Package required but not available: ‘ggformula’

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

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/MinimalRgg.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: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘William George Underwood <wgu2@princeton.edu>’

The Description field contains
  and Cucuringu (2020) <arXiv:2004.01293>.
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:
  '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:
  'ergm', '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: ‘Mark Puttick <marknputtick@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mark",
                      family = "Puttick",
                      role = c("aut", "cre", "cph"),
                      email = "marknputtick@gmail.com"),
               person(given = "Gavin",
                      family = "Thomas",
                      role = c("aut", "cph")),
               person(given = "Rob",
                      family = "Freckleton",
                      role = c("aut", "cph")),
               person(given = "Magnus",
                      family = "Clarke",
                      role = "ctb"),
               person(given = "Travis",
                      family = "Ingram",
                      role = "ctb"),
               person(given = "David",
                      family = "Orme",
                      role = "ctb"),
               person(given = "Emmanuel",
                      family = "Paradis",
                      role = "ctb"))
as necessary.
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?
Maintainer: ‘Andrew Tweedell <atweedell315@gmail.com>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘bin.Rd’:
    \keyword{bin,}
    \keyword{group,}
    \keyword{potentials,}
    \keyword{unit,}
  File ‘cumsum_mu_synch.Rd’:
    \keyword{recurrence,}
    \keyword{synchronization,}
    \keyword{unit,}
  File ‘mu_synch.Rd’:
    \keyword{Zscore,}
    \keyword{recurrence,}
    \keyword{sigmax,}
    \keyword{synchronization,}
    \keyword{unit,}
    \keyword{visual,}
  File ‘plot_bins.Rd’:
    \keyword{bin,}
    \keyword{plot,}
    \keyword{trains,}
    \keyword{unit,}
  File ‘recurrence_intervals.Rd’:
    \keyword{potentials,}
    \keyword{recurrence,}
    \keyword{unit,}
  File ‘visual_mu_synch.Rd’:
    \keyword{recurrence,}
    \keyword{synchronization,}
    \keyword{unit,}
  File ‘zscore_mu_synch.Rd’:
    \keyword{recurrence,}
    \keyword{synchronization,}
    \keyword{unit,}
Package required but not available: ‘dygraphs’

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: ‘Birgit Erni <birgit.erni@uct.ac.za>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Birgit", "Erni.", "Based", "on", "models", "developed", "by"),
                      family = "Underhill",
                      role = "aut",
                      email = "birgit.erni@uct.ac.za"),
               person(family = "Zucchini.",
                      role = "aut",
                      comment = "1988, 1990"),
               person(given = "Birgit",
                      family = "Erni",
                      role = "cre",
                      email = "birgit.erni@uct.ac.za"))
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: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'keyring', 'rmarkdown'

VignetteBuilder package required 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:
  'bsplus', 'config', 'ggiraph', 'golem', 'quarto', 'reactable',
  'shinybusy'

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

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

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

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: ‘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 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/moveHMM-custom-plots.Rnw’
   ‘inst/doc/moveHMM-guide.Rnw’
   ‘inst/doc/moveHMM-starting-values.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', '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?
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', 'tidyverse', 'plotly', '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?
Package required but not available: ‘RcmdrMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Zhu Wang <zwang145@uthsc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhu",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "zwang145@uthsc.edu"),
               person(given = c("with", "contributions", "from", "Achim"),
                      family = "Zeileis",
                      role = "aut"),
               person(given = "Simon",
                      family = "Jackman",
                      role = "aut"),
               person(given = "Brian",
                      family = "Ripley",
                      role = "aut"),
               person(given = "Patrick",
                      family = "Breheny",
                      role = "aut"))
as necessary.

The BugReports field in DESCRIPTION has
  https://github.com/zhuwang46/mpath
which should likely be
  https://github.com/zhuwang46/mpath/issues
instead.
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/brcancer.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', '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:
  'kableExtra', '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: ‘Ignacio López-de-Ullibarri <ignacio.lopezdeullibarri@udc.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ignacio",
                    family = "López-de-Ullibarri",
                    role = c("aut", "cre"),
                    email = "ignacio.lopezdeullibarri@udc.es")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'pinp', 'rmarkdown'

VignetteBuilder package required 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: ‘Edgar Santos-Fernandez <edgar.santosfdez@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Edgar",
                      family = "Santos-Fernandez",
                      role = c("aut", "cre"),
                      email = "edgar.santosfdez@gmail.com"),
               person(given = "Michele",
                      family = "Scagliarini.",
                      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’
checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
checkRd: (-1) genotype_data.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) phenotype_data.Rd:15: Escaped LaTeX specials: \_
Package has ‘vignettes’ subdirectory 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', 'gt'

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:
    ‘compute-contribution.R’ ‘compute-headcount-ratio-adjusted.R’
    ‘compute-headcount-ratio.R’ ‘compute-mpi.R’ ‘compute_mpi.Rd’
    ‘create-deprivation-matrix.R’ ‘define-deprivation.R’
    ‘define-mpi-specs.R’ ‘define_deprivation.Rd’ ‘define_mpi_specs.Rd’
    ‘helpers.R’ ‘save_mpi.R’ ‘write-as-excel.R’
Package has ‘vignettes’ subdirectory 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'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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?
checkRd: (-1) glmfence.Rd:21: Lost braces; missing escapes or markup?
    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
checkRd: (-1) lmfence.Rd:21: Lost braces; missing escapes or markup?
    21 | is performed where the boundary is cstar*hat(sigma)_{M,tildeM}.}
       |                                                     ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Chris Pardy <cooliomcdude@gmail.com>’

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

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: ‘Phuc H. Nguyen <phuc.nguyen.rcran@gmail.com>’

The Description field contains
  Nguyen et al. (2022) <arXiv:2209.08036>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘qtl’

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: ‘Francisco M. Fatore <fmfatore@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Francisco", "M."),
                      family = "Fatore",
                      role = c("aut", "cre"),
                      email = "fmfatore@gmail.com"),
               person(given = c("Samuel", "G."),
                      family = "Fadel",
                      role = "aut"))
as necessary.
Maintainer: ‘Kevin Burke <kevin.burke@ul.ie>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kevin",
                    family = "Burke",
                    role = c("aut", "cre"),
                    email = "kevin.burke@ul.ie")
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: ‘Mahdi Teimouri <teimouri@aut.ac.ir>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mahdi",
                      family = "Teimouri",
                      role = c("aut", "cre"),
                      email = "teimouri@aut.ac.ir"),
               person(given = "Saralees",
                      family = "Nadarajah",
                      role = "aut"))
as necessary.
Maintainer: ‘Henrik Singmann <singmann@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 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/mptinr_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: 'knitr', 'rmarkdown'

VignetteBuilder package required 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:
  'flextable', 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Paolo Frumento <paolo.frumento@unipi.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Paolo",
                    family = "Frumento",
                    role = c("aut", "cre"),
                    email = "paolo.frumento@unipi.it")
as necessary.
Packages required but not available: 'pch', '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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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 J. Rothman <arothman@umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Adam", "J."),
                    family = "Rothman",
                    role = c("aut", "cre"),
                    email = "arothman@umn.edu")
as necessary.
Maintainer: ‘Jeremy Oguamalam <jeremy.oguamalam@tuwien.ac.at>’

The Description field contains
  implementation of Oguamalam et al. (2023) <arXiv:2307.13509>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘fdapace’

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

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

Packages suggested but not available for checking:
  'ows4R', 'knitr', 'leaflet', 'leaflet.extras2', 'mapview',
  '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: ‘Chih-Li Sung <sungchih@msu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Chih-Li",
                    family = "Sung",
                    role = c("aut", "cre"),
                    email = "sungchih@msu.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', 'bookdown', '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'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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?
Running examples in ‘mrgsolve-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mread_yaml
> ### Title: Read a model from yaml format
> ### Aliases: mread_yaml yaml_to_cpp
> 
> ### ** Examples
> 
> mod <- house()
> 
> temp <- tempfile(fileext = ".yaml")
> 
> mwrite_yaml(mod, file = temp)
Error in `require_yaml()`:
! The package "yaml" is required.
Backtrace:
    ▆
 1. └─mrgsolve::mwrite_yaml(mod, file = temp)
 2.   └─mrgsolve:::require_yaml()
 3.     └─rlang::abort("The package \"yaml\" is required.")
Execution halted
Maintainer: ‘Tom Stindl <t.stindl@unsw.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Tom",
                      family = "Stindl",
                      role = c("aut", "cre"),
                      email = "t.stindl@unsw.edu.au"),
               person(given = "Feng",
                      family = "Chen",
                      role = "aut"))
as necessary.
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?
Maintainer: ‘Jon Clayden <code@clayden.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: ‘Qi Yan <qy2253@cumc.columbia.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Qi",
                    family = "Yan",
                    role = c("aut", "cre"),
                    email = "qy2253@cumc.columbia.edu")
as necessary.
Maintainer: ‘Yuanming Zhang<soyzhang@mail.hzau.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhang",
                      family = "Ya-Wen",
                      role = "aut"),
               person(given = "Li",
                      family = "Pei",
                      role = "aut"),
               person(given = "Zhang",
                      family = "Yuan-Ming",
                      role = "aut"),
               person(given = "Yuanming",
                      family = "Zhang",
                      role = "cre",
                      email = "soyzhang@mail.hzau.edu.cn"))
as necessary.
checkRd: (-1) MultiManhattan.Rd:33: Lost braces; missing escapes or markup?
    33 |         \item{LogTimes}{Magnification of {-log10(P-value)}; the default is
       |                                          ^
checkRd: (-1) MultiManhattan.Rd:35: Lost braces; missing escapes or markup?
    35 |     \item{LODTimes}{Magnification of {LOD score}; the default is 1.2.}
       |                                      ^
Maintainer: ‘Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Abirami S <abirami89@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Abirami",
                    family = "S",
                    role = c("aut", "cre"),
                    email = "abirami89@gmail.com")
as necessary.
Packages required but not available: 'Hmisc', 'WGCNA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Siqi Xu <sqxu@hku.hk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Siqi",
                    family = "Xu",
                    role = c("aut", "cre"),
                    email = "sqxu@hku.hk")
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: ‘Leo N. Geppert <geppert@statistik.uni-dortmund.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Esther",
                      family = "Denecke",
                      role = "aut"),
               person(given = c("Leo", "N."),
                      family = "Geppert",
                      role = c("aut", "cre"),
                      email = "geppert@statistik.uni-dortmund.de"),
               person(given = "Steffen",
                      family = "Maletz",
                      role = "ctb"),
               person(given = c("R", "Core"),
                      family = "Team",
                      role = "ctb"))
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', 'SuperLearner'

VignetteBuilder package required 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: ‘Tianchen Qian <t.qian@uci.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Eliot",
                      family = "Wong-Toi",
                      role = "aut"),
               person(given = "Thabat",
                      family = "Dahdoul",
                      role = "aut"),
               person(given = "Tianchen",
                      family = "Qian",
                      role = c("aut", "cre"),
                      email = "t.qian@uci.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?
Packages required but not available: 'knitr', 'rmarkdown', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Novia Permatasari <novia.permatasari@bps.go.id>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Azka",
                      family = "Ubaidillah",
                      role = "aut"),
               person(given = "Novia",
                      family = "Permatasari",
                      role = c("aut", "cre"),
                      email = "novia.permatasari@bps.go.id"))
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: ‘Novia Permatasari <novia.permatasari@bps.go.id>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Novia",
                      family = "Permatasari",
                      role = c("aut", "cre"),
                      email = "novia.permatasari@bps.go.id"),
               person(given = "Azka",
                      family = "Ubaidillah",
                      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) n.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) n.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) n.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
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: ‘Yonghui Dong <yonghui.dong@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yonghui",
                    family = "Dong",
                    role = c("aut", "cre"),
                    email = "yonghui.dong@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: 'cp4p', 'mixOmics'

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’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MSCMT.Rcheck/00install.out’ for details.
Maintainer: ‘Monica Calderon-Santiago <b42casam@uco.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Monica",
                    family = "Calderon-Santiago",
                    role = c("aut", "cre"),
                    email = "b42casam@uco.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: ‘Phil Ferriere <pferriere@hotmail.com>’

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

VignetteBuilder package required 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: ‘Phil Ferriere <pferriere@hotmail.com>’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Chris Bradley <cbradley05@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Chris",
                    family = "Bradley",
                    role = c("aut", "cre"),
                    email = "cbradley05@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: ‘Kei Hirose <mail@keihirose.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kei",
                    family = "Hirose",
                    role = c("aut", "cre"),
                    email = "mail@keihirose.com")
as necessary.
'data(package=)' call not declared from: ‘MASS’
Packages required but not available: 'do', 'set', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Steven Rozen <steverozen@pm.me>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘David Moriña Soler <dmorina@ub.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "David",
                      family = "Moriña",
                      role = c("aut", "cre"),
                      email = "dmorina@ub.edu",
                      comment = "Universitat de Barcelona"),
               person(given = "Pedro",
                      family = "Puig",
                      role = "aut",
                      comment = "Universitat Autònoma de Barcelona"),
               person(given = "Mireia",
                      family = "Diaz",
                      role = "aut",
                      comment = "Institut Català d'Oncologia"))
as necessary.
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/MSinference.Rnw’
(Is a VignetteBuilder field missing?)

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: ‘Luca Scrucca <luca.scrucca@unipg.it>’

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', 'rgl'

VignetteBuilder package required 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’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Phil J Watson <philwatson.slr@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Phil", "J"),
                    family = "Watson",
                    role = c("aut", "cre"),
                    email = "philwatson.slr@gmail.com")
as necessary.
Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
Maintainer: ‘Atsushi Kawaguchi <kawa_a24@yahoo.co.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Atsushi",
                    family = "Kawaguchi",
                    role = c("aut", "cre"),
                    email = "kawa_a24@yahoo.co.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: ‘Hasan BULUT <hasan.bulut@omu.edu.tr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hasan",
                    family = "BULUT",
                    role = c("aut", "cre"),
                    email = "hasan.bulut@omu.edu.tr")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'tidyverse', '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: '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', 'relsurv'

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘Kevin Michael Frick <kmfrick98@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Kevin", "Michael"),
                    family = "Frick",
                    role = c("aut", "cre"),
                    email = "kmfrick98@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: ‘Zhibing He <zhibingh@asu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhibing",
                      family = "He",
                      role = c("aut", "cre"),
                      email = "zhibingh@asu.edu"),
               person(given = "Dan",
                      family = "Cheng",
                      role = "aut"))
as necessary.

The Description field contains
  Schwartzman (2015) <arXiv:1504.06384>.
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: ‘David Magis <david.magis@uliege.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "David",
                      family = "Magis",
                      role = c("aut", "cre"),
                      email = "david.magis@uliege.be",
                      comment = "U Liege, Belgium"),
               person(given = "Duanli",
                      family = "Yan",
                      role = "aut",
                      comment = "ETS, USA"),
               person(given = "Alina",
                      family = "von Davier",
                      role = "aut",
                      comment = "ACTNext, USA"))
as necessary.
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Elias Maciel <eliasmacielr@gmail.com>’

The Description field contains
  of Gustavo Sosa et al. (2016) <arXiv:1709.08730>, total correlation,
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) multivar_joint_shannon_entropy.Rd:20: Lost braces
    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
checkRd: (-1) total_correlation.Rd:20: Lost braces
    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'devtools', '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?
Maintainer: ‘Josep A. Sanchez-Espigares <josep.a.sanchez@upc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Josep", "A."),
                      family = "Sanchez-Espigares",
                      role = c("aut", "cre"),
                      email = "josep.a.sanchez@upc.edu"),
               person(given = "Alberto",
                      family = "Lopez-Moreno",
                      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?
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: ‘Didem Sari <dsari@iastate.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Didem",
                      family = "Sari",
                      role = c("aut", "cre"),
                      email = "dsari@iastate.edu"),
               person(given = c("Sarah", "M."),
                      family = "Ryan",
                      role = "aut",
                      email = "smryan@iastate.edu"))
as necessary.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ye Tian <ye.t@columbia.edu>’

The Description field contains
  Y., Weng, H., & Feng, Y. (2022) <arXiv:2209.15224>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Humza Haider <hshaider@ualberta.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Humza",
                    family = "Haider",
                    role = c("aut", "cre"),
                    email = "hshaider@ualberta.ca")
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: '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: ‘gam’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ruey S. Tsay <ruey.tsay@chicagobooth.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Ruey", "S."),
                      family = "Tsay",
                      role = c("aut", "cre"),
                      email = "ruey.tsay@chicagobooth.edu"),
               person(given = "David",
                      family = "Wood",
                      role = "aut"),
               person(given = "Jon",
                      family = "Lachmann",
                      role = "ctb"))
as necessary.
Packages required but not available: 'fGarch', 'fBasics'

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: ‘Oliver Keyes <ironholds@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Oliver",
                      family = "Keyes",
                      role = c("aut", "cre"),
                      email = "ironholds@gmail.com"),
               person(given = "MuckRock",
                      family = "Project",
                      role = "cph"))
as necessary.

