already defined
causalOT.html:2637:1 (OTProblem_-class.Rd:159): Warning: <a> anchor "method-OTProblem-setup_arguments" already defined
causalOT.html:2700:1 (OTProblem_-class.Rd:207): Warning: <a> anchor "method-OTProblem-solve" already defined
causalOT.html:2752:1 (OTProblem_-class.Rd:247): Warning: <a> anchor "method-OTProblem-choose_hyperparameters" already defined
causalOT.html:2789:1 (OTProblem_-class.Rd:272): Warning: <a> anchor "method-OTProblem-info" already defined
causalOT.html:2826:1 (OTProblem_-class.Rd:290): Warning: <a> anchor "method-OTProblem-clone" already defined
Namespace in Imports field not imported from: ‘GeneNet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) tblGroup.Rd:21: height/width attributes should be in pixels
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘atp_plot.Rd’ ‘bioscope_plot.Rd’ ‘energetics_lme_summary.Rd’
    ‘energetics_ols_summary.Rd’ ‘fit_lme.Rd’ ‘get_energetics.Rd’
    ‘get_energetics_summary.Rd’ ‘get_rate_summary.Rd’
    ‘make_bioscope_plot.Rd’ ‘normalize.Rd’ ‘partition_data.Rd’
    ‘pipelines.r’ ‘rate_plot.R’ ‘rate_plot.Rd’ ‘rates_lme_summary.Rd’
    ‘read_data.Rd’
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Running examples in ‘CensSpatial-Ex.R’ failed
The error most likely occurred in:

> ### Name: algnaive12
> ### Title: Naive 1 and Naive 2 method for spatial prediction.
> ### Aliases: algnaive12
> ### Keywords: Spatial Censored SAEM
> 
> ### ** Examples
> 
> ###simulated coordinates
> n<-200 ### sample size for estimation.
> n1=100 ### number of observation used in the prediction.
> 
> ###simulated coordinates
> r1=sample(seq(1,30,length=400),n+n1)
> r2=sample(seq(1,30,length=400),n+n1)
> coords=cbind(r1,r2)### total coordinates (used in estimation and prediction).
> 
> coords1=coords[1:n,]####coordinates used for estimation.
> 
> type="matern"### covariance structure.
> 
> xtot<-cbind(1,runif((n+n1)),runif((n+n1),2,3))## X matrix for estimation and prediction.
> xobs=xtot[1:n,]## X matrix for estimation.
> 
> ###simulated data
> obj=rspacens(cov.pars=c(3,.3,0),beta=c(5,3,1),x=xtot,coords=coords,kappa=1.2,
+ cens=0.25,n=(n+n1),n1=n1,cov.model=type,cens.type="left")
> 
> data2=obj$datare
> data2[,4:5]=xobs[,-1]
> 
> cc=obj$cc
> y=obj$datare[,3]
> cutoff=rep(obj$cutoff,length(y[cc==1]))
> 
> 
> aux2=algnaive12(data=data2,cc=obj$cc,covar=TRUE,covar.col=4:5,
+ copred=obj$coords1,thetaini=c(.1,.2),y.col=3,coords.col=1:2,
+ fix.nugget=TRUE,nugget=0,kappa=1.2,cutoff=cutoff,trend=~V4+V5,
+ cov.model=type)
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
checkRd: (-1) call_api_once.Rd:36: Lost braces
    36 | A code{data.frame} with the requested variables at the requested
       |       ^
checkRd: (-1) centroid.Rd:22: Lost braces; missing escapes or markup?
    22 | Centroid value C_{cen}(v) for node v defined as:
       |                  ^
checkRd: (-1) clusterrank.Rd:23: Lost braces; missing escapes or markup?
    23 | where the term f(c_{i}) accounts for the effect of i's local clustering and the term '+1' results from the contribution of \eqn{j}{j} itself. \cr
       |                    ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ce-hg.R’ ‘ce-mean.R’ ‘ce-prepdata.R’ ‘ce-quantiles.R’ ‘ce-uccs.R’
    ‘get-survey-files.R’ ‘read-expd.R’ ‘read-fmld.R’ ‘read-fmli.R’
    ‘read-mtbi.R’ ‘recode-ce-variables.R’
checkRd: (-1) cequre.Rd:31: Lost braces; missing escapes or markup?
    31 |   {epsi}^{# regression coefficients} times the initial value,
       |   ^
checkRd: (-1) cequre.Rd:31: Lost braces; missing escapes or markup?
    31 |   {epsi}^{# regression coefficients} times the initial value,
       |          ^
Namespaces in Imports field not imported from:
  ‘base’ ‘stats’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘batchtools’ ‘data.table’ ‘dplyr’ ‘ggplot2’ ‘htmltools’
  ‘jsonlite’ ‘magrittr’ ‘methods’ ‘plotly’ ‘reshape’ ‘rlang’ ‘shiny’
  ‘shinyWidgets’ ‘shinyjqui’ ‘shinyjs’ ‘shinymaterial’ ‘sortable’ ‘ssh’
  ‘xml2’
  All declared Imports should be used.
.run_shiny_RsNLME : server: no visible global function definition for
  ‘addTablesToColumnMapping’
Undefined global functions or variables:
  addTablesToColumnMapping
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
File ‘cgAUC/libs/cgAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
checkRd: (-1) Hausdorff.dist.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{vec1}{A \code{integer} vector forms a subset of {1, 2, ..., n}.}
       |                                                       ^
checkRd: (-1) Hausdorff.dist.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{vec2}{A \code{integer} vector forms a subset of {1, 2, ..., n}.}
       |                                                       ^
checkRd: (-1) online.univar.multi.Rd:47-57: Lost braces
    47 | online.univar.one2 = function(y_vec, gamma, tau_gamma, ...){
       |                                                            ^
checkRd: (-1) online.univar.multi.Rd:50-55: Lost braces
    50 |   while(FLAG == 0 & t <= length(y_vec)){
       |                                        ^
checkRd: (-1) online.univar.multi.Rd:71-89: Lost braces
    71 | online.univar.one3 = function(y_vec, tau_vec, ...){
       |                                                   ^
checkRd: (-1) online.univar.multi.Rd:72-74: Lost braces
    72 |   if(length(y_vec) != length(tau_vec)){
       |                                       ^
checkRd: (-1) online.univar.multi.Rd:77-87: Lost braces
    77 |   while(FLAG == 0 & t <= length(y_vec)){
       |                                        ^
checkRd: (-1) online.univar.multi.Rd:81-86: Lost braces
    81 |     while(j < J & FLAG == 0){
       |                             ^
Namespaces in Imports field not imported from:
  ‘AER’ ‘graphics’ ‘lmtest’
  All declared Imports should be used.
Found the following HTML validation problems:
charlatan.html:21530:1 (PhoneNumberProvider_no_NO.Rd:60): Warning: <a> anchor "method-PhoneNumberProvider_nn_NO-clone" already defined
checkRd: (-1) cql.Rd:28: Lost braces; missing escapes or markup?
    28 | {X} \code{<x_var>, <(x_facet)>}: \tab\tab\tab\tab  X-axis variable. May include a second categorical\cr
       | ^
checkRd: (-1) cql.Rd:30: Lost braces; missing escapes or markup?
    30 | {Y} \code{<y_var>}: \tab\tab\tab\tab Y-axis variable. *Not used for \code{hist}.\cr
       | ^
checkRd: (-1) cql.Rd:38: Lost braces; missing escapes or markup?
    38 | {Y_label} \code{'<ylab>'}: \tab\tab\tab\tab  Y-axis custom label. Defaults to <y_var>\cr
       | ^
checkRd: (-1) cql.Rd:39: Lost braces; missing escapes or markup?
    39 | {Legend} \code{'<legend>'}: \tab\tab\tab\tab  Legend custom label. Defaults to <x_category>\cr
       | ^
checkRd: (-1) cql.Rd:40: Lost braces; missing escapes or markup?
    40 | {Colorset} \code{'<clist>'}: \tab\tab\tab\tab  Custom set of colors for <x_category> levels.\cr
       | ^
checkRd: (-1) cql.Rd:42: Lost braces; missing escapes or markup?
    42 | {AggFunc} \code{'<func>'}: \tab\tab\tab\tab Summary function for \code{bar} type.\cr
       | ^
checkRd: (-1) cql.Rd:45: Lost braces; missing escapes or markup?
    45 | {Fit} \code{'<show_se>'}: \tab\tab\tab\tab Valid types: \code{true|false}. Fit quadratic line.\cr
       | ^
checkRd: (-1) cql.Rd:47: Lost braces; missing escapes or markup?
    47 | {ConfInt} \code{'<interval>'}: \tab\tab\tab\tab  Show error bars. Value is confidence interval value. E.g. '.95'
       | ^
checkRd: (-1) create_unit_tests.Rd:17: Lost braces; missing escapes or markup?
    17 | Create `{testthat}` test cases for the code.
       |         ^
Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown'
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
checkRd: (-1) chillR-package.Rd:7: height/width attributes should be in pixels
checkRd: (-1) plot_phenology_trends.Rd:82: height/width attributes should be in pixels
checkRd: (-1) plot_scenarios.Rd:108: height/width attributes should be in pixels
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 {
       |          ^
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘prettydoc’ ‘rmdformats’ ‘skimr’
  All declared Imports should be used.
Specified C++11: support will be removed soon
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 ?
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
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’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
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: support will be removed soon
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘networkD3’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("citation")
  Loading required package: citation
  cff-version: 1.2.0
  message: If you use this software, please cite it using the metadata from this file.
  type: software
  title: 'yaml: Methods to Convert R Data to YAML and Back'
  version: 2.3.11
  date-released: '2025-11-06'
  abstract: Implements the 'libyaml' 'YAML' 1.1 parser and emitter (<https://pyyaml.org/wiki/LibYAML>)
    for R.
  authors:
  - family-names: Garbett
    given-names: Shawn
    email: shawn.garbett@vumc.org
    orcid: 0000-0003-4079-5621
  - family-names: Stephens
    given-names: Jeremy
  - family-names: Simonov
    given-names: Kirill
  - family-names: Xie
    given-names: Yihui
    orcid: 0000-0003-0645-5666
  - family-names: Dong
    given-names: Zhuoer
  - family-names: Wickham
    given-names: Hadley
    orcid: 0000-0003-4757-117X
  - family-names: Horner
    given-names: Jeffrey
  - name: reikoch
  - family-names: Beasley
    given-names: Will
    orcid: 0000-0002-5613-5006
  - family-names: O'Connor
    given-names: Brendan
  - family-names: Quinn
    given-names: Michael
  - family-names: Gao
    given-names: Charlie
  - family-names: Warnes
    given-names:
    - Gregory
    - R.
  - family-names: Kamvar
    given-names:
    - Zhian
    - N.
  license: BSD-3-Clause
  repository-code: https://github.com/vubiostat/r-yaml/
  Saving _problems/test-r2cff-20.R
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 8 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • !file.exists(citationFile) is TRUE (1): 'test-cff2r.R:3:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-r2cff.R:20:3'): r2cff generally works ────────────────────────
  Expected `r2cff(yamlFile)` to throw a error.
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 8 ]
  Error:
  ! Test failures.
  Execution halted
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}
       |     ^
Missing dependency on R >= 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’
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}}
       |                                                                                                             ^
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be 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:
    ‘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’
File ‘ClickClust/libs/ClickClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 ?
File ‘clogitL1/libs/clogitL1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Missing dependency on R >= 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’
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.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Found the following files/directories:
  ‘clusterhap_reports’
Specified C++11: support will be removed soon
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.}
       |                  ^
File ‘clustering.sc.dp/libs/clustering.sc.dp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
File ‘ClusterStability/libs/ClusterStability.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘sp’ ‘spdep’
  All declared Imports should be used.
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘datasets’ ‘dplyr’ ‘klaR’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘CovarianceStructure.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘CovarianceStructure.Rmd’