The Description field contains
  the 'MuckRock' (https://www.muckrock.com/) project under the United
Please enclose URLs in angle brackets (<...>).
checkRd: (-1) coef.mdf.Rd:17: Lost braces; missing escapes or markup?
    17 |   \item{type}{: Argument that controls the type of parameters to be returned. If \code{type="persons"} (default), a vector with the person parameters is returned. When \code{type="items"} then a vector with the item ranks obtained by the MUDFOLD item selection algorithm is returned. If {type="all"} then a list with both person and item coefficients is returned to the user.
       |                                                                                                                                                                                                                                                                                                ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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 in Depends/Imports which should probably only be in LinkingTo: ‘RcppArmadillo’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘David Winsemius <dwinsemius@comcast.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("S", "original", "by", "Kenneth"),
                      family = "Hess",
                      role = "aut"),
               person(given = c("R", "port", "by", "R."),
                      family = "Gentleman",
                      role = "aut"),
               person(given = "David",
                      family = "Winsemius",
                      role = "cre",
                      email = "dwinsemius@comcast.net"))
as necessary.
Package required but not available: ‘DiagrammeR’

Package suggested but not available for checking: ‘htmlwidgets’

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

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'

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?
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: ‘Ivan Tomic <info@ivantomic.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.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘intersection.Rd’:
    \keyword{intersect,}
  File ‘mulset.Rd’:
    \keyword{intersection,}
    \keyword{mulset,}
Packages required but not available: 'Hmisc', 'knitr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Serguei Sokol <sokol@insa-toulouse.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Serguei",
                    family = "Sokol",
                    role = c("aut", "cre"),
                    email = "sokol@insa-toulouse.fr")
as necessary.
Maintainer: ‘Luciano Selzer <luciano.selzer@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Spencer",
                      family = "Graves",
                      role = "aut"),
               person(given = "Hans-Peter",
                      family = "Piepho",
                      role = "aut"),
               person(given = c("Luciano", "Selzer", "with", "help", "from", "Sundar"),
                      family = "Dorai-Raj",
                      role = "aut"),
               person(given = "Luciano",
                      family = "Selzer",
                      role = "cre",
                      email = "luciano.selzer@gmail.com"))
as necessary.
Package required but not available: ‘MTS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Mario Hasler <hasler@email.uni-kiel.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mario",
                    family = "Hasler",
                    role = c("aut", "cre"),
                    email = "hasler@email.uni-kiel.de")
as necessary.
checkRd: (-1) MultEq-package.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MultEq-package.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MultEq-package.Rd:30: Lost braces in \itemize; meant \describe ?
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: ‘Robin Ristl <robin.ristl@meduniwien.ac.at>’

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', 'rticles'

VignetteBuilder package required 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 Eichenberger <mike.eichenberger@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Michael",
                      family = "Eichenberger",
                      role = c("aut", "cre"),
                      email = "mike.eichenberger@gmail.com"),
               person(given = "Carlo",
                      family = "Rosa",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown', '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?
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/SIRtrans.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: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Ana Belen Nieto Librero <ananieto@usal.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Ana", "Belen", "Nieto"),
                      family = "Librero",
                      role = c("aut", "cre"),
                      email = "ananieto@usal.es"),
               person(given = "Nora",
                      family = "Baccala",
                      role = "aut",
                      email = "norabaccala@gmail.com"),
               person(given = c("Purificacion", "Vicente"),
                      family = "Galindo",
                      role = "aut",
                      email = "purivg@usal.es"),
               person(given = c("Purificacion", "Galindo"),
                      family = "Villardon",
                      role = "aut",
                      email = "pgalindo@usal.es"))
as necessary.
Packages required but not available: 'rgl', 'shapes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'FactoMineR', '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', '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?
Maintainer: ‘Nils Norman Schiborr <nils-norman.schiborr@uni-bamberg.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.
Packages required but not available: 'plotly', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Nour-al-dain Marzouka <Nour-al-dain.Marzouka@med.lu.se>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Nour-al-dain",
                    family = "Marzouka",
                    role = c("aut", "cre"),
                    email = "nour-al-dain.marzouka@med.lu.se")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'BiocStyle'

VignetteBuilder package required 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) dbivCMP.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{bivprob}{Bivariate probabilities, {p00, p01, p10, p11}.}
       |                                         ^
Maintainer: ‘R. Salmeron <romansg@ugr.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "R.",
                      family = "Salmeron",
                      role = c("aut", "cre"),
                      email = "romansg@ugr.es"),
               person(given = "C.",
                      family = "Garcia",
                      role = "aut"),
               person(given = "J.",
                      family = "Garcia",
                      role = "aut"))
as necessary.
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 = "Aaron",
                      family = "Williams",
                      role = "aut"),
               person(given = "Jerome",
                      family = "Kelleher",
                      role = "aut"),
               person(given = "Dave",
                      family = "Barber",
                      role = "aut"))
as necessary.
Packages required but not available:
  'DT', 'knitr', 'rmarkdown', 'visNetwork'

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:
  'devtools', 'knitr', 'rgl', 'rmarkdown', '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:
  '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: ‘Alexander Volkmann <alexandervolkmann8@gmail.com>’

The Description field contains
  (multiFAMM), see Volkmann et al. (2021, <arXiv:2103.06606>). It builds
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Lukasz Smaga <ls@amu.edu.pl>’

The Description field contains
  data (Munko et al., 2023, <arXiv:2306.15259>). These procedures enable
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', '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: ‘S. Gorsky <sgorsky@umass.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "S.",
                      family = "Gorsky",
                      role = c("aut", "cre"),
                      email = "sgorsky@umass.edu"),
               person(given = "L.",
                      family = "Ma",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'qgraph', 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Jarrett Byrnes <jarrett.byrnes@umb.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’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Panos Rontogiannis <p.g.ronto@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Panos",
                    family = "Rontogiannis",
                    role = c("aut", "cre"),
                    email = "p.g.ronto@gmail.com")
as necessary.
Maintainer: ‘Marina Gomtsyan <marina.gomtsyan@agroparistech.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Marina",
                    family = "Gomtsyan",
                    role = c("aut", "cre"),
                    email = "marina.gomtsyan@agroparistech.fr")
as necessary.

The Description field contains
  (2022), <arXiv:2208.14721>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
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?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘mlgraph.Rd’
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: 'rlist', 'qgraph', 'mgm', 'lemon'

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: ‘"Markus Loecher" <markus.loecher@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "\"Markus",
                      family = "Loecher",
                      role = c("aut", "cre"),
                      email = "markus.loecher@gmail.com"),
               person(given = c("Berlin", "School", "of"),
                      family = "Economics",
                      role = "aut"),
               person(family = "Law\"",
                      role = "aut",
                      email = "markus.loecher@gmail.com",
                      comment = "BSEL"))
as necessary.
Package required but not available: ‘gam’

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?
Packages required but not available: 'shinystan', 'plotly', 'DT'

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

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: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘usethis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Silvia D'Angelo <silvia.dangelo@ucd.ie>’

The Description field contains
  <arXiv:2006.02995>.
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', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘predict.R’ ‘sensitivity.R’ ‘treatment_profile.R’
Running examples in ‘multimedia-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ansi_aware_handler
> ### Title: Pretty Printing
> ### Aliases: ansi_aware_handler
> 
> ### ** Examples
> 
> knitr::knit_hooks$set(output = ansi_aware_handler)
Error in loadNamespace(x) : there is no package called ‘knitr’
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?
Maintainer: ‘Jose Ameijeiras-Alonso <jose.ameijeiras@usc.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jose",
                      family = "Ameijeiras-Alonso",
                      role = c("aut", "cre"),
                      email = "jose.ameijeiras@usc.es"),
               person(given = c("Rosa", "M."),
                      family = "Crujeiras",
                      role = "aut"),
               person(given = "Alberto",
                      family = "Rodríguez-Casal",
                      role = "aut"),
               person(given = c("The", "R", "Core", "Team"),
                      family = "1996-2012",
                      role = c("ctb", "cph"),
                      comment = "C function 'BinDist2' obtained from package 'stats'"),
               person(given = c("The", "R", "Foundation"),
                      family = "2005",
                      role = c("ctb", "cph"),
                      comment = "C function 'BinDist2' obtained from package 'stats'"))
as necessary.
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:
  'roxygen2', '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: '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', 'pkgdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
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', '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?
Package required but not available: ‘matchMulti’

Package suggested but not available for checking: ‘rrelaxiv’

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?
Maintainer: ‘Lachlan Coin <l.coin@imb.uq.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Lachlan",
                      family = "Coin",
                      role = c("aut", "cre"),
                      email = "l.coin@imb.uq.edu.au"),
               person(given = "Paul",
                      family = "O'Reilly",
                      role = "aut"),
               person(given = "Yotsawat",
                      family = "Pompyen",
                      role = "aut"),
               person(given = "Clive",
                      family = "Hoggart",
                      role = "aut"),
               person(given = "Federico",
                      family = "Calboli",
                      role = "aut"))
as necessary.
checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
Maintainer: ‘Nicolas Froelich <nicfroe@posteo.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Nicolas",
                    family = "Froelich",
                    role = c("aut", "cre"),
                    email = "nicfroe@posteo.de")
as necessary.
Maintainer: ‘Pedro Araujo <pharaujo1094@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Pedro", "Araujo", "Gustavo", "Lacerda", "<gustavolacerdas@gmail.com>", "Peter", "C.B.", "Phillips", "<peter.phillips@yale.edu>", "Shu-Ping", "Shi"),
                      family = "<shuping.shi@mq.edu.au>",
                      role = "aut",
                      email = "shuping.shi@mq.edu.au"),
               person(given = "Pedro",
                      family = "Araujo",
                      role = "cre",
                      email = "pharaujo1094@gmail.com"))
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘sadf.Rd’:
    \keyword{AugmentedDickey-FullerTest,}
Maintainer: ‘Yuqi Tian <yuqitian35@gmail.com>’

The Description field contains
  with Semiparametric Cumulative Probability Models". <arXiv:2207.02815>.
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', 'pec', 'randomForestSRC', '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?
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/TwoModeNetworks.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Aurobindh Kalathil Puthanpura <kalat2@pdx.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Aurobindh", "Kalathil"),
                    family = "Puthanpura",
                    role = c("aut", "cre"),
                    email = "kalat2@pdx.edu")
as necessary.
Maintainer: ‘Agnes Martine Nielsen <agni@dtu.dk>’

The Description field contains
  Dot Product Graph Model", arXiv preprint <arXiv:1811.12172> (Submitted
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) nullestimation.Rd:17: Lost braces; missing escapes or markup?
    17 |           \code{U}        \tab The common latent space vectors. U in R^{n x d}\cr
       |                                                                        ^
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: ‘Alexander Keyel <skeyel@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alexander",
                    family = "Keyel",
                    role = c("aut", "cre"),
                    email = "skeyel@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: ‘Mark A. van de Wiel <mark.vdwiel@amsterdamumc.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Mark", "A."),
                    family = "van de Wiel",
                    role = c("aut", "cre"),
                    email = "mark.vdwiel@amsterdamumc.nl")
as necessary.

The Description field contains
  be specified. See Van de Wiel et al. (2021), <arXiv:2005.09301>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
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.
Maintainer: ‘Shixiao Zhang <praetere@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Shixiao",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "praetere@gmail.com"),
               person(given = "Peisong",
                      family = "Han",
                      role = "aut"))
as necessary.
Package required but not available: ‘rgl’

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

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: ‘Allison Meisner <allison.meisner@gmail.com>’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Hervé Monod <herve.monod@inra.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Caroline",
                      family = "Bidot",
                      role = "aut",
                      email = "caroline.bidot@inra.fr"),
               person(given = "Matieyendou",
                      family = "Lamboni",
                      role = "aut",
                      email = "matieyendou.lamboni@gmail.com"),
               person(given = "Hervé",
                      family = "Monod",
                      role = c("aut", "cre"),
                      email = "herve.monod@inra.fr"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
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/multisensi-vignette.rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Xu Qin <xuqin@pitt.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xu",
                      family = "Qin",
                      role = c("aut", "cre"),
                      email = "xuqin@pitt.edu"),
               person(given = "Guanglei",
                      family = "Hong",
                      role = "aut"),
               person(given = "Jonah",
                      family = "Deutsch",
                      role = "aut"),
               person(given = "Edward",
                      family = "Bein",
                      role = "aut"))
as necessary.
Maintainer: ‘Cinzia Franceschini <cinziafranceschini@msn.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Cinzia",
                      family = "Franceschini",
                      role = c("aut", "cre"),
                      email = "cinziafranceschini@msn.com"),
               person(given = "Nicola",
                      family = "Loperfido",
                      role = "aut"))
as necessary.
Maintainer: ‘Sarra Chair <sarra.chair@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Sarra",
                      family = "Chair",
                      role = c("aut", "cre"),
                      email = "sarra.chair@gmail.com"),
               person(given = "Malika",
                      family = "Charrad",
                      role = "aut"))
as necessary.
Maintainer: ‘Adam Clark <adam.tclark@gmail.com>’

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

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'

VignetteBuilder package required 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: ‘Karim Rahim <karim.rahim@queensu.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Karim",
                      family = "Rahim",
                      role = c("aut", "cre"),
                      email = "karim.rahim@queensu.ca"),
               person(given = c("Wesley", "S."),
                      family = "Burr",
                      role = "aut",
                      email = "wesleyburr@trentu.ca"))
as necessary.
Package required but not available: ‘DiagrammeR’

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

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', 'devtools'

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: 'factoextra', 'candisc', '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.
Maintainer: ‘Raziur Rahman <razeeebuet@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Raziur",
                    family = "Rahman",
                    role = c("aut", "cre"),
                    email = "razeeebuet@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’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘concat_pre_processors.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Rawan Allozi <ralloz2@uic.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rawan",
                      family = "Allozi",
                      role = c("aut", "cre"),
                      email = "ralloz2@uic.edu"),
               person(given = "Hakan",
                      family = "Demirtas",
                      role = "aut"))
as necessary.
Maintainer: ‘Zachary Fisher <fish.zachary@gmail.com>’

The Description field contains
  <arXiv:2007.05052>.
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 packages required for checking but not installed:
  'knitr', 'rmarkdown'
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: ‘Robin K. S. Hankin <hankin.robin@gmail.com>’

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

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

VignetteBuilder package required 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: ‘Eric F. Lock <elock@umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Eric", "F."),
                    family = "Lock",
                    role = c("aut", "cre"),
                    email = "elock@umn.edu")
as necessary.
Maintainer: ‘Nathaniel Graham <npgraham1@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Nathaniel",
                      family = "Graham",
                      role = c("aut", "cre"),
                      email = "npgraham1@gmail.com"),
               person(given = "Mahmood",
                      family = "Arai",
                      role = "aut"),
               person(given = "Björn",
                      family = "Hagströmer",
                      role = "aut"))
as necessary.
Maintainer: ‘Gunther Schauberger <gunther.schauberger@tum.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Gunther",
                    family = "Schauberger",
                    role = c("aut", "cre"),
                    email = "gunther.schauberger@tum.de")
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: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Eric Nantz <eric.nantz@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alex",
                      family = "Dmitrienko",
                      role = "aut"),
               person(given = "Eric",
                      family = "Nantz",
                      role = c("aut", "cre"),
                      email = "eric.nantz@gmail.com"),
               person(given = "Gautier",
                      family = "Paux",
                      role = "aut"),
               person(given = c("with", "contributions", "by", "Thomas"),
                      family = "Brechenmacher",
                      role = "aut"))
as necessary.
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.
Maintainer: ‘Martin Elff <martin@elff.eu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Martin",
                    family = "Elff",
                    role = c("aut", "cre"),
                    email = "martin@elff.eu")
as necessary.
Package required but not available: ‘memisc’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Charlotte Wickham <cwickham@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Charlotte",
                    family = "Wickham",
                    role = c("aut", "cre"),
                    email = "cwickham@gmail.com")
as necessary.
Package required but not available: ‘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: ‘Ryan T. Moore <rtm@american.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Ryan", "T."),
                      family = "Moore",
                      role = c("aut", "cre"),
                      email = "rtm@american.edu"),
               person(given = "Andrew",
                      family = "Reeves",
                      role = "aut",
                      email = "reeves@wustl.edu"))
as necessary.
Maintainer: ‘Fabian Krueger <Fabian.Krueger83@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alexander",
                      family = "Jordan",
                      role = "aut"),
               person(given = "Fabian",
                      family = "Krueger",
                      role = c("aut", "cre"),
                      email = "fabian.krueger83@gmail.com"))
as necessary.
Maintainer: ‘Aljaz Jelenko <aljaz.jelenko@amis.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Aljaz",
                    family = "Jelenko",
                    role = c("aut", "cre"),
                    email = "aljaz.jelenko@amis.net")
as necessary.
Maintainer: ‘Alessandro Santuz <alessandro.santuz@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: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Henning Prömpers <henning@proempers.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Henning",
                      family = "Prömpers",
                      role = c("aut", "cre"),
                      email = "henning@proempers.net"),
               person(given = "André",
                      family = "Guimarães",
                      role = "aut"))
as necessary.

The BugReports field in DESCRIPTION has
  https://github.com/alsguimaraes/MUS
which should likely be
  https://github.com/alsguimaraes/MUS/issues
instead.
Maintainer: ‘Kornelius Rohmeyer <rohmeyer@small-projects.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("MuToss", "Coding"),
                      family = "Team",
                      role = "aut",
                      comment = "Berlin 2010"),
               person(given = "Gilles",
                      family = "Blanchard",
                      role = "aut"),
               person(given = "Thorsten",
                      family = "Dickhaus",
                      role = "aut"),
               person(given = "Niklas",
                      family = "Hack",
                      role = "aut"),
               person(given = "Frank",
                      family = "Konietschke",
                      role = "aut"),
               person(given = "Kornelius",
                      family = "Rohmeyer",
                      role = c("aut", "cre"),
                      email = "rohmeyer@small-projects.de"),
               person(given = "Jonathan",
                      family = "Rosenblatt",
                      role = "aut"),
               person(given = "Marsel",
                      family = "Scheer",
                      role = "aut"),
               person(given = "Wiebke",
                      family = "Werft",
                      role = "aut"))
as necessary.
Packages required but not available: 'rJava', 'JavaGD', 'JGR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Kornelius Rohmeyer <rohmeyer@small-projects.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("MuToss", "Coding"),
                      family = "Team",
                      role = "aut",
                      comment = "Berlin 2010"),
               person(given = "Gilles",
                      family = "Blanchard",
                      role = "aut"),
               person(given = "Thorsten",
                      family = "Dickhaus",
                      role = "aut"),
               person(given = "Niklas",
                      family = "Hack",
                      role = "aut"),
               person(given = "Frank",
                      family = "Konietschke",
                      role = "aut"),
               person(given = "Kornelius",
                      family = "Rohmeyer",
                      role = c("aut", "cre"),
                      email = "rohmeyer@small-projects.de"),
               person(given = "Jonathan",
                      family = "Rosenblatt",
                      role = "aut"),
               person(given = "Marsel",
                      family = "Scheer",
                      role = "aut"),
               person(given = "Wiebke",
                      family = "Werft",
                      role = "aut"))
as necessary.
Maintainer: ‘Damiano Fantini <damiano.fantini@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Damiano",
                      family = "Fantini",
                      role = c("aut", "cre"),
                      email = "damiano.fantini@gmail.com"),
               person(given = "Vania",
                      family = "Vidimar",
                      role = "aut"),
               person(given = c("Joshua", "J"),
                      family = "Meeks",
                      role = "aut"))
as necessary.
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: ‘Mohit Dayal <mohitdayal2000@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mohit",
                    family = "Dayal",
                    role = c("aut", "cre"),
                    email = "mohitdayal2000@gmail.com")
as necessary.
Specified C++11: support will be removed soon
checkRd: (-1) cv.glm1path.Rd:74: Lost braces
    74 | \code{\link{glm1path}}, \\code{\link{glm1}}, \code{\link{glm}}, \code{\link{family}}
       |                               ^
Maintainer: ‘Mohammed Sedki <mohammed.sedki@u-psud.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Matthieu",
                      family = "Marbac",
                      role = "aut"),
               person(given = "Mohammed",
                      family = "Sedki",
                      role = c("aut", "cre"),
                      email = "mohammed.sedki@u-psud.fr"))
as necessary.
Maintainer: ‘Mark V. Bravington <mark.bravington@csiro.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Mark", "V."),
                    family = "Bravington",
                    role = c("aut", "cre"),
                    email = "mark.bravington@csiro.au")
as necessary.
Maintainer: ‘Denis Larocque <denis.larocque@hec.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Denis",
                    family = "Larocque",
                    role = c("aut", "cre"),
                    email = "denis.larocque@hec.ca")
as necessary.
Maintainer: ‘Nelson Lee Afanador <nelson.afanador@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Nelson", "Lee"),
                      family = "Afanador",
                      role = c("aut", "cre"),
                      email = "nelson.afanador@gmail.com"),
               person(given = "Thanh",
                      family = "Tran",
                      role = "aut"),
               person(given = "Lionel",
                      family = "Blanchet",
                      role = "aut"),
               person(given = "Richard",
                      family = "Baumgartner",
                      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’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘DFA.R’ ‘mvDFA.R’ ‘simulate_Lorenz_noise.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘multiverse’

Packages suggested but not available for checking:
  'pkgdown', 'covr', 'knitr', 'rmarkdown', 'kableExtra', '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:
  'scoringRules', 'cmdstanr', '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: ‘Justin Williams <williazo@ucla.edu>’

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

The Description field contains
  Williams, J.R, and Crespi, C.M. (2020) <arxiv:2008.13767>. The methods
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) bal.Rd:156: Escaped LaTeX specials: \&
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'rgl', 'mvmesh'

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

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

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?
Maintainer: ‘John P. Nolan <jpnolan@american.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("John", "P."),
                    family = "Nolan",
                    role = c("aut", "cre"),
                    email = "jpnolan@american.edu")
as necessary.
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Antonio Gasparrini <antonio.gasparrini@lshtm.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Antonio",
                    family = "Gasparrini",
                    role = c("aut", "cre"),
                    email = "antonio.gasparrini@lshtm.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.
Maintainer: ‘Jiebiao Wang <randel.wang@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jiebiao",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "randel.wang@gmail.com"),
               person(given = c("Lin", "S."),
                      family = "Chen",
                      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
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: ‘Arthur Allignol <arthur.allignol@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Arthur",
                    family = "Allignol",
                    role = c("aut", "cre"),
                    email = "arthur.allignol@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.

Found the following (possibly) invalid file URI:
  URI: /https://cran.r-project.org/web/packages/mvna/index.html
    From: README.md
Maintainer: ‘ZHANG Chen <447974102@qq.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "ZHANG",
                    family = "Chen",
                    role = c("aut", "cre"),
                    email = "447974102@qq.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: ‘Frank Technow <mvnggrad@fastmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Frank",
                    family = "Technow",
                    role = c("aut", "cre"),
                    email = "mvnggrad@fastmail.com")
as necessary.
Maintainer: ‘Hesen Li <li.hesen.21@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hesen",
                    family = "Li",
                    role = c("aut", "cre"),
                    email = "li.hesen.21@gmail.com")
as necessary.
Package required but not available: ‘plotly’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', '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’
Maintainer: ‘P. Filzmoser <P.Filzmoser@tuwien.ac.at>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Peter",
                      family = "Filzmoser",
                      role = "aut",
                      email = "P.Filzmoser@tuwien.ac.at"),
               person(given = "Moritz",
                      family = "Gschwandtner",
                      role = "aut",
                      email = "e0125439@student.tuwien.ac.at"),
               person(given = "P.",
                      family = "Filzmoser",
                      role = "cre",
                      email = "P.Filzmoser@tuwien.ac.at"))
as necessary.
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
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: ‘Arne Henningsen <arne.henningsen@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Arne",
                    family = "Henningsen",
                    role = c("aut", "cre"),
                    email = "arne.henningsen@gmail.com")
as necessary.
Maintainer: ‘Constantin Weiser <constantin.weiser@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Constantin",
                    family = "Weiser",
                    role = c("aut", "cre"),
                    email = "constantin.weiser@gmail.com",
                    comment = "University Mainz / Germany")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rgl', 'rmarkdown'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot (plot.NIGrid)
> ### Title: plots an NIGrid-object
> ### Aliases: 'plot (plot.NIGrid)' plot.NIGrid
> 
> ### ** Examples
> 
> myGrid <- createNIGrid(dim=4, type=c("GHe", "cNC1", "GLe", "oNC1"),
+                        level=c(3,4,5,6))
> plot(myGrid) ## dimension 1-min(3,dim(myGrid)) are plotted
Error in plot.NIGrid(myGrid) : 
  wrong dimensions stated to be plotted (no 'rgl'-package for 3d-plot)
Calls: plot -> plot.NIGrid
Execution halted
'library' or 'require' call not declared from: ‘mvtnorm’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Douglas Whitaker <douglas.whitaker@msvu.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Douglas",
                    family = "Whitaker",
                    role = c("aut", "cre"),
                    email = "douglas.whitaker@msvu.ca")
as necessary.
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.

Found the following (possibly) invalid file URIs:
  URI: jean-eudes.dazard@case.edu
    From: README.md
  URI: huaxu77@gmail.com
    From: README.md
  URI: ahs4@case.edu
    From: README.md
Maintainer: ‘Tommy Jones <jones.thos.w@gmail.com>’

The Description field contains
  Jones (2019) <arXiv:1911.11061>.
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', '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: ‘Elizabeth Gonzalez Estrada <egonzalez@colpos.mx>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Elizabeth",
                      family = "Gonzalez-Estrada",
                      role = "aut"),
               person(given = c("Jose", "A."),
                      family = "Villasenor-Alva",
                      role = "aut"),
               person(given = c("Elizabeth", "Gonzalez"),
                      family = "Estrada",
                      role = "cre",
                      email = "egonzalez@colpos.mx"))
as necessary.
Package required but not available: ‘matlib’

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', '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?
Maintainer: ‘Antonio Parisi <antonio.parisi@uniroma2.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Antonio",
                      family = "Parisi",
                      role = c("aut", "cre"),
                      email = "antonio.parisi@uniroma2.it"),
               person(given = "Brunero",
                      family = "Liseo",
                      role = "aut"),
               person(given = "Dirk",
                      family = "Eddelbuettel",
                      role = "ctb"),
               person(given = "Romain",
                      family = "Francois",
                      role = "ctb"))
as necessary.
Maintainer: ‘Han Chen <Han.Chen.2@uth.tmc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Han",
                    family = "Chen",
                    role = c("aut", "cre"),
                    email = "han.chen.2@uth.tmc.edu")
as necessary.
Maintainer: ‘Roger D. Peng <roger.peng@austin.utexas.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Roger", "D."),
                    family = "Peng",
                    role = c("aut", "cre"),
                    email = "roger.peng@austin.utexas.edu")
as necessary.
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', '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?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'visNetwork', 'htmlwidgets'

VignetteBuilder package required 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: ‘iTensor’

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

VignetteBuilder package required 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: ‘B N Mandal <mandal.stat@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("B", "N"),
                    family = "Mandal",
                    role = c("aut", "cre"),
                    email = "mandal.stat@gmail.com")
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?
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’
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘get_individual_algebra_results.R’
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', 'kableExtra', 'rTubeDB'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘S. Ramachandran<ramu@igib.in>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Deepika",
                      family = "Kulshreshtha",
                      role = "aut"),
               person(given = "Rupanjali",
                      family = "Chaudhuri",
                      role = "aut"),
               person(given = "Surabhi",
                      family = "Seth",
                      role = "aut"),
               person(given = "S.",
                      family = "Ramachandran",
                      role = c("aut", "cre"),
                      email = "ramu@igib.in"))
as necessary.
Package required but not available: ‘ggtree’

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?
Package required but not available: ‘yaml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Fu-Chang Hu <fuchang.hu@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("International-Harvard", "Statistical", "Consulting"),
                      family = "Company",
                      role = "aut",
                      email = "nhsc2010@hotmail.com"),
               person(given = "Fu-Chang",
                      family = "Hu",
                      role = "cre",
                      email = "fuchang.hu@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'Seurat', 'taxize'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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’
checkRd: (-1) mzipmed_data.Rd:22: Lost braces; missing escapes or markup?
    22 | @source {Simulated to serve as an example}
       |         ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Evan Biederstedt <evan.biederstedt@gmail.com>’

The Description field contains
  <doi:10.1109/TPAMI.2018.2889473>, <arXiv:1603.09320>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Gregory Jefferis <jefferis@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Stephane",
                      family = "Mangenat",
                      role = "aut",
                      comment = "for 'libnabo'"),
               person(given = "Gregory",
                      family = "Jefferis",
                      role = c("aut", "cre"),
                      email = "jefferis@gmail.com"))
as necessary.
Packages required but not available: 'knitr', 'rmarkdown'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Yaofang Hu <yaofangh@smu.edu>’

The Description field contains
  Wang (2023) <arXiv:2306.15616>. In addition to NAC, this package
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘survminer’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Sun-joo Lee <sjlee@air.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Sun-joo",
                      family = "Lee",
                      role = c("aut", "cre"),
                      email = "sjlee@air.org"),
               person(given = "Eric",
                      family = "Buehler",
                      role = "aut"),
               person(given = "Paul",
                      family = "Bailey",
                      role = "ctb"))
as necessary.
Maintainer: ‘Emmanuel Sikali <Emmanuel.Sikali@ed.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("NAEP", "Primer", "data", "by", "Emmanuel", "Sikali.", "Creation", "of", "R", "package", "by", "Paul"),
                      family = "Bailey",
                      role = "aut"),
               person(given = "Michael",
                      family = "Lee.",
                      role = "aut"),
               person(given = "Emmanuel",
                      family = "Sikali",
                      role = "cre",
                      email = "Emmanuel.Sikali@ed.gov"))
as necessary.
checkRd: (-1) M36NT2PM.dat.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) M36NT2PM.dat.Rd:38: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'WikidataR'

VignetteBuilder package required 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', 'SensoMineR'

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’
checkRd: (-1) addNodeNetworkStats.Rd:7: height/width attributes should be in pixels
checkRd: (-1) plotNetworkGraph.Rd:7: 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?
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/intro_naivebayes.Rnw’
(Is a VignetteBuilder field missing?)