--- re-building ‘SpatialExMeuseData.Rmd’ using rmarkdown
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
SUMMARY: processing the following file failed:
  ‘SpatialExMeuseData.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  /data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
See ‘/data/gannet/ripley/R/packages/tests-clang/clv.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 21.1.6’
File ‘clv/libs/clv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
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}
       |                     ^
Namespace in Imports field not imported from: ‘MPV’
  All declared Imports should be used.
checkRd: (-1) cmb.search.Rd:50: Lost braces; missing escapes or markup?
    50 |   \item{order}{applied conditioning order {length p}}
       |                                           ^
checkRd: (-1) gp.realize.Rd:20: Lost braces; missing escapes or markup?
    20 | The list \code{l.v} is created by \code{makedistlist()} from a {n x p} design matrix on which to generate the unconditional GP realization.  The correlation parameters take on values in \code{(0,1)} and use the Gaussian correlation model, calculated as \code{rho^d(xi,xj)^2}.  This helper function is used to create the demonstration data used in the example for \code{calibrate()}.
       |                                                                ^
Specified C++11: support will be removed soon
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
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: \#
File ‘cmprsk/libs/cmprsk.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be 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:
    ‘basis.R’
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
       |                                                                       ^
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
Namespace in Imports field not imported from: 'Hmisc'
  All declared Imports should be used.
Unknown package ‘designmatch’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
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’
File ‘coenoflex/libs/coenoflex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘utils.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘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’
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘qpdf’
  All declared Imports should be used.
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’
Unexported object imported by a ':::' call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘chi’ ‘dplyr’ ‘spatstat.utils’ ‘utils’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
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
       |                                        ^
checkRd: (-1) comet.Rd:20: height/width attributes should be in pixels
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
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
Found the following significant warnings:
  hmm.cpp:1079:26: warning: 'max' is deprecated: use .index_max() instead [-Wdeprecated-declarations]
  hmm.cpp:1084:54: warning: 'max' is deprecated: use .index_max() instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/communication.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 21.1.6’
Specified C++11: support will be removed soon
Namespaces in Imports field not imported from:
  ‘GGally’ ‘RColorBrewer’ ‘abind’ ‘diagram’ ‘ggplot2’ ‘grid’ ‘gtable’
  ‘igraph’ ‘magrittr’ ‘plyr’ ‘purrr’ ‘reshape2’ ‘scales’ ‘useful’
  All declared Imports should be used.
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 ?
File ‘compareC/libs/compareC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Missing dependency on R >= 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}
       |                    ^
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
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
       |   ^
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Specified C++11: support will be removed soon
Missing dependency on R >= 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)})
       |                                                                    ^
Namespaces in Imports field not imported from:
  ‘kernlab’ ‘purrr’ ‘survminer’ ‘tidyverse’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
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
Namespaces in Imports field not imported from:
  ‘lwgeom’ ‘s2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘dplyr’ ‘foreign’ ‘lavaan’ ‘openxlsx’ ‘purrr’ ‘semTools’
  ‘shinyWidgets’ ‘stringr’ ‘summarytools’ ‘waiter’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘scales’ ‘sna’
  All declared Imports should be used.
Missing dependency on R >= 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’
File ‘ConsReg/libs/ConsReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