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: ‘Qingliang Fan <michaelqfan@xmu.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Qingliang",
                      family = "Fan",
                      role = c("aut", "cre"),
                      email = "michaelqfan@xmu.edu.cn"),
               person(given = "KongYu",
                      family = "He",
                      role = "aut"),
               person(given = "Wei",
                      family = "Zhong",
                      role = "aut"))
as necessary.
checkRd: (-1) DSIVdata.Rd:15-23: Lost braces
    15 | for(i in 1:50){
       |               ^
checkRd: (-1) DSIVdata.Rd:17-21: Lost braces
    17 |   for(j in 1:50){
       |                 ^
checkRd: (-1) DSIVdata.Rd:31-39: Lost braces
    31 | for(i in 1:20){
       |               ^
checkRd: (-1) DSIVdata.Rd:33-37: Lost braces
    33 |   for(j in 1:20){
       |                 ^
checkRd: (-1) DSLIVEdata.Rd:10-18: Lost braces
    10 | for(i in 1:200){
       |                ^
checkRd: (-1) DSLIVEdata.Rd:12-16: Lost braces
    12 |   for(j in 1:200){
       |                  ^
checkRd: (-1) DSLIVEdata.Rd:26-34: Lost braces
    26 | for(i in 1:20){
       |               ^
checkRd: (-1) DSLIVEdata.Rd:28-32: Lost braces
    28 |   for(j in 1:20){
       |                 ^
checkRd: (-1) DSLIVEdata.Rd:50-54: Lost braces
    50 | for(kk in 1:length(p)){
       |                       ^
Cannot process vignettes
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  'knitr', 'rcrossref', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) drop_name_crossref.Rd:49: Lost braces; missing escapes or markup?
    49 | Takes one or several dois and extracts information from Crossref, then processes them into visual citations with \code{\link{drop_name}}. Requires {rcrossref} > v1.1, see README for further details.
       |                                                                                                                                                    ^
Package has ‘vignettes’ subdirectory 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: ‘Alencar Xavier <alenxav@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alencar",
                      family = "Xavier",
                      role = c("aut", "cre"),
                      email = "alenxav@gmail.com"),
               person(given = "William",
                      family = "Muir",
                      role = "aut"),
               person(given = "Katy",
                      family = "Rainey",
                      role = "aut"),
               person(given = "Shizhong",
                      family = "Xu.",
                      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’
'::' or ':::' import not declared from: ‘Matrix’
Package has ‘vignettes’ subdirectory 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:
  'knitr', 'rmarkdown', 'covr', 'Hmisc', '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:
    ‘impute_below.Rd’ ‘impute_factor.Rd’ ‘impute_fixed.Rd’
    ‘impute_mean.Rd’ ‘impute_median.Rd’ ‘impute_mode.Rd’ ‘impute_zero.Rd’
    ‘replace_na_with.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
File ‘nanoparquet/libs/nanoparquet.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.
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: ‘Taha Zaghdoudi <zedtaha@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Taha",
                    family = "Zaghdoudi",
                    role = c("aut", "cre"),
                    email = "zedtaha@gmail.com")
as necessary.
checkRd: (-1) fod.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fod.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fod.Rd:14: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Eduardo Flores <eduardo@enelmargen.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Eduardo",
                    family = "Flores",
                    role = c("aut", "cre"),
                    email = "eduardo@enelmargen.org")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling', '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?
Packages required but not available: 'pak', 'usethis'

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

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

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.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
Packages required but not available: 'rgl', 'yaml'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'alphashape3d'

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', '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")
  > library("natserv")
  > 
  > test_check("natserv")
  Error in `source_dir()`:
  ! Failed to evaluate './helper-natserv.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("natserv")
    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-natserv.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?
Packages required but not available: 'nat', 'rgl'

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

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

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: ‘Guo Yu <gy63@cornell.edu>’

The Description field contains
  high-dimensional linear models of Yu, Bien (2017) <arXiv:1712.02412>.
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: ‘Kosei Abe <mail@recyclebin.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kosei",
                    family = "Abe",
                    role = c("aut", "cre"),
                    email = "mail@recyclebin.jp")
as necessary.
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', '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.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘activate.Rd’
Maintainer: ‘Hiroto Katsumata <hrt.katsumata@gmail.com>’

The Description field contains
  <arXiv:2005.10998>, which improves the inverse probability weighting by
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: ‘Richard Wen <rrwen.dev@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:
  'bookdown', 'knitr', 'rmarkdown'

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

VignetteBuilder package required 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: ‘Malika Charrad <malika.charrad.1@ulaval.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Malika",
                      family = "Charrad",
                      role = c("aut", "cre"),
                      email = "malika.charrad.1@ulaval.ca"),
               person(given = "Nadia",
                      family = "Ghazzali",
                      role = "aut"),
               person(given = "Veronique",
                      family = "Boiteau",
                      role = "aut"),
               person(given = "Azam",
                      family = "Niknafs",
                      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.
checkRd: (-1) NbClust.Rd:50: Lost braces; missing escapes or markup?
    50 |       \item \bold{Average} : The distance \eqn{D_{ij}}{D_ij} between two clusters \eqn{C_{i}}{C_i} and \eqn{C_{j}}{C_j} is the mean of the distances between the pair of points {x} and {y}, where \eqn{x \in C_{i}, y \in C_{j}}{x in C_i, y in C_j}.
       |                                                                                                                                                                                 ^
checkRd: (-1) NbClust.Rd:50: Lost braces; missing escapes or markup?
    50 |       \item \bold{Average} : The distance \eqn{D_{ij}}{D_ij} between two clusters \eqn{C_{i}}{C_i} and \eqn{C_{j}}{C_j} is the mean of the distances between the pair of points {x} and {y}, where \eqn{x \in C_{i}, y \in C_{j}}{x in C_i, y in C_j}.
       |                                                                                                                                                                                         ^
Maintainer: ‘Philipp Angerer <philipp.angerer@helmholtz-muenchen.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Philipp",
                    family = "Angerer",
                    role = c("aut", "cre"),
                    email = "philipp.angerer@helmholtz-muenchen.de")
as necessary.
checkRd: (-1) nbconvert.Rd:49: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) nbconvert.Rd:50: Lost braces in \enumerate; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking:
  'usethis', 'knitr', 'rmarkdown', 'NBDCtoolsData'

VignetteBuilder package required 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: ‘Feiming Chen <feimingchen@yahoo.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Feiming",
                    family = "Chen",
                    role = c("aut", "cre"),
                    email = "feimingchen@yahoo.com")
as necessary.
Package required but not available: ‘nbpMatching’

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: ‘Yanming Di <diy@stat.oregonstate.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yanming",
                      family = "Di",
                      role = c("aut", "cre"),
                      email = "diy@stat.oregonstate.edu"),
               person(given = c("Daniel", "W"),
                      family = "Schafer",
                      role = "aut",
                      email = "schafer@stat.oregonstate.edu"),
               person(given = c("with", "contributions", "from", "Jason", "S"),
                      family = "Cumbie",
                      role = "aut",
                      email = "cumbiej@onid.orst.edu"),
               person(given = c("Jeff", "H"),
                      family = "Chang.",
                      role = "aut",
                      email = "changj@cgrb.oregonstate.edu"))
as necessary.
Maintainer: ‘Zeus Gracia-Tabuenca <zgtabuenca@comunidad.unam.mx>’

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: ‘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.
Packages required but not available: 'rmarkdown', 'rhandsontable'

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.
Packages required but not available: 'rmarkdown', 'rhandsontable'

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.
Packages required but not available: 'rmarkdown', 'rhandsontable'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotRt
> ### Title: Creates a plot of the effective reproductive number
> ### Aliases: plotRt
> 
> ### ** Examples
> 
> 
> ## Use the nbResults data frame included in the package which has the results
> # of the nbProbabilities() function on a TB-like outbreak.
> 
> ## Getting initial estimates of the reproductive number
> # (without specifying nbResults and without confidence intervals)
> rInitial <- estimateR(nbResults, dateVar = "infectionDate",
+                indIDVar = "individualID", pVar = "pScaled",
+                timeFrame = "months")
Please choose the stable portion of the outbreak to calculate the average Rt
>                
> ## Finding the stable portion of the outbreak for rangeForAvg using the plot
> plotRt(rInitial)
Error in loadNamespace(x) : there is no package called ‘Hmisc’
Calls: plotRt ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Marina Gomtsyan <mgomtsian@gmail.com>’

The Description field contains
  <arXiv:2307.00929>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
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: 'knitr', 'rmarkdown', 'bookdown'

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.
Maintainer: ‘Kyun-Seop Bae <k@acr.kr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kyun-Seop",
                    family = "Bae",
                    role = c("aut", "cre"),
                    email = "k@acr.kr")
as necessary.
Maintainer: ‘Jon Eastman <jonathan.eastman@gmail.com>’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', '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?
Problems with news in ‘NEWS.md’:
No news entries found.
Maintainer: ‘Nicholas Cooper <njcooper@gmx.co.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Nicholas",
                    family = "Cooper",
                    role = c("aut", "cre"),
                    email = "njcooper@gmx.co.uk")
as necessary.
Maintainer: ‘Dongshin Kim <dongshin.kim@live.com>’

The Description field contains
  Kim, D., Lee, S. and Kwon, S. (2018) <arXiv:1811.05061>, Lee, S., Kwon,
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) ncpen.Rd:108: Lost braces; missing escapes or markup?
   108 |   \item{gamma}{extra shrinkage parameter for \code{classo} and {sridge} only.}
       |                                                                ^
checkRd: (-1) ncpen.reg.Rd:109: Lost braces; missing escapes or markup?
   109 |   \item{gamma}{extra shrinkage parameter for \code{classo} and {sridge} only.}
       |                                                                ^
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: ‘Gavin Melville <gavin.melville@dpi.nsw.gov.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "GJ",
                      family = "Melville",
                      role = "aut"),
               person(given = "Gavin",
                      family = "Melville",
                      role = "cre",
                      email = "gavin.melville@dpi.nsw.gov.au"))
as necessary.
Maintainer: ‘Bouchra R. Nasri <bouchra.nasri@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Bouchra", "R."),
                    family = "Nasri",
                    role = c("aut", "cre"),
                    email = "bouchra.nasri@gmail.com")
as necessary.
Maintainer: ‘Sebastian J. Teran Hidalgo <sebastianteranhidalgo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Sebastian", "J.", "Teran"),
                      family = "Hidalgo",
                      role = c("aut", "cre"),
                      email = "sebastianteranhidalgo@gmail.com"),
               person(given = "Shuangge",
                      family = "Ma",
                      role = "aut"),
               person(given = "Ruofan",
                      family = "Bie",
                      role = "aut"))
as necessary.

Found the following (possibly) invalid file URIs:
  URI: sebastianteranhidalgo@gmail.com
    From: man/ancut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/awncut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/ncut.Rd
  URI: commits/master
    From: README.md
  URI: /commits/master
    From: README.md
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: 'leidenAlg', 'visNetwork'

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

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

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: ‘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.
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking: 'tergm', 'ergm', 'knitr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Joseph Rigdon <jrigdon@wakehealth.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Joseph",
                    family = "Rigdon",
                    role = c("aut", "cre"),
                    email = "jrigdon@wakehealth.edu")
as necessary.
Package required but not available: ‘nbpMatching’

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

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: ‘fBasics’

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: ‘Seurat’

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', '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?
Package required but not available: ‘gam’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Edilberto Cepeda <ecepedac@unal.edu.co>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Edilberto",
                      family = "Cepeda-Cuervo",
                      role = "aut"),
               person(given = c("Maria", "Victoria"),
                      family = "Cifuentes-Amado",
                      role = "aut"),
               person(given = "Margarita",
                      family = "Marin",
                      role = "aut"),
               person(given = "Edilberto",
                      family = "Cepeda",
                      role = "cre",
                      email = "ecepedac@unal.edu.co"))
as necessary.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/negenes.Rcheck/00install.out’ for details.
Maintainer: ‘Mamadou Yauck <yauck.mamadou@uqam.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mamadou",
                      family = "Yauck",
                      role = c("aut", "cre"),
                      email = "yauck.mamadou@uqam.ca"),
               person(given = c("Erica", "E.", "M."),
                      family = "Moodie",
                      role = "aut"))
as necessary.
Package required but not available: ‘RDS’

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: ‘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?
Package required but not available: ‘plotly’

Packages suggested but not available for checking:
  'spelling', 'kableExtra', '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', '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’
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘functions.R’
Package has ‘vignettes’ subdirectory 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?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘neon_cloud.R’
Package required but not available: ‘leaflet’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Peifeng Ruan <pruan12@fudan.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Peifeng",
                    family = "Ruan",
                    role = c("aut", "cre"),
                    email = "pruan12@fudan.edu.cn")
as necessary.
Packages required but not available: 'plotly', '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 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: ‘Olanrewaju Akande <akandelanre13@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Quanli",
                      family = "Wang",
                      role = "aut"),
               person(given = "Olanrewaju",
                      family = "Akande",
                      role = c("aut", "cre"),
                      email = "akandelanre13@gmail.com"),
               person(given = "Jingchen",
                      family = "Hu",
                      role = "aut"),
               person(given = "Jerry",
                      family = "Reiter",
                      role = "aut"),
               person(given = "Andres",
                      family = "Barrientos",
                      role = "aut"))
as necessary.
Specified C++11: support will be removed soon
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'SuperLearner'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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 packages required for checking but not installed:
  'knitr', 'rmarkdown'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘as.data.frame.predict.R’
checkRd: (-1) GSS.Rd:17: Lost braces
    17 | code{2016}.}
       |     ^
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:
  'BiocStyle', '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?
Maintainer: ‘Sean J Westwood <seanjw@stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mike",
                      family = "Nowak",
                      role = "aut",
                      email = "michael.nowak@gmail.com"),
               person(given = "Solomon",
                      family = "Messing",
                      role = "aut",
                      email = "solomon.messing@gmail.com"),
               person(given = c("Sean", "J"),
                      family = "Westwood",
                      role = c("aut", "cre"),
                      email = "seanjw@stanford.edu"),
               person(given = "Dan",
                      family = "McFarland",
                      role = "aut",
                      email = "dmcfarla@stanford.edu"))
as necessary.
Maintainer: ‘Shuchismita Sarkar <ssarkar@bgsu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Shuchismita",
                      family = "Sarkar",
                      role = c("aut", "cre"),
                      email = "ssarkar@bgsu.edu"),
               person(given = "Volodymyr",
                      family = "Melnykov",
                      role = "aut"))
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?
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'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Li-Pang Chen <lchen723@nccu.edu.tw>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Li-Pang",
                    family = "Chen",
                    role = c("aut", "cre"),
                    email = "lchen723@nccu.edu.tw")
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: ‘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?
Package required but not available: ‘qtl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Tianshi Lu <tianshi.lu@utsouthwestern.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tianshi",
                    family = "Lu",
                    role = c("aut", "cre"),
                    email = "tianshi.lu@utsouthwestern.edu")
as necessary.
Maintainer: ‘Karline Soetaert <karline.soetaert@nioz.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Karline",
                      family = "Soetaert",
                      role = c("aut", "cre"),
                      email = "karline.soetaert@nioz.nl"),
               person(given = c("Julius", "Kipyegon"),
                      family = "Kones",
                      role = "aut",
                      email = "jkones@uonbi.ac.ke"),
               person(given = "Dick",
                      family = "van Oevelen",
                      role = "aut",
                      email = "dick.vanoevelen@nioz.nl"))
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: ‘visNetwork’

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 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: '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:
  'btergm', 'ergm', 'tergm', 'ergMargins', 'gam'

Package suggested but not available for checking: ‘statnet’

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

Packages suggested but not available for checking:
  'knitr', '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: ‘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?
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: ‘Frank W. Marrs <frank.marrs@colostate.edu>’

The Description field contains
  <arXiv:1701.05530>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
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: '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: ‘wTO’

Package suggested but not available for checking: ‘CoDiNA’

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?
Packages required but not available: 'DiagrammeR', 'htmlwidgets', '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:
  'colourpicker', 'DT', 'netgwas', 'plotly', 'visNetwork'

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.
Packages required but not available: 'rmarkdown', 'shinybusy', 'plotly'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Christian Brownlees <christian.brownlees@upf.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Christian",
                    family = "Brownlees",
                    role = c("aut", "cre"),
                    email = "christian.brownlees@upf.edu")
as necessary.
'library' or 'require' call not declared from: ‘MASS’
Maintainer: ‘Arash A. Amini <aaamini@ucla.edu>’

The Description field contains
  <doi:10.1214/16-AOS1457> Zhang and Amini (2020) <arXiv:2012.15047> Le
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', 'mixtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) spec_clust.Rd:33: Lost braces; missing escapes or markup?
    33 | A label vector of size n x 1 with elements in {1,2,...,K}
       |                                               ^
Running examples in ‘nett-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fast_cpl
> ### Title: CPL algorithm for community detection (fast)
> ### Aliases: fast_cpl
> ### Keywords: comm_detect
> 
> ### ** Examples
> 
> head(fast_cpl(igraph::as_adj(polblogs), 2), 50)
Error: Package "mixtools" needed for this function. Please install it.
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', 'spelling', 'vcr'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: has_codebook
> ### Title: Check if form has codebook
> ### Aliases: has_codebook
> 
> ### ** Examples
> 
> ## Don't show: 
> vcr::insert_example_cassette("has_codebook", package = "nettskjemar")
Error in loadNamespace(x) : there is no package called ‘vcr’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Load necessary libraries
  > library(nettskjemar)
  > library(testthat)
  > 
  > test_check("nettskjemar")
  Error in `source_dir()`:
  ! Failed to evaluate './helpers.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("nettskjemar")
    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 ./helpers.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: ‘fGarch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Minghui Wang <m.h.wang@live.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Minghui",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "m.h.wang@live.com"),
               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) rc.plot.ideogram.Rd:20: Lost braces; missing escapes or markup?
    20 |  \item{las}{numeric in {0,1,2,3}; the style of chromosome labels. 0, always parallel to the track [default]; 1, always horizontal; 2, always perpendicular to the track; 3, always vertical.}
       |                        ^
Package has ‘vignettes’ subdirectory 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: ‘Jong Hee Park <jongheepark@snu.ac.kr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Jong", "Hee"),
                      family = "Park",
                      role = c("aut", "cre"),
                      email = "jongheepark@snu.ac.kr"),
               person(given = "Yunkyu",
                      family = "Sohn",
                      role = "aut"))
as necessary.
Package required but not available: ‘qgraph’

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

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

Package suggested but not available for checking: ‘bootnet’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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?
checkRd: (-1) nodeLogic.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:46: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘map.png’ ‘maze.html’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Ian Laga <ilaga25@gmail.com>’

The Description field contains
  Niu, X (2021) <arXiv:2109.10204>, Zheng, T., Salganik, M. J., and
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: '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: ‘latentnet’

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

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

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

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

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

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?
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘plotly’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'roxygen2', '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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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 Buchsbaum <brad.buchsbaum@gmail.com>’

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

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: ‘Surya Tokdar <surya.tokdar@duke.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Surya",
                    family = "Tokdar",
                    role = c("aut", "cre"),
                    email = "surya.tokdar@duke.edu")
as necessary.

The Description field contains
  may be found at <arXiv:1911.04387>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘memisc’

Packages suggested but not available for checking:
  'BPST', 'ImageSCC', 'knitr', 'rmarkdown', 'roxygen2', 'Triangulation'

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: ‘ggpmisc’

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: ‘flipr’

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: ‘Saralees Nadarajah <Saralees.Nadarajah@manchester.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Saralees",
                      family = "Nadarajah",
                      role = c("aut", "cre"),
                      email = "saralees.nadarajah@manchester.ac.uk"),
               person(given = "Ricardo",
                      family = "Rocha",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(new.dist)
  > 
  > test_check("new.dist")
  Saving _problems/test_function-246.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 232 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_function.R:246:3'): functions returns a  vector with the expected size ──
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `expect_vector(dbwd(10, alpha = 2, sigma = 2), ptype = double(), size = 1)`: The package "vctrs" is required.
  Backtrace:
      ▆
   1. └─testthat::expect_vector(...) at test_function.R:246:3
   2.   └─rlang::check_installed("vctrs")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 232 ]
  Error:
  ! Test failures.
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ningning Xu <n.xu@lumc.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ningning",
                    family = "Xu",
                    role = c("aut", "cre"),
                    email = "n.xu@lumc.nl")
as necessary.

The Description field contains
  (2021) <arXiv:2001.01541> for detailed description.
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?
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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: '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', '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?
Maintainer: ‘Carlos Martinez <cmmm7031@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Dr", "Carlos", "Miguel", "Martinez"),
                      family = "Manrique",
                      role = "aut"),
               person(given = "Carlos",
                      family = "Martinez",
                      role = "cre",
                      email = "cmmm7031@gmail.com"))
as necessary.
Maintainer: ‘Obinna Obianom <idonshayo@gmail.com>’

The BugReports field in DESCRIPTION has
  https://github.com/oobianom/nextGenShinyApps
which should likely be
  https://github.com/oobianom/nextGenShinyApps/issues
instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'r2resize'

VignetteBuilder package required for checking but 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?
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.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', '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'

VignetteBuilder package required 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: ‘nflplotR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Aaron Robotham <aaron.robotham@uwa.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Aaron",
                    family = "Robotham",
                    role = c("aut", "cre"),
                    email = "aaron.robotham@uwa.edu.au")
as necessary.

The Description field contains
  Robotham & Howlett (2018) <arXiv:1805.09550>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
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: ‘htmlwidgets’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Chung-hong Chan <chainsawtiney@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Chung-hong",
                    family = "Chan",
                    role = c("aut", "cre"),
                    email = "chainsawtiney@gmail.com")
as necessary.
Maintainer: ‘John Hughes <drjphughesjr@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "John",
                      family = "Hughes",
                      role = c("aut", "cre"),
                      email = "drjphughesjr@gmail.com"),
               person(given = "Xiaohui",
                      family = "Cui",
                      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.

The Description field contains
  Bayesian spatial filtering model of Hughes (2017) <arXiv:1706.04651>.
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: ‘Randall Pruim <rpruim@calvin.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Randall",
                    family = "Pruim",
                    role = c("aut", "cre"),
                    email = "rpruim@calvin.edu")
as necessary.

The Description field contains
  http://www.cdc.gov/nchs/nhanes.htm for details.
Please enclose URLs in angle brackets (<...>).
checkRd: (-1) NHANES.Rd:278: Lost braces
   278 | \code{AgeFirstMarij}{Age participant first tried marijuana. Reported for participants aged 18 to 59 years.}
       |                     ^
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', '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:
  '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: ‘D. Lukke Sweet <dls229@zips.uakron.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("D.", "Lukke"),
                    family = "Sweet",
                    role = c("aut", "cre"),
                    email = "dls229@zips.uakron.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: ‘Ana C. Cebrian <acebrian@unizar.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Ana", "C."),
                    family = "Cebrian",
                    role = c("aut", "cre"),
                    email = "acebrian@unizar.es")
as necessary.
checkRd: (-1) graphresU.fun.Rd:72: 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', '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: ‘Giovanni Tramonti <giovanni.tramonti@ed.ac.uk>’

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

VignetteBuilder package required 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:
  'covr', 'hexSticker', 'knitr', 'lintr', 'rmarkdown', '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'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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) bootstrap_param_est.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootstrap_param_est.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootstrap_param_est.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_data.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_data.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_data.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Charles J. Geyer <geyer@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 = "geyer@umn.edu"),
               person(given = c("Charles", "J."),
                      family = "Geyer",
                      role = "cre",
                      email = "geyer@umn.edu"))
as necessary.
Maintainer: ‘Cai-qing YANG <yangcq_ivy@163.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.

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

Packages suggested but not available for checking:
  'rmarkdown', 'covr', '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’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘create_comparison.R’ ‘create_comparisons.Rd’
    ‘extract_group_metrics.R’ ‘extract_group_metrics.Rd’
    ‘extract_layman.R’ ‘extract_layman.Rd’ ‘extract_mu.R’ ‘extract_mu.Rd’
    ‘extract_niche_size.R’ ‘extract_overlap.R’ ‘extract_sigma.R’
    ‘extract_similarities.R’ ‘extract_similarities.Rd’ ‘niche_ellipse.R’
Package has ‘vignettes’ subdirectory 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 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/nieve.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Timothy Koscik <timothy-koscik@uiowa.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Timothy", "R."),
                      family = "Koscik",
                      role = c("aut", "cre", "cph")),
               person(given = "Timothy",
                      family = "Koscik",
                      role = "cre",
                      email = "timothy-koscik@uiowa.edu"))
as necessary.
Maintainer: ‘Max Hughes-Brandl <gordonmax@hotmail.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Max",
                    family = "Hughes-Brandl",
                    role = c("aut", "cre"),
                    email = "gordonmax@hotmail.de")
as necessary.
Maintainer: ‘Natalya Pya Arnqvist <nat.pya@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Natalya", "Pya"),
                      family = "Arnqvist",
                      role = c("aut", "cre"),
                      email = "nat.pya@gmail.com"),
               person(given = "Vassilly",
                      family = "Voinov",
                      role = "aut"),
               person(given = "Rashid",
                      family = "Makarov",
                      role = "aut"),
               person(given = "Yevgeniy",
                      family = "Voinov",
                      role = "aut"))
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?
Packages required but not available:
  'plotly', 'skimr', 'missMDA', 'networkD3', 'visNetwork'

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: ‘rcarbon’

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: '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
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: ‘David Pleydell <david.pleydell@inrae.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "David",
                    family = "Pleydell",
                    role = c("aut", "cre", "cph"),
                    email = "david.pleydell@inrae.fr",
                    comment = c("Package developer", ORCID = "0000-0002-6450-1475"))
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', 'tufte', 'spelling', 'covr', '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: ‘Lennart Johansson <l.johansson@umcg.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dirk",
                      family = "de Weerd",
                      role = "aut"),
               person(given = "Lennart",
                      family = "Johansson",
                      role = c("aut", "cre"),
                      email = "l.johansson@umcg.nl"))
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: ‘Yikai Wang <johnzon.wyk@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yikai",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "johnzon.wyk@gmail.com"),
               person(given = "Xiao",
                      family = "Wang",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  '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")
  > test_check("nisrarr")
  Loading required package: nisrarr
  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("nisrarr")
    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: ‘Douglas Bates <bates@stat.wisc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("original", "from", "National", "Institutes", "for"),
                      family = "Standards",
                      role = "aut"),
               person(given = c("Technology", "http://www.itl.nist.gov/div898/strd/nls/nls_main.shtml", "R", "port", "by", "Douglas"),
                      family = "Bates",
                      role = "aut",
                      email = "bates@stat.wisc.edu",
                      comment = "NIST"),
               person(given = "Douglas",
                      family = "Bates",
                      role = "cre",
                      email = "bates@stat.wisc.edu"))
as necessary.
Malformed Description field: should contain one or more complete sentences.
Maintainer: ‘Troy D. Hill <Hill.Troy@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Troy", "D."),
                      family = "Hill",
                      role = c("aut", "cre"),
                      email = "hill.troy@gmail.com"),
               person(given = c("Nathalie", "R."),
                      family = "Sommer",
                      role = "aut"),
               person(given = c("Caroline", "R."),
                      family = "Kanaskie",
                      role = "aut"),
               person(given = c("Emily", "A."),
                      family = "Santos",
                      role = "aut"),
               person(given = c("Autumn", "J."),
                      family = "Oczkowski",
                      role = "aut"))
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘CN_mass_data.Rd’:
    \keyword{data,}
    \keyword{isotopes,}
  File ‘allometry.Rd’:
    \keyword{data,}
  File ‘dea.Rd’:
    \keyword{data,}
    \keyword{denitrification,}
  File ‘stemHeights.Rd’:
    \keyword{NAPP,}
    \keyword{biomass,}
    \keyword{data,}
    \keyword{height,}

Found the following URLs which should use \doi (with the DOI name only):
  File ‘CN_mass_data.Rd’:
    https://doi.org/10.1016/j.dib.2018.09.133
    https://doi.org/10.1016/j.jembe.2018.07.006
  File ‘allometry.Rd’:
    https://doi.org/10.1016/j.dib.2018.09.133
    https://doi.org/10.1016/j.jembe.2018.07.006
  File ‘bCM.Rd’:
    https://doi.org/10.1002/ecy.1600
  File ‘dea.Rd’:
    https://doi.org/10.1016/j.dib.2018.09.133
    https://doi.org/10.1016/j.jembe.2018.07.006
  File ‘stemHeights.Rd’:
    https://doi.org/10.1016/j.dib.2018.09.133
    https://doi.org/10.1016/j.jembe.2018.07.006
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'usethis'

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:
    ‘get_model_params.R’ ‘level_from_quantiles.R’ ‘make_request.R’
    ‘nixtla_client_cross_validation.R’ ‘nixtla_client_detect_anomalies.R’
    ‘nixtla_client_forecast.R’ ‘nixtla_client_historic.R’
    ‘nixtla_client_plot.R’ ‘nixtla_validate_api_key.R’
    ‘validate_exogenous.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Xianyan Chen <xychen@uga.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xianyan",
                      family = "Chen",
                      role = c("aut", "cre"),
                      email = "xychen@uga.edu"),
               person(given = "Xiangrong",
                      family = "Yin",
                      role = "aut",
                      email = "yinxiangrong@uky.edu"))
as necessary.
Package required but not available: ‘MLInterfaces’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Berend Hasselman <bhh@xs4all.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Berend",
                    family = "Hasselman",
                    role = c("aut", "cre"),
                    email = "bhh@xs4all.nl")
as necessary.
Specified C++11: support will be removed soon
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: 'nlraa', 'knitr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Author field differs from that derived from Authors@R
  Author:    ‘José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), Johannes Ranke [ctb] (varConstProp()), R Core Team [aut, cre] (02zz1nj61)’
  Authors@R: ‘José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), Johannes Ranke [ctb] (varConstProp()), R Core Team [aut, cre] (ROR: <https://ror.org/02zz1nj61>)’
Running ‘Pwr1.R’ [1s/1s]
  Running ‘Pwr2.R’ [0s/1s]
  Running ‘logLik1.R’ [0s/1s]
  Running ‘missPat.R’ [0s/0s]
  Running ‘roxygen.R’ [0s/0s]
  Running ‘runScript.R’ [0s/0s]
  Running ‘simY.R’ [1s/1s]
Running the tests in ‘tests/roxygen.R’ failed.
Complete output:
  > library(roxygen2)
  Error in library(roxygen2) : there is no package called 'roxygen2'
  Execution halted
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nlmixr2', 'nlmixr2est', '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: 'devtools', 'xgxr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'knitr', 'nlmixr2est'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nlmixr2est’

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.
Packages required but not available: 'nlmixr2est', 'nlmixr2extra', 'xgxr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'nlmixr2est', 'nlmixr2extra', 'nlmixr2plot'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'flextable', 'nlmixr2est', 'nlmixr2extra', 'onbrand',
  'xpose.nlmixr2', 'yaml'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Carme Font <carme.font.moragon@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Carme",
                    family = "Font",
                    role = c("aut", "cre"),
                    email = "carme.font.moragon@gmail.com")
as necessary.
Maintainer: ‘Tianwei Yu<yutianwei@cuhk.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Tianwei",
                      family = "Yu",
                      role = c("aut", "cre"),
                      email = "yutianwei@cuhk.edu.cn"),
               person(given = "Haodong",
                      family = "Liu",
                      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?
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: ‘David Benkeser <benkeser@emory.edu>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘wine.Rd’:
    https://doi.org/10.1016/j.dss.2009.05.016
Package required but not available: ‘SuperLearner’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jin Liu <Veronica.Liu0206@gmail.com>’

The Description field contains
  <arXiv:2302.03237v2>.
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: ‘qdap’

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.
Packages required but not available: 'rms', 'Hmisc'

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?
Maintainer: ‘G. Grothendieck <ggrothendieck@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "G.",
                      family = "Grothendieck",
                      role = c("aut", "cre"),
                      email = "ggrothendieck@gmail.com"),
               person(given = c("R", "Core"),
                      family = "Team",
                      role = "aut",
                      comment = "nls"))
as necessary.
checkRd: (-1) anova.Rd:19: Lost braces
    19 |   Returns an object of class code{anova}.  These objects represent
       |                                  ^
Cannot process vignettes
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'nlraa'

VignetteBuilder package required 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: ‘Rafael Benitez <rabesua@uv.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mariano",
                      family = "Rodriguez-Arias",
                      role = "aut",
                      email = "arias@unex.es"),
               person(given = c("Juan", "Antonio"),
                      family = "Fernandez",
                      role = "aut",
                      email = "jfernandck@alumnos.unex.es"),
               person(given = "Javier",
                      family = "Cabello",
                      role = "aut",
                      email = "coco@unex.es"),
               person(given = "Rafael",
                      family = "Benitez",
                      role = c("aut", "cre"),
                      email = "rabesua@uv.es"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rticles'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', '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?
Cannot process vignettes
Packages suggested but not available for checking:
  'Hmisc', 'knitr', 'lintr', 'rmarkdown', 'TESS'

VignetteBuilder package required 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: ‘Oleh Komashko <oleg_komashko@ukr.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Oleh",
                    family = "Komashko",
                    role = c("aut", "cre"),
                    email = "oleg_komashko@ukr.net")
as necessary.
Package required but not available: ‘rlist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Burak Kuersad Guenhan <burakgunhan@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: 'INLA', 'knitr'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/nmaINLA.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?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nmarank.Rd: netmeta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Maintainer: ‘David Phillippo <david.phillippo@bristol.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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Suhai (Timothy) Liu <tim.liu@alumni.duke.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Suhai",
                      family = "Liu",
                      role = "aut",
                      comment = "Timothy"),
               person(given = "Suhai",
                      family = "Liu",
                      role = "cre",
                      email = "tim.liu@alumni.duke.edu",
                      comment = "Timothy"))
as necessary.
Packages suggested but not available for checking: 'devtools', 'knitr'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/NMF-vignette.Rnw’
   ‘inst/doc/heatmaps.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:
  '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: ‘Joseph Lipoff <josephlipoff@msn.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Joseph", "V."),
                      family = "Lipoff",
                      role = "aut"),
               person(given = "Will",
                      family = "Pauls",
                      role = "aut"),
               person(given = c("Kaylin", "C."),
                      family = "Dobbs",
                      role = "aut"),
               person(given = c("Jordan", "L."),
                      family = "Jensen",
                      role = "aut"),
               person(given = "Kevin",
                      family = "Woods",
                      role = "aut"),
               person(given = c("Evan", "T."),
                      family = "Johnson",
                      role = "aut"),
               person(given = c("Benjamin", "F."),
                      family = "Timson",
                      role = "aut"),
               person(given = c("Scott", "D.", "Zimmerman,and", "Paul"),
                      family = "Plummer",
                      role = "aut"),
               person(given = "Joseph",
                      family = "Lipoff",
                      role = "cre",
                      email = "josephlipoff@msn.com"))
as necessary.
Maintainer: ‘Kyun-Seop Bae <k@acr.kr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kyun-Seop",
                    family = "Bae",
                    role = c("aut", "cre"),
                    email = "k@acr.kr")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'keras', 'tensorflow', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Specified C++14: 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: '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
Maintainer: ‘Brian Ripley <Brian.Ripley@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.
Maintainer: ‘Anthony Christidis <anthony.christidis@stat.ubc.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Anthony",
                      family = "Christidis",
                      role = c("aut", "cre"),
                      email = "anthony.christidis@stat.ubc.ca"),
               person(given = "Stefan",
                      family = "Van Aelst",
                      role = "aut",
                      email = "stefan.vanaelst@kuleuven.be"),
               person(given = "Ruben",
                      family = "Zamar",
                      role = "aut",
                      email = "ruben@stat.ubc.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: ‘Baidya Nath Mandal <mandal.stat@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Baidya", "Nath"),
                      family = "Mandal",
                      role = c("aut", "cre"),
                      email = "mandal.stat@gmail.com"),
               person(given = "Jun",
                      family = "Ma",
                      role = "aut",
                      email = "jun.ma@mq.edu.au"))
as necessary.
Maintainer: ‘Chiu-Hsieh Hsu <pablo1639@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Di",
                      family = "Ran",
                      role = "aut"),
               person(given = "Chiu-Hsieh",
                      family = "Hsu",
                      role = c("aut", "cre"),
                      email = "pablo1639@gmail.com"),
               person(given = "Mandi",
                      family = "Yu",
                      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: ‘Elvan Ceyhan <elvanceyhan@gmail.com>’