> ### Name: CKrige
> ### Title: Constrained, Covariance-matching Constrained and Universal
> ###   Kriging
> ### Aliases: CKrige CKrige.points CKrige.polygons CKrige-methods
> ###   CKrige,formula,data.frame,formula,preCKrigePoints-method
> ###   CKrige,formula,data.frame,formula,preCKrigePolygons-method
> ###   print.CKrige.exout.polygons summary.CKrige.exout.polygons
> ###   print.CKrige.exout.points summary.CKrige.exout.points
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> 
> 
> ### example 7: universal block Kriging of mean over whole domain
> ### cf chapter 4 of vignette of package georob
> ### (https://CRAN.R-project.org/package=georob)
> if(!requireNamespace("gstat", quietly = TRUE)){
+   stop("install package gstat to run example")
+ }
> ### load coalash data
> data(coalash, package="gstat")
> 
> ### generate SpatialPointsDataFrame covering entire domain of coalash data
> coalash.domain <- rbind(c(0.5,0), c(16.5,0), c(16.5,24), c(0.5,24), c(0.5,0))
> coalash.domain <- SpatialPolygonsDataFrame(
+   SpatialPolygons(list(Polygons(list(Polygon(coalash.domain)), ID= "domain"))),
+   data=data.frame(x=8.5,y=12,row.names="domain"))
> 
> ### universal block Kriging
> preCK_coalash <- preCKrige(newdata = coalash.domain, model = covmodel(modelname =
+     "exponential", mev = 1.023, nugget = 0, variance = 0.268,
+     scale = 1.907), pwidth = 16, pheight = 24)
> UK_coalash <- CKrige(formula = coalash ~ x, data = coalash,
+   locations = ~ x+y, object = preCK_coalash, method = 1)
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
Specified C++11: support will be removed soon
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 ?
File ‘contoureR/libs/contoureR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: support will be removed soon
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 ?
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.
       |                                                                                                                                                                                  ^
Missing dependency on R >= 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’
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘re2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be 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:
    ‘corrRect.hclust.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:
    ‘corrBarplot.R’ ‘corrNetwork.R’
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
File ‘covBM/libs/covBM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘covfefe_inauguration.txt’
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httr’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mapview’ ‘plotly’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Specified C++11: support will be removed soon
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be 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:
    ‘coxphf-tidiers.R’
Specified C++11: support will be removed soon
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
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
Specified C++11: support will be removed soon
File ‘cpm/libs/cpm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘cpp11qpdf/libs/cpp11qpdf.so’:
  Found ‘_ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘libqpdf/libstatqpdf.a’
  Found ‘_ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Object: ‘libqpdf/libstatqpdf.a’
  Found ‘__vprintf_chk’, possibly from ‘vprintf’ (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.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
Specified C++11: support will be removed soon
File ‘cqrReg/libs/cqrReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) sharedat.Rd:23: Lost braces
    23 | \doi{10.7910/DVN/YXMQZM}{Harvard dataverse}
       |                         ^
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 
       |                                  ^
Problems with news in ‘NEWS.md’:
No news entries found.
File ‘credule/libs/credule.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
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{
       |           ^
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Running examples in ‘csmpv-Ex.R’ failed
The error most likely occurred in:

> ### Name: LASSO2_XGBtraining
> ### Title: Variable Selection with LASSO2 and Modeling with XGBoost
> ### Aliases: LASSO2_XGBtraining
> 
> ### ** Examples
> 
> # Load in data sets:
> data("datlist", package = "csmpv")
> tdat = datlist$training
> 
> # The function saves files locally. You can define your own temporary directory. 
> # If not, tempdir() can be used to get the system's temporary directory.
> temp_dir = tempdir()
> # As an example, let's define Xvars, which will be used later:
> Xvars = c("highIPI", "B.Symptoms", "MYC.IHC", "BCL2.IHC", "CD10.IHC", "BCL6.IHC")
> # The function can work with three different outcome types. 
> # Here, we use binary as an example:
> blxfit = LASSO2_XGBtraining(data = tdat, biomks = Xvars, Y = "DZsig",
+                            outfile = paste0(temp_dir, "/binary_LASSO2_XGBoost"))
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized),  :
  Passed unrecognized parameters: verbose. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'data' has been renamed to 'x'. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'gamma' has been renamed to 'min_split_loss'. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'eta' has been renamed to 'learning_rate'. This warning will become an error in a future version.
Error in xgboost::xgboost(objective = "binary:logistic", data = Dtrain,  : 
  argument "y" is missing, with no default
Calls: LASSO2_XGBtraining ... <Anonymous> -> process.y.margin.and.objective -> NROW
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘csmpv_vignette.rmd’ using rmarkdown

Quitting from csmpv_vignette.rmd:421-425 [unnamed-chunk-34]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `xgboost::xgboost()`:
! argument "y" is missing, with no default
---
Backtrace:
    ▆
 1. └─csmpv::XGBtraining(...)
 2.   └─xgboost::xgboost(...)
 3.     └─xgboost:::process.y.margin.and.objective(...)
 4.       └─base::NROW(y)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'csmpv_vignette.rmd' failed with diagnostics:
argument "y" is missing, with no default
--- failed re-building ‘csmpv_vignette.rmd’

SUMMARY: processing the following file failed:
  ‘csmpv_vignette.rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
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:
    ‘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’
Missing dependency on R >= 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’
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be 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:
    ‘create_cure_dataframe.R’ ‘cure_plot.R’ ‘resample_residuals.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_curriculum_graph.R’
Found the following files/directories:
  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Specified C++11: support will be removed soon
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 ?
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be 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:
    ‘d3TreeFunctions.R’
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{  A small, positive scalar that determines when iterations
       |               ^
checkRd: (-1) fpiter.Rd:60-61: Lost braces
    60 |     \code{maxiter}{  An integer denoting the maximum limit on the number of
       |                   ^
checkRd: (-1) fpiter.Rd:63-65: Lost braces
    63 |     \code{trace}{  A logical variable denoting whether some of the intermediate
       |                 ^
checkRd: (-1) formatScientificTeX.Rd:33: Lost braces; missing escapes or markup?
    33 | function will return  " 3.0\\\\times 10^{2}"
       |                                         ^
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Running examples in ‘DALEXtra-Ex.R’ failed
The error most likely occurred in:

> ### Name: explain_xgboost
> ### Title: Create explainer from your xgboost model
> ### Aliases: explain_xgboost
> 
> ### ** Examples
> 
> library("xgboost")
> library("DALEXtra")
> library("mlr")
Loading required package: ParamHelpers
> # 8th column is target that has to be omitted in X data
> data <- as.matrix(createDummyFeatures(titanic_imputed[,-8]))
> model <- xgboost(data, titanic_imputed$survived, nrounds = 10,
+                  params = list(objective = "binary:logistic"),
+                 prediction = TRUE)
Warning in throw_err_or_depr_msg("Parameter(s) have been removed from this function: ",  :
  Parameter(s) have been removed from this function: params. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized),  :
  Passed unrecognized parameters: prediction. This warning will become an error in a future version.
> # explainer with encode functiom
> explainer_1 <- explain_xgboost(model, data = titanic_imputed[,-8],
+                                titanic_imputed$survived,
+                                encode_function = function(data) {
+  as.matrix(createDummyFeatures(data))
+ })
Preparation of a new explainer is initiated
  -> model label       :  xgb.Booster  ( [33m default [39m )
  -> data              :  2207  rows  7  cols 
  -> target variable   :  2207  values 
  -> predict function  :  yhat.xgb.Booster  will be used ( [33m default [39m )
  -> predicted values  :  No value for predict function target column. ( [33m default [39m )
Error in strsplit(model$params$objective, ":", fixed = TRUE) : 
  non-character argument
Calls: explain_xgboost ... explain -> model_info -> model_info.xgb.Booster -> strsplit
Execution halted
File ‘DALY/libs/DALY.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
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
       |     ^
File ‘DataGraph/libs/DataGraph.so’:
  Found non-API call to R: ‘Rf_isFrame’
This entry point may be removed soon.