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

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: ‘Roger Day <day01@pitt.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Roger",
                    family = "Day",
                    role = c("aut", "cre"),
                    email = "day01@pitt.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) ROCplots.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:40: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory 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: ‘Zhao Yang <yangz98@connect.hku.hk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Zhao",
                    family = "Yang",
                    role = c("aut", "cre"),
                    email = "yangz98@connect.hku.hk")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'scoringutils'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Yang Tian <tianyang1211@126.com>’

The Description field contains
  Grover, Jure Leskovec(2016),available at <arXiv:1607.00653>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘rlist’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Arnaud Le Rouzic <arnaud.le-rouzic@universite-paris-saclay.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Arnaud",
                      family = "Le Rouzic",
                      role = c("aut", "cre"),
                      email = "arnaud.le-rouzic@universite-paris-saclay.fr",
                      comment = c(ROR = "2007-2015")),
               person(given = c("Arne", "B."),
                      family = "Gjuvsland",
                      role = "aut",
                      comment = "2010"),
               person(given = "Olivier",
                      family = "Ariste",
                      role = "aut",
                      comment = "2010"))
as necessary.
checkRd: (-1) simulatePop.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:45: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) imp_int_an.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imp_int_an.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ndmodel.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ndmodel.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ndmodel.Rd:18: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Audrey Q. Fu <audreyqyfu@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Audrey", "Qiuyan"),
                      family = "Fu",
                      role = "aut"),
               person(given = "Lior",
                      family = "Pachter",
                      role = "aut"),
               person(given = c("Audrey", "Q."),
                      family = "Fu",
                      role = "cre",
                      email = "audreyqyfu@gmail.com"))
as necessary.
Maintainer: ‘Flavio Santi <flavio.santi@univr.it>’

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 ‘noisyCE2-package.Rd’:
    https://doi.org/10.1080/10618600.2016.1278003
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: ‘Valentin Kilian <valentin.kilian@ens-rennes.fr>’

The Description field contains
  <arXiv:2402.19021>.
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 in Depends/Imports which should probably only be in LinkingTo: ‘RcppArmadillo’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tabea Rebafka <tabea.rebafka@sorbonne-universite.fr>’

The Description field contains
  Roquain, F. Villers (2020) <arXiv:1907.10176>.
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?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘libr_called.R’ ‘libr_unused.R’ ‘libr_used.R’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', '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?
Package required but not available: ‘htmlwidgets’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Zhicheng Du<dgdzc@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhicheng",
                      family = "Du",
                      role = c("aut", "cre"),
                      email = "dgdzc@hotmail.com"),
               person(given = "Yuantao",
                      family = "Hao",
                      role = "aut"))
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘nomogramEx.Rd’:
    \keyword{nomogram, survival probability}
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jing Zhang<zj391120@163.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jing",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "zj391120@163.com"),
               person(given = "Zhi",
                      family = "Jin",
                      role = "aut"))
as necessary.
Packages required but not available: 'rms', 'do', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Kyun-Seop Bae <k@acr.kr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kyun-Seop",
                    family = "Bae",
                    role = c("aut", "cre"),
                    email = "k@acr.kr")
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?
Packages required but not available: 'rlist', '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.
Maintainer: ‘Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Christina",
                      family = "Heinze-Deml",
                      role = c("aut", "cre"),
                      email = "heinzedeml@stat.math.ethz.ch"),
               person(given = "Jonas",
                      family = "Peters",
                      role = "aut",
                      email = "jonas.peters@math.ku.dk"))
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
  <arXiv:1501.01332>, to nonlinear settings. For more details, see C.
  for Nonlinear Models', <arXiv:1706.08576>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Burak Guris <bguris@istanbul.edu.tr>’

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

VignetteBuilder package required 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 Astrand <magnus.astrand@astrazeneca.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Magnus",
                    family = "Astrand",
                    role = c("aut", "cre"),
                    email = "magnus.astrand@astrazeneca.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:
  'devtools', 'xgxr', '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: ‘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'

VignetteBuilder package required 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’

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: ‘D. Lukke Sweet <dlukkesweet@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("D.", "Lukke"),
                    family = "Sweet",
                    role = c("aut", "cre"),
                    email = "dlukkesweet@gmail.com")
as necessary.
Maintainer: ‘Luis Castro Martín <luiscastro193@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Luis", "Castro"),
                      family = "Martín",
                      role = c("aut", "cre"),
                      email = "luiscastro193@gmail.com"),
               person(given = c("Ramón", "Ferri"),
                      family = "García",
                      role = "aut",
                      email = "rferri@ugr.es"),
               person(given = c("María", "del", "Mar"),
                      family = "Rueda",
                      role = "aut",
                      email = "mrueda@ugr.es"))
as necessary.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘valliant_weights.Rd’:
    https://doi.org/10.1093/jssam/smz003
Maintainer: ‘Brian P. O'Connor  <brian.oconnor@ubc.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Brian", "P."),
                    family = "O'Connor",
                    role = c("aut", "cre"),
                    email = "brian.oconnor@ubc.ca")
as necessary.
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?
Package required but not available: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Angelo M. Mineo <angelo.mineo@unipa.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Angelo", "M."),
                    family = "Mineo",
                    role = c("aut", "cre"),
                    email = "angelo.mineo@unipa.it")
as necessary.
Maintainer: ‘Kevin Chang <k.chang@auckland.ac.nz>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Shan Gao <gao_shan@mail.nankai.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhenfeng",
                      family = "Wu",
                      role = "aut"),
               person(given = "Shan",
                      family = "Gao",
                      role = c("aut", "cre"),
                      email = "gao_shan@mail.nankai.edu.cn"))
as necessary.
Packages required but not available: 'plotly', 'badger', 'hexSticker'

Packages suggested but not available for checking:
  'knitr', 'learnr', '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: ‘Cecile Proust-Lima <cecile.proust-lima@inserm.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Cecile",
                      family = "Proust-Lima",
                      role = c("aut", "cre"),
                      email = "cecile.proust-lima@inserm.fr"),
               person(given = "Viviane",
                      family = "Philipps",
                      role = "aut"))
as necessary.
Maintainer: ‘John Fox <jfox@mcmaster.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Ported", "to", "R", "by", "Alvaro", "A.", "Novo.", "Original", "by", "Joseph", "L.", "Schafer"),
                      family = "<jls@stat.psu.edu>.",
                      role = "aut",
                      email = "jls@stat.psu.edu"),
               person(given = "John",
                      family = "Fox",
                      role = "cre",
                      email = "jfox@mcmaster.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: ‘Pierre Lafaye de Micheaux <lafaye@unsw.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Pierre",
                      family = "Duchesne",
                      role = "aut"),
               person(given = c("Pierre", "Lafaye"),
                      family = "de Micheaux",
                      role = c("aut", "cre"),
                      email = "lafaye@unsw.edu.au"))
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', 'ggtree', '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: ‘Hien D. Nguyen <h.nguyen7@uq.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Hien", "D."),
                    family = "Nguyen",
                    role = c("aut", "cre"),
                    email = "h.nguyen7@uq.edu.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?
Running ‘testthat.R’ [1s/1s]
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(notionapi)
  > 
  > test_check("notionapi")
  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("notionapi")
    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>`(`<S3: packageNotFoundError>`)
   17.   └─cli::cli_abort(...)
   18.     └─rlang::abort(...)
  Execution halted
Packages required but not available: 'DT', 'knitr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Mutua Kilai <kilaimutua@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mutua",
                      family = "Kilai",
                      role = c("aut", "cre"),
                      email = "kilaimutua@gmail.com"),
               person(given = "Gichuhi",
                      family = "Waititu",
                      role = "aut"),
               person(given = "Wanjoya",
                      family = "Kibira",
                      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?
Package required but not available: ‘NoviceDeveloperResources’

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: ‘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.
Maintainer: ‘Terry Therneau <terry.therneau@mayo.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Terry",
                    family = "Therneau",
                    role = c("aut", "cre"),
                    email = "terry.therneau@mayo.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: ‘Kerstin Rubarth <kerstin.rubarth@charite.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Frank",
                      family = "Konietschke",
                      role = c("aut", "cre")),
               person(given = "Kimihiro",
                      family = "Noguchi",
                      role = "ctr"),
               person(given = "Kerstin",
                      family = "Rubarth",
                      role = "cre",
                      email = "kerstin.rubarth@charite.de"))
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: ‘Frank Konietschke <frank.konietschke@charite.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Kimihiro",
                      family = "Noguchi",
                      role = "aut",
                      email = "noguchk@wwu.edu"),
               person(given = "Mahbub",
                      family = "Latif",
                      role = "aut",
                      email = "mlatif@isrt.ac.bd"),
               person(given = "Karthinathan",
                      family = "Thangavelu",
                      role = "aut"),
               person(given = "Frank",
                      family = "Konietschke",
                      role = c("aut", "cre"),
                      email = "frank.konietschke@charite.de"),
               person(given = c("Yulia", "R."),
                      family = "Gel",
                      role = "aut",
                      email = "yxg142030@utdallas.edu"),
               person(given = "Edgar",
                      family = "Brunner",
                      role = "aut",
                      email = "ebrunne1@gwdg.de"))
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', 'fGarch', 'mmints', 'npboottprm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Thibault Laurent <thibault.laurent@univ-tlse1.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Abdelaati",
                      family = "Daouia",
                      role = "aut",
                      email = "Abdelaati.Daouia@tse-fr.eu"),
               person(given = "Thibault",
                      family = "Laurent",
                      role = c("aut", "cre"),
                      email = "thibault.laurent@univ-tlse1.fr"),
               person(given = "Hohsuk",
                      family = "Noh",
                      role = "aut",
                      email = "word5810@gmail.com"))
as necessary.
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’
Package has ‘vignettes’ subdirectory 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', 'pinp', 'rmarkdown'

VignetteBuilder package required 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: ‘Ignacio López-de-Ullibarri <ignacio.lopezdeullibarri@udc.es>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘beran.Rd’:
    https://doi.org/10.1093/biostatistics/kxx034
  File ‘berancv.Rd’:
    https://doi.org/10.1177/1471082X0700700404
    https://doi.org/10.1093/biostatistics/kxx034
  File ‘hpilot.Rd’:
    https://doi.org/10.1080/10485259308832566
    https://doi.org/10.1023/A:1014644700806
    https://doi.org/10.1016/j.csda.2016.08.002
    https://doi.org/10.1007/s11749-016-0515-1
  File ‘latency.Rd’:
    https://doi.org/10.1007/s11749-016-0515-1
  File ‘latencyhboot.Rd’:
    https://doi.org/10.1023/A:1014644700806
    https://doi.org/10.1007/s11749-016-0515-1
  File ‘npcure-package.Rd’:
    https://doi.org/10.1016/j.csda.2016.08.002
    https://doi.org/10.1007/s11749-016-0515-1
  File ‘probcure.Rd’:
    https://doi.org/10.1016/j.csda.2016.08.002
    https://doi.org/10.1002/cjs.11197
  File ‘probcurehboot.Rd’:
    https://doi.org/10.1023/A:1014644700806
    https://doi.org/10.1016/j.csda.2016.08.002
  File ‘testmz.Rd’:
    https://doi.org/10.1093/biomet/79.4.731
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Dimitrios Bagkavos <dimitrios.bagkavos@gmail.com>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘DefVarBandRule.Rd’:
    http://dx.doi.org/10.1080/03610920802364088
  File ‘DiscHazRateAuxFunctions.Rd’:
    https://doi.org/10.1007/BF00128979
  File ‘TransHazRateEst.Rd’:
    http://dx.doi.org/10.1080/10485250802440184
  File ‘TutzPritscher.Rd’:
    https://doi.org/10.1007/BF00128979
  File ‘VarBandHazEst.Rd’:
    http://dx.doi.org/10.1080/03610920802364088
  File ‘WeibHazFunctionals.Rd’:
    http://dx.doi.org/10.1080/03610920802364088
checkRd: (-1) DiscHazRateAuxFunctions.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiscHazRateAuxFunctions.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiscHazRateAuxFunctions.Rd:48: Lost braces in \itemize; meant \describe ?
Maintainer: ‘Huan Cheng <hcheng1118@hotmail.com>’

The Description field contains
  Cheng and He (2021) <arXiv:2110.03833>. The references for sample size
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Robin Ristl <robin.ristl@meduniwien.ac.at>’

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', '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: ‘Jos Feys <jos.feys@faber.kuleuven.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jos",
                    family = "Feys",
                    role = c("aut", "cre"),
                    email = "jos.feys@faber.kuleuven.be")
as necessary.
Maintainer: ‘Frank Farach <frank.farach@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:
  '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'

VignetteBuilder package required 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: ‘Daniel E. Weeks <weeks@pitt.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Robert", "V"),
                      family = "Baron",
                      role = "aut",
                      email = "rvb5@pitt.edu"),
               person(given = "Nandita",
                      family = "Mukhopadhyay",
                      role = "aut"),
               person(given = "Xinyu",
                      family = "Tang",
                      role = "aut"),
               person(given = c("Daniel", "E."),
                      family = "Weeks",
                      role = c("aut", "cre"),
                      email = "weeks@pitt.edu"))
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/nplr.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: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Xin Tian <tianxtt@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xin",
                      family = "Tian",
                      role = c("aut", "cre"),
                      email = "tianxtt@gmail.com"),
               person(given = "Colin",
                      family = "Wu",
                      role = "aut"))
as necessary.
Maintainer: ‘Chung-Hsing Chen <chchen@nhri.org.tw>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chung-Hsing",
                      family = "Chen",
                      role = c("aut", "cre"),
                      email = "chchen@nhri.org.tw"),
               person(given = "I-Shou",
                      family = "Chang",
                      role = "aut"),
               person(given = c("Chao", "A."),
                      family = "Hsiung",
                      role = "aut"))
as necessary.
Maintainer: ‘Jochen Einbeck <jochen.einbeck@durham.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jochen",
                      family = "Einbeck",
                      role = c("aut", "cre"),
                      email = "jochen.einbeck@durham.ac.uk"),
               person(given = "Ross",
                      family = "Darnell",
                      role = "aut"),
               person(given = "John",
                      family = "Hinde",
                      role = "aut"))
as necessary.
Maintainer: ‘Scott Powers <saberpowers@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Scott",
                      family = "Powers",
                      role = c("aut", "cre"),
                      email = "saberpowers@gmail.com"),
               person(given = "Trevor",
                      family = "Hastie",
                      role = "aut"),
               person(given = "Robert",
                      family = "Tibshirani",
                      role = "aut"))
as necessary.
Maintainer: ‘Bulent Altunkaynak <bulenta@gazi.edu.tr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Bulent",
                      family = "Altunkaynak",
                      role = c("aut", "cre"),
                      email = "bulenta@gazi.edu.tr"),
               person(given = "Hamza",
                      family = "Gamgam",
                      role = "aut"))
as necessary.
Maintainer: ‘David Allingham <David.Allingham@newcastle.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "David",
                      family = "Allingham",
                      role = c("aut", "cre"),
                      email = "david.allingham@newcastle.edu.au"),
               person(given = "D.J.",
                      family = "Best",
                      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.
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
'::' or ':::' import not declared from: ‘crs’
'library' or 'require' call not declared from: ‘crs’
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'bookdown', 'rmarkdown'

VignetteBuilder package required 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: ‘Nathaniel E. Helwig <helwig@umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Nathaniel", "E."),
                    family = "Helwig",
                    role = c("aut", "cre"),
                    email = "helwig@umn.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?
Maintainer: ‘Oleg Badunenko <oleg.badunenko@brunel.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Oleg",
                      family = "Badunenko",
                      role = c("aut", "cre"),
                      email = "oleg.badunenko@brunel.ac.uk"),
               person(given = "Pavlo",
                      family = "Mozharovskyi",
                      role = "aut"),
               person(given = "Yaryna",
                      family = "Kolomiytseva",
                      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: ‘Yong Wang <yongwang@auckland.ac.nz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yong",
                    family = "Wang",
                    role = c("aut", "cre"),
                    email = "yongwang@auckland.ac.nz")
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: ‘Nathaniel E. Helwig <helwig@umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Nathaniel", "E."),
                    family = "Helwig",
                    role = c("aut", "cre"),
                    email = "helwig@umn.edu")
as necessary.
checkRd: (-1) np.reg.test.Rd:148: Lost braces
   148 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
checkRd: (-1) nptest-package.Rd:73: Lost braces
    73 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
Maintainer: ‘Gordon J. Ross <gordon.ross@ed.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Gordon", "J."),
                    family = "Ross",
                    role = c("aut", "cre"),
                    email = "gordon.ross@ed.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.