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’
Missing dependency on R >= 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’
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘methods’
  All declared Imports should be used.
File ‘data.table/libs/data_table.so’:
  Found non-API calls to R: ‘OBJECT’, ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_OBJECT’, ‘SET_TRUELENGTH’, ‘TRUELENGTH’
This entry point may be removed soon:
‘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.
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
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tidyverse’ ‘vctrs’
  All declared Imports should be used.
Running examples in ‘dblr-Ex.R’ failed
The error most likely occurred in:

> ### Name: dblr_train
> ### Title: Discrete Boosting Logistic Regression Training
> ### Aliases: dblr_train
> 
> ### ** Examples
> 
> # use iris data for example
> dat <- iris
> # create two categorical variables
> dat$Petal.Width <- as.factor((iris$Petal.Width<=0.2)*1+(iris$Petal.Width>1.0)*2)
> dat$Sepal.Length <- (iris$Sepal.Length<=3.0)*2+(iris$Sepal.Length>6.0)*1.25
> # create the response variable
> dat$Species <- as.numeric(dat$Species=='versicolor')
> set.seed(123)
> # random sampling
> index <- sample(1:150,100,replace = FALSE)
> # train the dblr model using the training data
> dblr_fit <- dblr_train(train_x=dat[index,c(1:4)],
+ train_y=dat[index,5],category_cols = c('Petal.Width','Sepal.Length'),
+ metric = 'logloss',subsample = 0.5,eta = 0.05,colsample = 1.0,
+ lambda = 1.0,cv_early_stops = 10,verbose=FALSE)
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized),  :
  Passed unrecognized parameters: metrics. This warning will become an error in a future version.
Error in begin_iteration:end_iteration : argument of length 0
Calls: dblr_train -> <Anonymous>
Execution halted
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
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}}
       |                                                ^
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘html5’
  All declared Imports should be used.
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.
Specified C++11: support will be removed soon
Namespaces in Imports field not imported from:
  ‘MASS’ ‘qpdf’
  All declared Imports should be used.
Running ‘testthat.R’ [70s/196s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ddml)
  > 
  > test_check("ddml")
  Saving _problems/test-ml_wrappers-35.R
  
  sample fold 1/3
  sample fold 2/3
  sample fold 3/3[ FAIL 1 | WARN 6 | SKIP 0 | PASS 134 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ml_wrappers.R:35:3'): mdl_xgboost is working ───────────────────
  Error in `process.y.margin.and.objective(as.vector(y), base_margin, objective, params)`: Got numeric 'y' - supported objectives for this data are: reg:squarederror, reg:squaredlogerror, reg:logistic, reg:pseudohubererror, reg:absoluteerror, reg:quantileerror, count:poisson, reg:gamma, reg:tweedie. Was passed: binary:logistic
  Backtrace:
      ▆
   1. └─ddml::mdl_xgboost(y, X, objective = "binary:logistic") at test-ml_wrappers.R:35:3
   2.   └─xgboost::xgboost(...)
   3.     └─xgboost:::process.y.margin.and.objective(...)
   4.       └─xgboost:::process.y.margin.and.objective(...)
  
  [ FAIL 1 | WARN 6 | SKIP 0 | PASS 134 ]
  Error:
  ! Test failures.
  Execution halted
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}}
       |     ^
Namespace in Imports field not imported from: ‘shinydisconnect’
  All declared Imports should be used.
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: support will be removed soon
checkRd: (-1) make_deadata_fuzzy.Rd:96: height/width attributes should be in pixels
Specified C++14: support will be removed soon
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}),
       |                                                           ^
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
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: support will be removed soon
Missing dependency on R >= 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’
Namespaces in Imports field not imported from:
  ‘knitr’ ‘shinyBS’ ‘shinyMatrix’
  All declared Imports should be used.
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’
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be 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:
    ‘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: \&
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be 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:
    ‘mod_template_srv.R’
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
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: support will be removed soon
Specified C++11: support will be removed soon
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).
       |                                       ^
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be 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:
    ‘diario.R’
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
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘purrr’
  All declared Imports should be used.
checkRd: (-1) Diderot-package.Rd:20: height/width attributes should be in pixels
Specified C++11: support will be removed soon
checkRd: (-1) did_imputation.Rd:74: Lost braces; missing escapes or markup?
    74 | form average treatment effects for groups of {it}.
       |                                              ^
File ‘diffIRT/libs/diffIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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}}}
       |   ^
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(digitize)
  > 
  > test_check("digitize")
  Saving _problems/test-reverse_compatible-38.R
  Saving _problems/test-unit-15.R
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-reverse_compatible.r:32:13'): `digitize` gives same ────────────
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: `with_mock()` was deprecated in testthat 3.2.0 and is now defunct.
  ℹ Please use `with_mocked_bindings()` instead.
  Backtrace:
      ▆
   1. └─testthat::with_mock(...) at test-reverse_compatible.r:32:13
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  ── Error ('test-unit.r:9:13'): Digitize skips point input ──────────────────────
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: `with_mock()` was deprecated in testthat 3.2.0 and is now defunct.
  ℹ Please use `with_mocked_bindings()` instead.
  Backtrace:
      ▆
   1. └─testthat::with_mock(...) at test-unit.r:9:13
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]
  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:
    ‘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
       |                                   ^
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
Specified C++11: support will be removed soon
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:
    ‘dev_package.R’
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘proxy’
  All declared Imports should be used.
checkRd: (-1) dapply.Rd:27-30: Lost braces
    27 | udf <- function(x){
       |                   ^
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rlang’
  All declared Imports should be 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:
    ‘mixture.R’
Namespace in Imports field not imported from: ‘truncnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggmulti’ ‘loon’ ‘loon.data’ ‘loon.ggplot’ ‘loon.shiny’ ‘loon.tourr’
  ‘stats’ ‘zenplots’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plotly’ ‘pryr’ ‘rpart’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
Running ‘testthat.R’ [107s/173s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dmlalg)
  > 
  > test_check("dmlalg")
  Saving _problems/test-data_formats_regsdml-1332.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1113 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-data_formats_regsdml.R:1332:5'): return_results outputs right data formats ──
  Error in `expect(nrow(results$beta_test), d)`: `ok` must be `TRUE` or `FALSE`, not the number 3.
  Backtrace:
      ▆
   1. └─dmlalg (local) check_return_results_format(beta = beta, var = var, xx_colnames = xx_colnames) at test-data_formats_regsdml.R:1356:3
   2.   └─testthat::expect(ok = nrow(results$beta_test)) at test-data_formats_regsdml.R:1332:5
   3.     └─testthat:::check_bool(ok)
   4.       └─testthat:::stop_input_type(...)
   5.         └─rlang::abort(message, ..., call = call, arg = arg)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1113 ]
  Error:
  ! Test failures.
  Execution halted
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
Problems with news in ‘NEWS.md’:
No news entries found.
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
       |            ^
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})}
       |                                              ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New features
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘DoseFinding’ ‘Rsolnp’ ‘ggplot2’ ‘kableExtra’ ‘knitr’
  ‘latticeExtra’ ‘purrr’ ‘readxl’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  ‘stringr’ ‘utils’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘case_study.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘case_study.Rmd’