The Description field contains
  Segmentation" <arxiv:2107.01742>. This uses a version of Wild Binary
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: ‘covr’

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.
Maintainer: ‘Maya B. Mathur <mmathur@stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Maya", "B."),
                      family = "Mathur",
                      role = c("aut", "cre"),
                      email = "mmathur@stanford.edu"),
               person(given = c("Tyler", "J."),
                      family = "VanderWeele",
                      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: ‘Eisuke Inoue <eisuke.inoue@marianna-u.ac.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Eisuke",
                    family = "Inoue",
                    role = c("aut", "cre"),
                    email = "eisuke.inoue@marianna-u.ac.jp")
as necessary.
Maintainer: ‘Benjamin Groebe <ben.groebe@gmail.com>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘mde.arfima.Rd’:
    https://doi.org/10.1111/j.1368-423X.2007.00202.x
  File ‘mle.arfima.Rd’:
    https://doi.org/10.1111/j.2517-6161.1995.tb02054.x
Maintainer: ‘Ming-Chang (Alan) Lee <alan9956@ydu.edu.tw>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ching-Shih",
                      family = "Tsou",
                      role = "aut",
                      email = "cstsou@mail.ntcb.edu.tw",
                      comment = "Vince"),
               person(given = "Ming-Chang",
                      family = "Lee",
                      role = "cre",
                      email = "alan9956@ydu.edu.tw",
                      comment = "Alan"))
as necessary.
Maintainer: ‘Artem Shramko <art.shramko@gmail.com>’

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

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘nsga3-package.Rd’:
    \keyword{algorithm,}
    \keyword{nsga3,}
    \keyword{omptimisation,}
    \keyword{optimisation,}
    \keyword{preprocessing,}
    \keyword{selection,}
    \keyword{wrapper,}
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Sonia Perez Fernandez <uo217889@uniovi.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Sonia", "Perez"),
                    family = "Fernandez",
                    role = c("aut", "cre"),
                    email = "uo217889@uniovi.es")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools', '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(NSR)
  > 
  > 
  > test_check("NSR")
  Error in `source_dir()`:
  ! Failed to evaluate './setup-nsr.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("NSR")
    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-nsr.R:12:1
   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?
Maintainer: ‘Daliang Ning <ningdaliang@ou.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Daliang",
                    family = "Ning",
                    role = c("aut", "cre"),
                    email = "ningdaliang@ou.edu")
as necessary.
Package required but not available: ‘iCAMP’

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) MSM.fit.Rd:21: Lost braces
    21 | \code{MSM.fit} returns an object of class code{MSM.lm} or \code{MSM.glm}, depending on the input model.
       |                                               ^
checkRd: (-1) SMC.Smooth.Rd:25: Lost braces; missing escapes or markup?
    25 | observation at current time step. It should return {xx} (the samples xt) and
       |                                                    ^
checkRd: (-1) SMC.Smooth.Rd:26: Lost braces; missing escapes or markup?
    26 | {logww} (their corresponding log weight).}
       | ^
Maintainer: ‘Volker Schmid <volker.schmid@lmu.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.
Packages required but not available: 'EBImage', 'bioimagetools'

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: 'DT', '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
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: 'ggtree', 'scistreer'

Package suggested but not available for checking: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Author field differs from that derived from Authors@R
  Author:    ‘Chris Hartgerink [rev] (<https://orcid.org/0000-0003-1050-6809>), Ulysse Boucherie [ctb] (https://www.linkedin.com/in/ulysse-boucherie-7a3b2b111/), Joshua W. Lambert [ctb] (<https://orcid.org/0000-0001-5218-3046>), Karim Mané [ctb] (<https://orcid.org/0000-0002-9892-2999>), Hugo Gruson [aut] (<https://orcid.org/0000-0002-4094-1476>), Bankole Ahadzie [aut, cre], London School of Hygiene and Tropical Medicine, LSHTM [cph] (00a0jsq62)’
  Authors@R: ‘Chris Hartgerink [rev] (ORCID: <https://orcid.org/0000-0003-1050-6809>), Ulysse Boucherie [ctb] (https://www.linkedin.com/in/ulysse-boucherie-7a3b2b111/), Joshua W. Lambert [ctb] (ORCID: <https://orcid.org/0000-0001-5218-3046>), Karim Mané [ctb] (ORCID: <https://orcid.org/0000-0002-9892-2999>), Hugo Gruson [aut] (ORCID: <https://orcid.org/0000-0002-4094-1476>), Bankole Ahadzie [aut, cre], London School of Hygiene and Tropical Medicine, LSHTM [cph] (ROR: <https://ror.org/00a0jsq62>)’
Maintainer: ‘Maarten Kruijver <maarten.kruijver@esr.cri.nz>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Packages required but not available: 'pedtools', 'ribd'

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.
Problems with news in ‘NEWS.md’:
No news entries found.
Maintainer: ‘Paul Gilbert <pgilbert.ttv9z@ncf.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Paul",
                      family = "Gilbert",
                      role = c("aut", "cre"),
                      email = "pgilbert.ttv9z@ncf.ca"),
               person(given = "Ravi",
                      family = "Varadhan",
                      role = "aut"))
as necessary.
Packages required but not available: 'gam', 'reactable', 'reactablefmtr'

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

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

Depends: includes the non-default packages:
  'Cubist', 'Metrics', 'arm', 'brnn', 'broom', 'car', 'caret',
  'corrplot', 'doParallel', 'dplyr', 'e1071', 'earth', 'gam', 'gbm',
  'ggplot2', 'glmnet', 'gridExtra', 'ipred', 'leaps', 'nnet', 'olsrr',
  'parallel', 'pls', 'purrr', 'randomForest', 'reactable',
  'reactablefmtr', 'readr', 'rpart', 'tidyr', 'tree', 'xgboost'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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?
Maintainer: ‘Tyler Rinker <tyler.rinker@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Zhicheng Du<dgdzc@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhicheng",
                      family = "Du",
                      role = c("aut", "cre"),
                      email = "dgdzc@hotmail.com"),
               person(given = "Yuantao",
                      family = "Hao",
                      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: ‘Moritz Hennicke <AAoritz@posteo.de>’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) cross_track_intersection.Rd:32: height/width attributes should be in pixels
checkRd: (-1) xyz2R.Rd:31: Lost braces
    31 |    \item Finally, code{T} is rotated an angle \code{z} about its NEWEST z-axis.
       |                       ^
Package has ‘vignettes’ subdirectory 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: ‘Finnbar Lee <lee.finnbar@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 required but not available: 'gghalves', 'smacof'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'visNetwork', 'outbreaker2'

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', 'outbreaker2', 'mixtree', 'epicontacts'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘o2ools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_accuracy
> ### Title: Calculate the accuracy of outbreak reconstruction
> ### Aliases: get_accuracy
> 
> ### ** Examples
> 
> true_tree <- data.frame(from = as.character(outbreaker2::fake_outbreak$ances), to = linelist$id)
Error in loadNamespace(x) : there is no package called ‘outbreaker2’
Calls: data.frame ... 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?
Maintainer: ‘Jason Waddell <jason.waddell@openanalytics.eu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jason",
                    family = "Waddell",
                    role = c("aut", "cre"),
                    email = "jason.waddell@openanalytics.eu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: '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: ‘Jason Waddell <jason.waddell@openanalytics.eu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jason",
                      family = "Waddell",
                      role = c("aut", "cre"),
                      email = "jason.waddell@openanalytics.eu"),
               person(given = "Willem",
                      family = "Ligtenberg",
                      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: ‘Robin K. S. Hankin <hankin.robin@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jonathan",
                      family = "Rougier",
                      role = "aut",
                      email = "j.c.rougier@bristol.ac.uk"),
               person(given = c("Robin", "K.", "S."),
                      family = "Hankin",
                      role = "cre",
                      email = "hankin.robin@gmail.com"))
as necessary.
Maintainer: ‘Marek Hlavac <mhlavac@alumni.princeton.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Marek",
                    family = "Hlavac",
                    role = c("aut", "cre"),
                    email = "mhlavac@alumni.princeton.edu")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Philip Stubbings <phil@parasec.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Philip",
                    family = "Stubbings",
                    role = c("aut", "cre"),
                    email = "phil@parasec.net")
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?
Maintainer: ‘Alejandro Ordonez <ordonezjosealejandro@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alejandro",
                      family = "Ordonez",
                      role = c("aut", "cre"),
                      email = "ordonezjosealejandro@gmail.com"),
               person(given = c("Marcos", "O."),
                      family = "Prates",
                      role = "aut"),
               person(given = c("Larissa", "A."),
                      family = "Matos",
                      role = "aut"),
               person(given = c("Victor", "H."),
                      family = "Lachos.",
                      role = "aut"))
as necessary.

The Description field contains
  Details can be found in Ordonez et al. (2020) <arXiv:2004.04341>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘modeest’

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', '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?
Maintainer: ‘Michael Lawrence <michafla@gene.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Michael",
                      family = "Lawrence",
                      role = c("aut", "cre"),
                      email = "michafla@gene.com"),
               person(given = "Tengfei",
                      family = "Yin",
                      role = "aut"))
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: ‘pec’

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: ‘John Snyder <jcs8v6@mail.missouri.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dan",
                      family = "Zheng",
                      role = "aut"),
               person(given = "John",
                      family = "Snyder",
                      role = "cre",
                      email = "jcs8v6@mail.missouri.edu"))
as necessary.
checkRd: (-1) OBMb.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
Maintainer: ‘Paul R. Hibbing <paulhibbing@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 package required 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 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.
Package required but not available: ‘leaflet’

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

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: ‘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.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'devtools', 'shinytest2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(occupationMeasurement)
  > 
  > # Limit number of threads used by data.table
  > # More info here: https://github.com/Rdatatable/data.table/issues/5658
  > data.table::setDTthreads(1)
  > 
  > test_check("occupationMeasurement")
  
  Attaching package: 'data.table'
  
  The following object is masked from 'package:base':
  
      %notin%
  
  Error in `source_dir()`:
  ! Failed to evaluate './setup.R'.
  Caused by error in `loadNamespace()`:
  ! there is no package called 'shinytest2'
  Backtrace:
       ▆
    1. ├─testthat::test_check("occupationMeasurement")
    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::suppressWarnings(shinytest2::load_app_env()) at ./setup.R:8:1
   15. │                         └─base::withCallingHandlers(...)
   16. ├─base::loadNamespace(x)
   17. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   18. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
   19. │ │   └─base (local) doWithOneRestart(return(expr), restart)
   20. │ └─base::stop(cond)
   21. └─testthat (local) `<fn>`(`<S3: packageNotFoundError>`)
   22.   └─cli::cli_abort(...)
   23.     └─rlang::abort(...)
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yudong Chen <yudong.chen@statslab.cam.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yudong",
                      family = "Chen",
                      role = c("aut", "cre"),
                      email = "yudong.chen@statslab.cam.ac.uk"),
               person(given = "Tengyao",
                      family = "Wang",
                      role = "aut"),
               person(given = c("Richard", "J."),
                      family = "Samworth",
                      role = "aut"))
as necessary.

The Description field contains
  <arxiv:2003.03668> for online detection of sudden mean changes in a
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) ChangepointDetector.Rd:93: Lost braces; missing escapes or markup?
    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                               ^
checkRd: (-1) ChangepointDetector.Rd:93: Lost braces; missing escapes or markup?
    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                                         ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |        ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |                  ^
Package required but not available: ‘DT’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'shinytest', '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:
  'DT', 'leaflet', 'leaflet.extras', '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: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plot3Drgl', 'rgl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Luke Miller <contact@lukemiller.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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'bookdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Andrea Pagotto <ajpagotto@gmail.com>’

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

The Description field contains
  and MacKay (2007) <arXiv:0710.3742> for univariate or multivariate
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) onlineCPD.Rd:35: Lost braces
    35 |  function(x, lambda){const_hazard(x, lambda=100)}
       |                     ^
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.
Package required but not available: ‘usethis’

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: ‘DT’

Packages suggested but not available for checking:
  'keyring', '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:
    ‘octopus_api.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:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) dbConnect-OdbcDriver-method.Rd:137: 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: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Sevvandi Kandanaarachchi <sevvandik@gmail.com>’

The Description field contains
  anomalies (Kandanaarachchi, Hyndman 2022) <arXiv:2210.07407>.
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:
  'DDoutlier', 'knitr', 'rmarkdown'

VignetteBuilder package required 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 Blume <marco.blume@pinnaclesports.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Marco",
                      family = "Blume",
                      role = c("aut", "cre"),
                      email = "marco.blume@pinnaclesports.com"),
               person(given = "Sascha",
                      family = "Thomsen",
                      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?
Package required but not available: ‘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.
Cannot process vignettes
Packages suggested but not available for checking:
  'gam', 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Zeynel Cebeci <zcebeci@cukurova.edu.tr>’

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', '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: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Muntashir-Al-Arefin <muntashir.a2i@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(family = "Muntashir-Al-Arefin",
                    role = c("aut", "cre"),
                    email = "muntashir.a2i@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?
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: '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?
Package required but not available: ‘DiagrammeR’

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: ‘hexSticker’

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?
Maintainer: ‘Christopher Mann <cmann3@unl.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Christopher",
                    family = "Mann",
                    role = c("aut", "cre"),
                    email = "cmann3@unl.edu")
as necessary.
Maintainer: ‘Christopher Mann <cmann3@unl.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Christopher",
                    family = "Mann",
                    role = c("aut", "cre"),
                    email = "cmann3@unl.edu")
as necessary.
Packages required but not available: 'knitr', 'rmarkdown', 'yaml'

Packages suggested but not available for checking: 'bookdown', 'flextable'

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?
Maintainer: ‘Jiebiao Wang <randel.wang@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jiebiao",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "randel.wang@gmail.com"),
               person(given = "Qianying",
                      family = "Liu",
                      role = "aut"),
               person(given = c("Lin", "S."),
                      family = "Chen",
                      role = "aut"))
as necessary.
Packages required but not available:
  'ggExtra', 'rmarkdown', 'tmap', 'bookdown', 'leaflet'

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.
Package required but not available: ‘DT’

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

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:
  'CirceR', 'DatabaseConnector', 'gt', 'kableExtra', 'quarto',
  'reactable', 'rmarkdown'

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

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:
  'DatabaseConnector', 'devtools', 'ResultModelManager'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Hai-Tang Chiou <htchiou1@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hai-Tang",
                      family = "Chiou",
                      role = c("aut", "cre"),
                      email = "htchiou1@gmail.com"),
               person(given = "Ching-Kang",
                      family = "Ing",
                      role = "aut"),
               person(given = c("Tze", "Leung"),
                      family = "Lai",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'mapview', '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:
    ‘set_parameters.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘warbleR’

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: ‘Deducer’

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: ‘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
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: ‘rmarkdown’

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

VignetteBuilder packages required for checking but not installed:
  'kableExtra', 'knitr'
Package has ‘vignettes’ subdirectory 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: ‘Matheus H. J. Saldanha <mhjsaldanha@gmail.com>’