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

Quitting from introduction.Rmd:84-86 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'introduction.Rmd' failed with diagnostics:
`replacement` function must return a vector the same length as the input
(8), not length 1.
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
checkRd: (-1) Downscale-package.Rd:23: height/width attributes should be in pixels
checkRd: (-1) upgrain.Rd:74: height/width attributes should be in pixels
checkRd: (-1) upgrain.threshold.Rd:42: height/width attributes should be in pixels
checkRd: (-1) upgrain.threshold.Rd:80: height/width attributes should be in pixels
Missing dependency on R >= 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’
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
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’
These entry points may be removed soon:
‘OBJECT’, ‘R_shallow_duplicate_attr’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘ggplot2’ ‘nloptr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
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}}
       |                                                               ^
Specified C++11: support will be removed soon
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 ?
Specified C++11: support will be removed soon
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
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rJava’ ‘tools’
  All declared Imports should be used.
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.
Specified C++11: support will be removed soon
Missing dependency on R >= 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: support will be removed soon
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: support will be removed soon
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
       |                                                  ^
checkRd: (-1) Mena.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 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
File ‘dualtrees/libs/dualtrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘roxygen2’
  All declared Imports should be used.
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’
Namespaces in Imports field not imported from:
  ‘GenEst’ ‘expint’ ‘numDeriv’
  All declared Imports should be used.
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: support will be removed soon
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
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) 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: \&
File ‘dynpred/libs/dynpred.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Missing dependency on R >= 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: support will be removed soon
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) plot.earlyR.Rd:34-46: Lost braces
    34 | if (require(incidence)) {
       |                         ^
Missing dependency on R >= 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’
Namespace in Imports field not imported from: ‘rprojroot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qcr’
  All declared Imports should be used.
Missing dependency on R >= 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’
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
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 significant warnings:
  /data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
See ‘/data/gannet/ripley/R/packages/tests-clang/eco.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 21.1.6’
File ‘ECOSolveR/libs/ECOSolveR.so’:
  Found ‘__vprintf_chk’, possibly from ‘vprintf’ (C)
    Objects: ‘ecos/libecos.a’, ‘ecos/libecos_bb.a’
  Found ‘printf’, possibly from ‘printf’ (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.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘rlang’
  All declared Imports should be used.
checkRd: (-1) transformFitness.Rd:25: Lost braces; missing escapes or markup?
    25 | minimization (most others). This function computes a factor from {-1, 1} for
       |                                                                  ^
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’
Running ‘test-all.R’ [10s/27s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("EDISON")
  Loading required package: EDISON
  Loading required package: corpcor
  Loading required package: MASS
  [1] "Initialisation successful."
  [1] "Starting tvDBN iterations..."
  5 % 10 % 15 % 20 % 25 % 30 % 35 % 40 % 45 % 50 % 55 % 60 % 65 % 70 % 75 % 80 % 85 % 90 % 95 % 100 % [1] ""
  [1] "End of iterations"
  [1] "Initialisation successful."
  [1] "Starting tvDBN iterations..."
  5 % 10 % 15 % 20 % 25 % 30 % 35 % 40 % 45 % 50 % 55 % 60 % 65 % 70 % 75 % 80 % 85 % 90 % 95 % 100 % [1] ""
  [1] "End of iterations"
  Saving _problems/test-structure-moves-329.R
  Saving _problems/test-structure-moves-333.R
  Saving _problems/test-structure-moves-337.R
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 17 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-structure-moves.r:328:1'): network info the same before and after  ──
  Error in `is_true()`: could not find function "is_true"
  Backtrace:
      ▆
   1. └─testthat::expect_that(updateCorrectly(), is_true())
  ── Error ('test-structure-moves.r:332:1'): rejected moves make no change ───────
  Error in `is_true()`: could not find function "is_true"
  Backtrace:
      ▆
   1. └─testthat::expect_that(noChangeOnReject(), is_true())
  ── Error ('test-structure-moves.r:336:1'): output not null ─────────────────────
  Error in `is_false()`: could not find function "is_false"
  Backtrace:
      ▆
   1. └─testthat::expect_that(...)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 17 ]
  Error:
  ! Test failures.
  Execution halted
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘tibble’
  All declared Imports should be used.
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
Namespace in Imports field not imported from: ‘PCovR’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Missing dependency on R >= 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’
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/EIX.Rcheck/00install.out’ for details.
Running examples in ‘eks-Ex.R’ failed
The error most likely occurred in:

> ### Name: tidyst_kdr
> ### Title: Tidy and geospatial kernel density ridge estimates
> ### Aliases: tidy_kdr st_kdr
> ### Keywords: smooth
> 
> ### ** Examples
> ## tidy density ridge estimate
> library(ggplot2)
>  
> 
> ## geospatial density ridge estimate
> data(wa)
> data(grevilleasf)
> hakeoides <- dplyr::filter(grevilleasf, species=="hakeoides")
> ## gridsize=c(21,21) is for illustrative purposes only 
> ## remove for more complete KDR
> s1 <- st_kdr(hakeoides, gridsize=c(21,21))
> 
> ## base R plot
> xlim <- c(1.2e5, 1.1e6); ylim <- c(6.1e6, 7.2e6)
> plot(wa, xlim=xlim, ylim=ylim)
> plot(sf::st_geometry(hakeoides), add=TRUE, col=3, pch=16, cex=0.5)
> plot(s1, add=TRUE)
Error in center_h[i] <- center_h[i - 1] - max_sizes[i - 1]/2 - y_spacing -  : 
  replacement has length zero
Calls: plot ... <Anonymous> -> <Anonymous> -> do.call -> <Anonymous>
Execution halted
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)
       |                                          ^
Specified C++11: support will be removed soon
Namespaces in Imports field not imported from:
  ‘distr’ ‘distrEllipse’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
checkRd: (-1) elo.run.Rd:80: Lost braces
    80 | \code{\link{score}}, \link{elo.run.helpers}{elo.run helpers}, \code{\link{elo.calc}},
       |                                            ^
File ‘elsa/libs/elsa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  /data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
See ‘/data/gannet/ripley/R/packages/tests-clang/EmbedSOM.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 21.1.6’
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Licence stub is invalid DCF.
Found the following HTML validation problems:
EmiR.html:386:1 (bohachevsky_func.Rd:16): Warning: <script> anchor "MathJax-script" already defined
EmiR.html:1635:1 (freudenstein_roth_func.Rd:16): Warning: <script> anchor "MathJax-script" already defined
EmiR.html:1725:1 (griewank_func.Rd:16): Warning: <script> anchor "MathJax-script" already defined
EmiR.html:1821:1 (miele_cantrell_func.Rd:16): Warning: <script> anchor "MathJax-script" already defined
EmiR.html:2145:1 (rastrigin_func.Rd:19): Warning: <script> anchor "MathJax-script" already defined
EmiR.html:2175:1 (rosenbrock_func.Rd:16): Warning: <script> anchor "MathJax-script" already defined
EmiR.html:2228:1 (schwefel_func.Rd:16): Warning: <script> anchor "MathJax-script" already defined
EmiR.html:2280:1 (styblinski_tang_func.Rd:16): Warning: <script> anchor "MathJax-script" already defined
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’
Specified C++11: support will be removed soon
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.
       |                       ^
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
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}.
       |                                                                                              ^
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
       |                                                       ^
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘DECIPHER’ ‘ggplot2’ ‘reshape2’ ‘usethis’
  All declared Imports should be used.
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’
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},
       |                                                        ^
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tinytest’
  All declared Imports should be used.
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
checkRd: (-1) datagen.Rd:81: height/width attributes should be in pixels
checkRd: (-1) datagen.Rd:88: height/width attributes should be in pixels
checkRd: (-1) datagen.Rd:95: height/width attributes should be in pixels
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 | }{
       |  ^
Namespace in Imports field not imported from: ‘xts’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘cubature’ ‘rootSolve’
  All declared Imports should be used.
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’
Missing dependency on R >= 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’
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
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,
       |                                                                                                                       ^
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) 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’, ‘SET_OBJECT’,
    ‘UNSET_S4_OBJECT’
These entry points may be removed soon:
‘UNSET_S4_OBJECT’, ‘IS_S4_OBJECT’, ‘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: support will be removed soon
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: \&
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 ?
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’
checkRd: (-1) ebc_allmeasures.Rd:17-18: height/width attributes should be in pixels
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}"
       |                                                       ^
Namespaces in Imports field not imported from:
  ‘forcats’ ‘rqPen’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘KMsurv’ ‘MLEcens’ ‘lubridate’ ‘msm’ ‘perm’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) glr.Rd:5: Lost braces
     5 |   Conducts a generalized likelihood ratio test testing whether {\eqn{\beta \in}  (-\code{c},\code{c})}. Covariates can be accommodated.
       |                                                                ^
checkRd: (-1) glr.Rd:34: Lost braces
    34 |   This is a similar function to the main function \code{evian}. Instead of testing H0: \eqn{\beta}=0, it tests for whether H0:{\eqn{\beta \in} (-\code{c},\code{c})}.
       |                                                                                                                               ^
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) fmgammagpd.Rd:183: Lost braces; missing escapes or markup?
   183 |  \item {nlumgammagpd} and {proflumgammagpd} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], sigmau, xi)}
       |                           ^
checkRd: (-1) fmgammagpdcon.Rd:181: Lost braces; missing escapes or markup?
   181 |  \item {nlumgammagpdcon} and {proflumgammagpdcon} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], xi)}
       |                              ^
checkRd: (-1) kernels.Rd:87: Lost braces
    87 | code{\link[evmix:kernels]{kd*}}  and \code{\link[evmix:kernels]{kp*}} give the
       |     ^
Found the following files/directories:
  ‘sample .nwk’
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.
       |                                                                                  ^
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
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 significant warnings:
  /data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
See ‘/data/gannet/ripley/R/packages/tests-clang/excursions.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 21.1.6’
* used C++ compiler: ‘clang version 21.1.6’
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.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
checkRd: (-1) ExpAnalysis3d-package.Rd:10: height/width attributes should be in pixels
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
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
       |       ^
Missing dependency on R >= 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’
Namespace in Imports field not imported from: ‘ggpmisc’
  All declared Imports should be used.
Running examples in ‘explore-Ex.R’ failed
The error most likely occurred in:

> ### Name: explain_xgboost
> ### Title: Explain a binary target using xgboost
> ### Aliases: explain_xgboost
> 
> ### ** Examples
> 
> data <- use_data_iris()
> data$is_versicolor <- ifelse(data$Species == "versicolor", 1, 0)
> data$Species <- NULL
> explain_xgboost(data, target = is_versicolor, log = FALSE)
Warning in check.deprecation(deprecated_cv_params, match.call(), ...) :
  Passed invalid function arguments: eval_metric, nthread. These should be passed as a list to argument 'params'. Conversion from argument to 'params' entry will be done automatically, but this behavior will become an error in a future version.
Warning in check.custom.obj(params, objective) :
  Argument 'objective' is only for custom objectives. For built-in objectives, pass the objective under 'params'. This warning will become an error in a future version.
Error in all_nrounds[k] <- cv$best_iteration : 
  replacement has length zero
Calls: explain_xgboost
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:
    ‘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’
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.}
       |                                                   ^
File ‘extremis/libs/extremis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
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 ?
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
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’
Namespace in Imports field not imported from: ‘tsibbledata’
  All declared Imports should be used.
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
       |             ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    minor changes
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
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}}
       |                      ^
Namespaces in Imports field not imported from:
  ‘base’ ‘data.table’
  All declared Imports should be used.
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
       |                    ^
File ‘falcon/libs/falcon.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: support will be removed soon
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
File ‘FastBandChol/libs/FastBandChol.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: support will be removed soon
File ‘fastcmh/libs/fastcmh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: support will be removed soon
Specified C++11: support will be removed soon
File ‘FastGP/libs/FastGP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: support will be removed soon
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grDevices’ ‘utils’
  All declared Imports should be used.
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’
These entry points may be removed soon:
‘VECTOR_PTR’, ‘SET_NAMED’, ‘EXTPTR_PTR’, ‘NAMED’, ‘OBJECT’, ‘STRING_PTR’, ‘DATAPTR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
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 ?
Note: information on .o files is not available
File ‘FastRWeb/libs/null.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  /data/gannet/ripley/R/R-clang/include/R_ext/Callbacks.h:33:2: warning: include R_ext/ObjectTable.h for R_ObjectTable declarations [-W#warnings]
See ‘/data/gannet/ripley/R/packages/tests-clang/fastSOM.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 21.1.6’
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘collapse’ ‘data.table’ ‘kit’ ‘magrittr’
  All declared Imports should be used.
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)} {
       |                                   ^
Found the following significant warnings:
  /data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
See ‘/data/gannet/ripley/R/packages/tests-clang/fBasics.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 21.1.6’
Namespace in Imports field not imported from: ‘agridat’
  All declared Imports should be used.
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}}
       |                                          ^
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
Found the following files/directories:
  ‘.Rprofile’
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 ?
Namespaces in Imports field not imported from:
  ‘data.table’ ‘ggplot2’ ‘randomcoloR’ ‘sqldf’
  All declared Imports should be used.
File ‘FD/libs/FD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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}.}
       |                                                                                                                                                                     ^
Namespaces in Imports field not imported from:
  ‘e1071’ ‘lattice’ ‘randomForest’ ‘tibble’ ‘utils’
  All declared Imports should be used.
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: \#
File ‘fechner/libs/fechner.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Missing dependency on R >= 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:
    ‘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’
Specified C++11: support will be removed soon
checkRd: (-1) contemParametros.Rd:19: Lost braces
    19 | \item{exclui3pontos}{verify por ... ? in f<-function(a, ...){ }}
       |                                                             ^
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘numDeriv’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rclipboard’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
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’
File ‘fishMod/libs/fishMod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
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}.
       |                               ^
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
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’
Missing dependency on R >= 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: support will be removed soon
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
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 ?
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: support will be removed soon
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: \&
File ‘flashClust/libs/flashClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Missing dependency on R >= 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’
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
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)
       |                         ^
File ‘flock/libs/flock.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 files/directories:
  ‘flux.CH4.txt’
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Specified C++11: support will be removed soon
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
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) 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 ?
Missing dependency on R >= 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 ?
Missing dependency on R >= 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’
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘forrel’ ‘pedtools’ ‘plotly’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pkgKitten’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tibble’ ‘viridis’
  All declared Imports should be used.
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},
       |                                                                          ^
Namespaces in Imports field not imported from:
  ‘spatstat’ ‘spatstat.data’
  All declared Imports should be used.
checkRd: (-1) ForIT_DataBase.Rd:40: height/width attributes should be in pixels
Namespaces in Imports field not imported from:
  ‘R6’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘utils’
  All declared Imports should be used.
Missing dependency on R >= 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’
Namespaces in Imports field not imported from:
  ‘TreeSim’ ‘shinyjs’
  All declared Imports should be used.
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: support will be removed soon
Namespace in Imports field not imported from: ‘LaplacesDemon’
  All declared Imports should be used.
2270c2270
< Package 'mclust' version 6.1.2
---
> Package 'mclust' version 6.1.1
2951c2951
< Package 'mclust' version 6.1.2
---
> Package 'mclust' version 6.1.1
3038c3038
< Package 'mclust' version 6.1.2
---
> Package 'mclust' version 6.1.1
3096c3096
< Package 'mclust' version 6.1.2
---
> Package 'mclust' version 6.1.1
3989c3989
< Package 'mclust' version 6.1.2
---
> Package 'mclust' version 6.1.1
Running ‘fpctests_notallin.R’ [14s/17s]
  Comparing ‘fpctests_notallin.Rout’ to ‘fpctests_notallin.Rout.save’ ...9c9
< Package 'mclust' version 6.1.2
---
> Package 'mclust' version 6.1.1
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
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
       |   ^
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
File ‘fractional/libs/fractional.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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: \&
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
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 
       |          ^
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Specified C++11: support will be removed soon
checkRd: (-1) maximin.Rd:197: Lost braces
   197 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
Error(s) in re-building vignettes:
Warning: elapsed-time limit of 1 hours reached for sub-process
--- re-building ‘FRK_intro.Rnw’ using knitr
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
--- re-building ‘FRK_non-Gaussian.Rnw’ using knitr
--- finished re-building ‘FRK_non-Gaussian.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Missing dependency on R >= 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: support will be removed soon
Specified C++11: support will be removed soon
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be 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:
    ‘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’
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
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’
Namespaces in Imports field not imported from:
  ‘bigalgebra’ ‘biganalytics’
  All declared Imports should be used.
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’
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.
       |                                                                                                          ^
File ‘gafit/libs/gafit.so’:
  Found non-API calls to R: ‘FRAME’, ‘HASHTAB’
File ‘gafit/libs/gafit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
These entry points may be removed soon:
‘FRAME’, ‘HASHTAB’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
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
       |                                           ^
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gargle’ ‘getProxy’ ‘rappsflyer’ ‘rfacebookstat’ ‘rgoogleads’
  ‘rmytarget’ ‘rvkstat’ ‘ryandexdirect’ ‘rym’ ‘tidyr’
  All declared Imports should be used.
Package required but not available: ‘tidyjson’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
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.  
       |                                                                                                                                                                                                                                         ^
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
checkRd: (-1) pc.Rd:17: Lost braces
    17 | The functions \code{gamlss.pcr()} and \code{gamlss.pc()} are supporting functions. The  are not intended to be called directly by users. The function \code{gamlss.pc()} is using the linear model function \code{lm()} to fit the first principal components while the function code{gamlss.pcr()} uses \code{fitPCR()}.
       |                                                                                                                                                                                                                                                                                      ^
Found the following significant warnings:
  /data/gannet/ripley/R/R-clang/include/R_ext/PrtUtil.h:31:2: warning: non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-W#warnings]
See ‘/data/gannet/ripley/R/packages/tests-clang/gam.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 21.1.6’
* used Fortran compiler: ‘flang version 21.1.6’
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
       |               ^
Missing dependency on R >= 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’
Specified C++11: support will be removed soon
File ‘gbp/libs/gbp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
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) 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,
       | ^
File ‘GCPM/libs/GCPM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

> ### Name: eigcv
> ### Title: Compute cross-validate eigenvalues
> ### Aliases: eigcv
> 
> ### ** Examples
> 
> 
> library(fastRG)
> 
> set.seed(27)
> 
> B <- matrix(0.1, 5, 5)
> diag(B) <- 0.3
> 
> model <- sbm(
+   n = 1000,
+   k = 5,
+   B = B,
+   expected_degree = 40,
+   poisson_edges = FALSE,
+   allow_self_loops = FALSE
+ )
Error: Must specify only one of `B` and `k`, not both.
Execution halted
Running ‘testthat.R’ [22s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(gdim)
  Loading required package: Matrix
  > 
  > test_check("gdim")
  
  Attaching package: 'fastRG'
  
  The following object is masked from 'package:testthat':
  
      expectation
  
  Saving _problems/test-eigcv-17.R
  Saving _problems/test-eigcv-81.R
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-eigcv.R:10:3'): symmetric eigcv, calculations on A ─────────────
  Error: Must specify only one of `B` and `k`, not both.
  Backtrace:
      ▆
   1. └─fastRG::sbm(...) at test-eigcv.R:10:3
   2.   └─fastRG::dcsbm(...)
  ── Error ('test-eigcv.R:74:3'): symmetric eigcv, calculations on L ─────────────
  Error: Must specify only one of `B` and `k`, not both.
  Backtrace:
      ▆
   1. └─fastRG::sbm(...) at test-eigcv.R:74:3
   2.   └─fastRG::dcsbm(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ]
  Error:
  ! Test failures.
  Execution halted
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).
       |            ^
File ‘GEEaSPU/libs/GEEaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) gelnet.logreg.obj.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{y}{n-by-1 binary response vector sampled from {0,1}}
       |                                                     ^
File ‘gelnet/libs/gelnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘pracma’ ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
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}}
       |                     ^
train.xgboost: no visible global function definition for
  ‘cb.evaluation.log’
Undefined global functions or variables:
  cb.evaluation.log
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) cpm.Rd:70: Lost braces; missing escapes or markup?
    70 | covariates included in \code{formula_l} or {formula_s} (required).}
       |                                            ^
Namespaces in Imports field not imported from:
  ‘GGEBiplots’ ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’
  ‘reshape2’
  All declared Imports should be used.
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
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.
Missing dependency on R >= 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’
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 
       |                                            ^
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be 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:
    ‘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: support will be removed soon
Specified C++11: support will be removed soon
Missing dependency on R >= 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’
Running examples in ‘geomander-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_lewis
> ### Title: Get historical United States Congressional District Shapefiles
> ### Aliases: get_lewis
> 
> ### ** Examples
> 
> get_lewis(state = 'NM', congress = 111)
Data sourced from the United States Congressional District Shapefiles
<https://cdmaps.polisci.ucla.edu/>.
This message is displayed once per session.
Warning in CPL_read_ogr(dsn, layer, query, as.character(options), quiet,  :
  GDAL Error 1: HTTP error code : 404
Error: Cannot open "https://raw.githubusercontent.com/JeffreyBLewis/congressional-district-boundaries/master/New_Mexico_108_to_112.geojson"; The file doesn't seem to exist.
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:
    ‘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’
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘georob_vignette.Rnw’ using Sweave
Loading required package: sp

Attaching package: ‘georob’

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

    step

OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
recomputing robust Mahalanobis distances
saving the robust distances 'MD' as part of ‘r.lmrob’
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’ ‘spData’
  All declared Imports should be used.
Running examples in ‘geostatsp-Ex.R’ failed
The error most likely occurred in:

> ### Name: RFsimulate
> ### Title: Simulation of Random Fields
> ### Aliases: RFsimulate modelRandomFields RFsimulate RFsimulate-methods
> ###   RFsimulate,ANY,SpatRaster-method RFsimulate,numeric,SpatRaster-method
> ###   RFsimulate,numeric,SpatVector-method
> ###   RFsimulate,RMmodel,SpatVector-method
> ###   RFsimulate,RMmodel,SpatRaster-method
> ###   RFsimulate,matrix,SpatRaster-method
> ###   RFsimulate,matrix,SpatVector-method RFsimulate,data.frame,ANY-method
> ### Keywords: spatial
> 
> ### ** Examples
> 
> library('geostatsp')
> 
> # exclude this line to use the RandomFields package
> options(useRandomFields = FALSE)
> 
> model1 <- c(var=5, range=1,shape=0.5)
> 
> 
> myraster = rast(nrows=20,ncols=30,extent = ext(0,6,0,4), 
+ 	crs="+proj=utm +zone=17 +datum=NAD27 +units=m +no_defs")
> 
> set.seed(0) 
> 
> simu <- RFsimulate(model1, x=myraster, n=3)
install the RandomFields package for faster simulations
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
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 HTML validation problems:
germinationmetrics.html:272:1 (EmergenceRateIndex.Rd:53): Warning: <script> anchor "MathJax-script" already defined
germinationmetrics.html:513:2 (FirstGermTime.Rd:54): Warning: <script> anchor "MathJax-script" already defined
germinationmetrics.html:716:63 (FourPHFfit.Rd:84): Warning: <script> anchor "MathJax-script" already defined
germinationmetrics.html:1154:30 (GermIndex.Rd:39): Warning: <script> anchor "MathJax-script" already defined
germinationmetrics.html:1344:14 (GermPercent.Rd:38): Warning: <script> anchor "MathJax-script" already defined
germinationmetrics.html:1430:2 (GermSpeed.Rd:72): Warning: <script> anchor "MathJax-script" already defined
germinationmetrics.html:1678:2 (GermSynchrony.Rd:36): Warning: <script> anchor "MathJax-script" already defined
germinationmetrics.html:1797:1 (GermValue.Rd:51): Warning: <script> anchor "MathJax-script" already defined
germinationmetrics.html:1997:2 (MeanGermPercent.Rd:43): Warning: <script> anchor "MathJax-script" already defined
germinationmetrics.html:2139:2 (MeanGermRate.Rd:70): Warning: <script> anchor "MathJax-script" already defined
germinationmetrics.html:2351:1 (MeanGermTime.Rd:53): Warning: <script> anchor "MathJax-script" already defined
germinationmetrics.html:2531:24 (TimsonsIndex.Rd:54): Warning: <script> anchor "MathJax-script" already defined
germinationmetrics.html:2785:34 (WeightGermPercent.Rd:28): Warning: <script> anchor "MathJax-script" already defined
germinationmetrics.html:2996:59 (germination.indices.Rd:245): Warning: <script> anchor "MathJax-script" already defined
germinationmetrics.html:3818:61 (t50.Rd:28): Warning: <script> anchor "MathJax-script" already defined
Missing dependency on R >= 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: support will be removed soon
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
Missing dependency on R >= 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’
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 ?
Namespaces in Imports field not imported from:
  ‘googlesheets4’ ‘tidyr’
  All declared Imports should be used.
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}}
       |                                      ^
Missing dependency on R >= 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’
Namespace in Imports field not imported from: ‘png’
  All declared Imports should be 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:
    ‘girder_experiment.Rd’
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘utils’
  All declared Imports should be used.
Found the following assignments to the global environment:
File ‘ggExtra/R/ggMarginalGadget.R’:
  assign(plotname, eval(parse(text = origPlot)), envir = .GlobalEnv)
Missing dependency on R >= 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’
Specified C++11: support will be removed soon
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘vdiffr’
  All declared Imports should be 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:
    ‘inset_shape_circle.R’ ‘inset_shape_rectangle.R’ ‘inset_shape_sf.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:
    ‘ggmugs.R’
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
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 ?
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘RPostgres’ ‘colourpicker’ ‘ggpmisc’
  ‘ggpubr’ ‘glue’ ‘gridExtra’ ‘markdown’ ‘patchwork’ ‘plotly’
  ‘quantreg’ ‘shinyFiles’ ‘shinyjqui’ ‘shinyjs’ ‘table1’ ‘zoo’
  All declared Imports should be used.
Missing dependency on R >= 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’
Namespaces in Imports field not imported from:
  ‘nomogramFormula’ ‘survival’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘utils’
  All declared Imports should be used.
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}
       |                                                                           ^
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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
Missing dependency on R >= 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’
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘mockery’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MCMCpack’ ‘ggplot2’ ‘moments’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: support will be removed soon
File ‘gllm/libs/gllm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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) 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}.}
       |                                                                                                                                                                                                                                                                                                                                                                                                          ^
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiceKriging’ ‘rgenoud’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘AER’ ‘MASS’ ‘Matrix’ ‘censReg’ ‘effects’ ‘foreign’ ‘lme4’ ‘lmtest’
  ‘nnet’ ‘pBrackets’ ‘plm’ ‘pscl’ ‘sandwich’
  All declared Imports should be used.
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.
File ‘globalOptTests/libs/globalOptTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
checkRd: (-1) gmac.Rd:56: height/width attributes should be in pixels
checkRd: (-1) rtheta.Rd:50-76: Lost braces in \itemize; meant \describe ?
Unknown package ‘registr’ in Rd xrefs
Specified C++11: support will be removed soon
Missing dependency on R >= 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’
Namespaces in Imports field not imported from:
  ‘base’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Specified C++11: support will be removed soon
Namespaces in Imports field not imported from:
  ‘rhandsontable’ ‘shiny’ ‘stats’
  All declared Imports should be used.
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: \&
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘future’ ‘httr’
  All declared Imports should be 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:
    ‘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).}
       |     ^
Missing dependency on R >= 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.
Namespace in Imports field not imported from: ‘BiocManager’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
File ‘gplm/libs/gplm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: support will be removed soon
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’
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 ?
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}.
       |                                                                                ^
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘PairedData’ ‘RColorBrewer’ ‘agricolae’ ‘corrplot’ ‘desplot’
  ‘dplyr’ ‘ggplot2’ ‘ggpubr’ ‘gridGraphics’ ‘gtools’ ‘kableExtra’
  ‘knitr’ ‘magrittr’ ‘pastecs’ ‘reshape2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘summarytools’
  All declared Imports should be used.
checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) crdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) descApp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) layoutApp.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) rbdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) ttApp.Rd:43: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(graphhopper)
  > 
  > test_check("graphhopper")
  Saving _problems/test_route-22.R
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 6 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • gh_is_avialable() is not TRUE (2): 'test_route-local-gh-instance.R:10:3',
    'test_spt-local-gh-instance.R:4:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_route.R:9:3'): sf LINESTRING ───────────────────────────────────
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: `with_mock()` was deprecated in testthat 3.2.0 and is now defunct.
  ℹ Please use `with_mocked_bindings()` instead.
  Backtrace:
      ▆
   1. └─testthat::with_mock(...) at test_route.R:9:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 6 ]
  Error:
  ! Test failures.
  Execution halted
Specified C++11: support will be removed soon
File ‘graphpcor/libs/graphpcor.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) 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.
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
Specified C++11: support will be removed soon
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
checkRd: (-1) cost.Rd:13: height/width attributes should be in pixels
checkRd: (-1) invprob.Rd:12: height/width attributes should be in pixels
checkRd: (-1) sensitivity.Rd:13: height/width attributes should be in pixels
checkRd: (-1) synthetic.Rd:16: height/width attributes should be in pixels
Namespace in Imports field not imported from: ‘msm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘methods’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘rjags’
  All declared Imports should be used.
File ‘grove/libs/grove.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Found the following files/directories:
  ‘p1_20up-vs-p2_25up_in_str1.txt’ ‘p1_20up-vs-p2_25up_in_str2.txt’
  ‘p2_25up-vs-p1_20up_in_str1.txt’ ‘p2_25up-vs-p1_20up_in_str2.txt’
  ‘s0_20up.txt’ ‘s0_30up.txt’ ‘s0_f2up.txt’ ‘strs.vec_01mx.txt’
  ‘strs.vec_02mx.txt’ ‘strs.vec_03mx.txt’ ‘strs.vec_04mx.txt’
  ‘strs.vec_05mx.txt’ ‘strs.vec_06mx.txt’ ‘strs.vec_30up.txt’
  ‘strs.vec_50up.txt’ ‘strs.vec_f2up.txt’ ‘uni_p1_20up-p2_25up.txt’
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’
File ‘grr/libs/grr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
This entry point may be removed soon:
‘STRING_PTR’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
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
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 ?
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Specified C++11: support will be removed soon
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 ?
Missing dependency on R >= 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) 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.}
       |                                                          ^
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘gumbel.Rnw’ using Sweave
Error: processing vignette 'gumbel.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'gumbel.tex' failed.
LaTeX errors:
! Undefined control sequence.
\__hook begindocument ...fter {\bbl@main@language 
                                                  }\ifbbl@single \renewcomma...
l.55 \begin{document}
                     
! Emergency stop.
\__hook begindocument ...fter {\bbl@main@language 
                                                  }\ifbbl@single \renewcomma...
l.55 \begin{document}
                     
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘gumbel.Rnw’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Missing dependency on R >= 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’
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘spgwr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘attempt’ ‘corpcor’ ‘glue’ ‘htmltools’ ‘pkgload’ ‘processx’
  ‘tools’
  All declared Imports should be used.
Found the following files/directories:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
Specified C++11: support will be removed soon
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’
File ‘hawkes/libs/hawkes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++14: support will be removed soon
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 ?
checkRd: (-1) phenowheat.Rd:18: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) phenowheat.Rd:19: Lost braces in \enumerate; meant \describe ?
File ‘HDGLM/libs/HDGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) pain.Rd:114: height/width attributes should be in pixels
Missing dependency on R >= 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’
Namespaces in Imports field not imported from:
  ‘RandomWalker’ ‘TidyDensity’ ‘healthyR’ ‘healthyR.ai’ ‘healthyR.data’
  ‘healthyR.ts’ ‘tidyAML’
  All declared Imports should be used.
Malformed Title field: should not end in a period.