The BugReports field in DESCRIPTION has
  https://github.com/matheushjs/ollggamma
which should likely be
  https://github.com/matheushjs/ollggamma/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:
  '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:
    ‘OLStraj.R’ ‘cbc_lm.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'config', 'golem', 'shinybusy'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Yujiao Mai <yujiaomai@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yujiao",
                      family = "Mai",
                      role = c("cre", "aut"),
                      email = "yujiaomai@gmail.com"),
               person(given = c("Deo", "Kumar"),
                      family = "Srivastava",
                      role = "aut"),
               person(given = c("Kevin", "R."),
                      family = "Krull",
                      role = "aut"))
as necessary.
Maintainer: ‘Hae Kyung Im <haky@uchicago.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Hae", "Kyung"),
                      family = "Im",
                      role = c("aut", "cre"),
                      email = "haky@uchicago.edu"),
               person(given = c("Heather", "E."),
                      family = "Wheeler",
                      role = "aut"),
               person(given = c("Keston", "Aquino"),
                      family = "Michaels",
                      role = "aut"),
               person(given = "Vassily",
                      family = "Trubetskoy",
                      role = "aut"))
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘krigr_cross_validation.Rd’:
    \keyword{prediction,}
  File ‘make_PCs_irlba.Rd’:
    \keyword{PCA,}
    \keyword{covariate,}
  File ‘make_PCs_svd.Rd’:
    \keyword{PCA,}
    \keyword{covariate,}
Error(s) in re-building vignettes:
  ...
--- re-building ‘OmicNavigatorAPI.Rnw’ using Sweave
OmicNavigator R package version: 1.16.0
The app is not installed. Install it with installApp()
Installing study "ABC" in /tmp/RtmprbGkvM/file1606a264232c7b
Exporting study "ABC" as an R package
Note: No maintainer email was specified. Using the placeholder: Unknown <unknown@unknown>
Calculating pairwise overlaps. This may take a while...
Exported study to /tmp/RtmprbGkvM/ONstudyABC

Error: processing vignette 'OmicNavigatorAPI.Rnw' failed with diagnostics:
 chunk 3 (label = test-data) 
Error in utils::install.packages(tmpPkgDir, lib = library, repos = NULL,  : 
  (converted from warning) installation of package ‘/tmp/RtmprbGkvM/ONstudyABC’ had non-zero exit status

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

--- re-building ‘OmicNavigatorUsersGuide.Rnw’ using Sweave
OmicNavigator R package version: 1.16.0
The app is not installed. Install it with installApp()
Installing study "vignetteExample" in /tmp/RtmpXdH5Gq/file160b625f817717
Exporting study "vignetteExample" as an R package
Note: No maintainer email was specified. Using the placeholder: Unknown <unknown@unknown>
Calculating pairwise overlaps. This may take a while...
Exported study to /tmp/RtmpXdH5Gq/ONstudyvignetteExample
Success!
Returning "default" features for modelID "modelThatDoesntExistYet"
--- finished re-building ‘OmicNavigatorUsersGuide.Rnw’

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

Error: Vignette re-building failed.
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'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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'

VignetteBuilder package required 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'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Fumihiko Takeuchi <fumihiko@takeuchi.name>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘ctassoc.Rd’:
    https://doi.org/10.1080/03610927608827353
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Patrick O'Keefe <okeefep@ohsu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Patrick",
                    family = "O'Keefe",
                    role = c("aut", "cre"),
                    email = "okeefep@ohsu.edu")
as necessary.
Maintainer: ‘Qi Yan <qiy17@pitt.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Qi",
                    family = "Yan",
                    role = c("aut", "cre"),
                    email = "qiy17@pitt.edu")
as necessary.
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:
  'bookdown', 'gt', 'knitr', 'rmarkdown', 'visOmopResults'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'sparklyr', 'DatabaseConnector'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'flextable', 'gt', 'knitr', 'OmopViewer', 'sortable',
  'reactable', 'rmarkdown', 'covr', 'visOmopResults', '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?
Packages required but not available:
  'DT', 'gt', 'usethis', 'visOmopResults', 'yaml'

Packages suggested but not available for checking:
  'devtools', 'DiagrammeR', 'htmlwidgets', 'knitr', 'plotly',
  'reactable', 'rmarkdown', 'rsconnect', 'shinyTree', 'sortable'

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’

Packages suggested but not available for checking: 'covr', '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: ‘keras3’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) dot-discoveryRequest.Rd:15-16: Lost braces
    15 | \item{service}{One of {"locations", "deployments", "deviceCategories", "devices",
       |                       ^
checkRd: (-1) dot-discoveryRequest.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{method}{One of {"get", "getTree"}}
       |                      ^
checkRd: (-1) dot-saveAsFile.Rd:19: Lost braces; missing escapes or markup?
    19 | (numeric) Result code from {0: done, -1: error, -2: fileExists}
       |                            ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'cmdstanr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘survminer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', '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?
Maintainer: ‘Dadong Zhang <dadong.zhang.shared@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Dadong",
                    family = "Zhang",
                    role = c("aut", "cre"),
                    email = "dadong.zhang.shared@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: ‘Aniko Szabo <aszabo@mcw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Aniko",
                      family = "Szabo",
                      role = c("aut", "cre"),
                      email = "aszabo@mcw.edu"),
               person(given = "Lisa",
                      family = "Pappas",
                      role = "aut"))
as necessary.
checkRd: (-1) oncotree.fit.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘validate’

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

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?
Maintainer: ‘Eric E. Graves <gravcon5@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Eric", "E."),
                    family = "Graves",
                    role = c("aut", "cre"),
                    email = "gravcon5@gmail.com")
as necessary.
Packages required but not available: 'plotly', 'smacof', '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?
Maintainer: ‘Holger von Jouanne-Diedrich <holger.jouanne-diedrich@h-ab.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Holger",
                    family = "von Jouanne-Diedrich",
                    role = c("aut", "cre"),
                    email = "holger.jouanne-diedrich@h-ab.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?
Package required but not available: ‘survminer’

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:
  'covr', 'devtools', 'doctest', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Jun Li <jli49@kent.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Lingjun",
                      family = "Li",
                      role = "aut"),
               person(given = "Jun",
                      family = "Li",
                      role = c("aut", "cre"),
                      email = "jli49@kent.edu"))
as necessary.

The Description field contains
  <arXiv:1911.07762>.
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', '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: ‘David Degras <ddegrasv@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "David",
                      family = "Degras",
                      role = c("aut", "cre"),
                      email = "ddegrasv@gmail.com"),
               person(given = "Herve",
                      family = "Cardot",
                      role = "ctb"))
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?
Package required but not available: ‘gt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Sergei Tarasov <sergei.tarasov@helsinki.fi>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sergei",
                    family = "Tarasov",
                    role = c("aut", "cre"),
                    email = "sergei.tarasov@helsinki.fi")
as necessary.
Packages required but not available: 'visNetwork', 'sunburstR', 'usethis'

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: ‘rdflib’

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: ‘Daniel Greene <dg333@cam.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Daniel",
                    family = "Greene",
                    role = c("aut", "cre"),
                    email = "dg333@cam.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?
Maintainer: ‘Daniel Greene <dg333@cam.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Daniel",
                    family = "Greene",
                    role = c("aut", "cre"),
                    email = "dg333@cam.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?
Maintainer: ‘Daniel Greene <dg333@cam.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Daniel",
                    family = "Greene",
                    role = c("aut", "cre"),
                    email = "dg333@cam.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?
Packages required but not available: 'seededlda', 'quanteda'

Packages suggested but not available for checking:
  'keyATM', 'stm', 'covr', 'knitr', 'rmarkdown', 'quanteda.textmodels',
  'shinytest2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Stijn Hawinkel <stijn.hawinkel@psb.ugent.be>’

The BugReports field in DESCRIPTION has
  https://github.com/sthawinke/oosse
which should likely be
  https://github.com/sthawinke/oosse/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: ‘Philipp Külpmann <philipp@kuelpmann.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', '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', 'knitrBootstrap', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Jorn Lotsch <j.lotsch@em.uni-frankfurt.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jorn",
                      family = "Lotsch",
                      role = c("aut", "cre"),
                      email = "j.lotsch@em.uni-frankfurt.de",
                      comment = c(ORCID = "0000-0002-5818-6958")),
               person(given = "Sebastian",
                      family = "Malkusch",
                      role = "aut",
                      comment = c(ORCID = "0000-0001-6766-140X")),
               person(given = "Alfred",
                      family = "Ultsch",
                      role = "aut",
                      comment = c(ORCID = "0000-0002-7845-3283")))
as necessary.
Maintainer: ‘Albrecht Gebhardt <albrecht.gebhardt@aau.at>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Petr",
                      family = "Simecek",
                      role = "aut",
                      email = "simecek@gmail.com"),
               person(given = "Juergen",
                      family = "Pilz",
                      role = "aut",
                      email = "juergen.pilz@aau.at"),
               person(given = "Mingui",
                      family = "Wang",
                      role = "aut",
                      email = "mail.mwang@gmail.com"),
               person(given = "Albrecht",
                      family = "Gebhardt.",
                      role = "aut",
                      email = "albrecht.gebhardt@aau.at"),
               person(given = "Albrecht",
                      family = "Gebhardt",
                      role = "cre",
                      email = "albrecht.gebhardt@aau.at"))
as necessary.
Package required but not available: ‘leaflet’

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

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:
  'lintr', '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: ‘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 = "Aaron",
                      family = "Puchert",
                      role = "aut",
                      email = "aaronpuchert@alice-dsl.net"))
as necessary.
License stub is invalid DCF.
File ‘OpenCL/libs/R_OpenCL.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.
Running ‘buffer.R’ [0s/1s]
  Comparing ‘buffer.Rout’ to ‘buffer.Rout.save’ ...5,10d4
< > 
< > if (!length(oclPlatforms())) {
< +     cat("== Cannot run tests as there is no platform")
< +     q("no")
< + }
< > 
  Running ‘kernel.R’ [2s/3s]
  Comparing ‘kernel.Rout’ to ‘kernel.Rout.save’ ...5,10d4
< > 
< > if (!length(oclPlatforms())) {
< +     cat("== Cannot run tests as there is no platform")
< +     q("no")
< + }
< >
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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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:
  'covr', 'ggiraph', 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Kari Gunnarsson <kari.gunnarsson@outlook.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kari",
                    family = "Gunnarsson",
                    role = c("aut", "cre"),
                    email = "kari.gunnarsson@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:
  'knitr', 'pkgdown', 'rmarkdown', 'kableExtra', 'DT'

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

VignetteBuilder package required 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’

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.
Package required but not available: ‘networkD3’

Packages suggested but not available for checking:
  'tmap', 'knitr', 'rmarkdown', '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: ‘yaml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Maintainer: ‘Giuseppe Casalicchio <giuseppe.casalicchio@stat.uni-muenchen.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Giuseppe",
                      family = "Casalicchio",
                      role = c("aut", "cre"),
                      email = "giuseppe.casalicchio@stat.uni-muenchen.de"),
               person(given = "Bernd",
                      family = "Bischl",
                      role = "aut",
                      email = "bernd_bischl@gmx.net"),
               person(given = "Dominik",
                      family = "Kirchhoff",
                      role = "aut",
                      email = "dom.kirchhoff@gmail.com"),
               person(given = "Michel",
                      family = "Lang",
                      role = "aut",
                      email = "michellang@gmail.com"),
               person(given = "Benjamin",
                      family = "Hofner",
                      role = "aut",
                      email = "benjamin.hofner@fau.de"),
               person(given = "Jakob",
                      family = "Bossek",
                      role = "aut",
                      email = "j.bossek@gmail.com"),
               person(given = "Pascal",
                      family = "Kerschke",
                      role = "aut",
                      email = "kerschke@uni-muenster.de"),
               person(given = "Joaquin",
                      family = "Vanschoren",
                      role = "aut",
                      email = "joaquin.vanschoren@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: ‘SAMtool’

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

VignetteBuilder package required 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: 'openNLPdata', 'rJava'

Package suggested but not available for checking: ‘openNLPmodels.en’

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

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:
    ‘OpenRange_api_load_species.Rd’ ‘OpenRange_api_species.Rd’
    ‘OpenRange_load_species.Rd’ ‘OpenRange_sf.R’ ‘OpenRange_species.Rd’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OpenRange)
  Loading required package: RPostgreSQL
  Loading required package: DBI
  > 
  > test_check("OpenRange")
  Error in `source_dir()`:
  ! Failed to evaluate './setup-OpenRange.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("OpenRange")
    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-OpenRange.R:12:1
   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?
Packages required but not available: 'formattable', 'DT', 'tidyverse'

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

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

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

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:    ‘Jakub Jędrusiak [aut, cre, cph] (<https://orcid.org/0000-0002-6481-8210>, University of Wroclaw), Peter Organisciak [ctb] (<https://orcid.org/0000-0002-9058-2280>, University of Denver), Selcuk Acar [ctb] (<https://orcid.org/0000-0003-4044-985X>, University of North Texas), Denis Dumas [ctb] (<https://orcid.org/0000-0002-8446-4720>, University of Georgia), Pier-Luc de Chantal [ctb] (<https://orcid.org/0000-0002-6974-6172>, Université du Québec à Montréal), Kelly Berthiaume [ctb] (<https://orcid.org/0000-0002-5285-0512>, University of North Texas)’
  Authors@R: ‘Jakub Jędrusiak [aut, cre, cph] (ORCID: <https://orcid.org/0000-0002-6481-8210>, affiliation: University of Wroclaw), Peter Organisciak [ctb] (ORCID: <https://orcid.org/0000-0002-9058-2280>, affiliation: University of Denver), Selcuk Acar [ctb] (ORCID: <https://orcid.org/0000-0003-4044-985X>, affiliation: University of North Texas), Denis Dumas [ctb] (ORCID: <https://orcid.org/0000-0002-8446-4720>, affiliation: University of Georgia), Pier-Luc de Chantal [ctb] (ORCID: <https://orcid.org/0000-0002-6974-6172>, affiliation: Université du Québec à Montréal), Kelly Berthiaume [ctb] (ORCID: <https://orcid.org/0000-0002-5285-0512>, affiliation: University of North Texas)’

  Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘oscai.R’
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'BiocStyle', 'rmarkdown'

VignetteBuilder package required 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: ‘Win Cowger <wincowger@gmail.com>’

Found the following (possibly) invalid URLs:
  URL: https://app.gitter.im/#/room/#Open-Specy_community:gitter.im
    From: README.md
    Message: Invalid URL: '#' not allowed in fragment
Packages required but not available: 'yaml', 'plotly'

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

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: ‘rJava’

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: ‘InSilicoVA’

Packages suggested but not available for checking: 'covr', '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?
Maintainer: ‘Romain Francois <romain@r-enthusiasts.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Romain",
                    family = "Francois",
                    role = c("aut", "cre"),
                    email = "romain@r-enthusiasts.com")
as necessary.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(operator.tools)
  > 
  > test_check("operator.tools")
  Saving _problems/test-operators-11.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-operators.R:6:1'): opetators ───────────────────────────────────
  Error in `is_true()`: could not find function "is_true"
  Backtrace:
      ▆
   1. └─testthat::expect_that(...) at test-operators.R:6:1
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
  Error:
  ! Test failures.
  Execution halted
Maintainer: ‘Jorn Lotsch <j.lotsch@em.uni-frankfurt.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jorn",
                      family = "Lotsch",
                      role = c("aut", "cre"),
                      email = "j.lotsch@em.uni-frankfurt.de",
                      comment = c(ORCID = "0000-0002-5818-6958")),
               person(given = "Sebastian",
                      family = "Malkusch",
                      role = "aut",
                      comment = c(ORCID = "0000-0001-6766-140X")),
               person(given = "Martin",
                      family = "Maechler",
                      role = "ctb"),
               person(given = "Peter",
                      family = "Rousseeuw",
                      role = "ctb"),
               person(given = "Anja",
                      family = "Struyf",
                      role = "ctb"),
               person(given = "Mia",
                      family = "Hubert",
                      role = "ctb"),
               person(given = "Kurt",
                      family = "Hornik",
                      role = "ctb"))
as necessary.
Packages required but not available:
  'AdaptGauss', 'DistributionOptimization', 'mixtools'

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

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.
Maintainer: ‘Monsuru Adepeju <monsuur2010@yahoo.com>’

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

The BugReports field in DESCRIPTION has
  https://github.com/MAnalytics/opitools/issues/1
which should likely be
  https://github.com/MAnalytics/opitools/issues/1/issues
instead.
Package required but not available: ‘wordcloud2’

Packages suggested but not available for checking:
  '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?
No examples, no tests, no vignettes
Maintainer: ‘Christian E. Galarza <cgalarza88@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Christian", "E."),
                      family = "Galarza",
                      role = c("aut", "cre"),
                      email = "cgalarza88@gmail.com"),
               person(given = c("Jonathan", "M."),
                      family = "Olate",
                      role = "aut"))
as necessary.
checkRd: (-1) MonteCarlo.Rd:23: Lost braces
    23 | N is computed from \code{p} length. M is code{10^4} by default.
       |                                              ^
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'roxygen2', 'rmarkdown', 'gurobi', 'ggtree', 'rhandsontable'

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: ‘Seung Won Hyun <yellowatom09@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Seung", "Won"),
                      family = "Hyun",
                      role = c("aut", "cre"),
                      email = "yellowatom09@gmail.com"),
               person(given = c("Weng", "Kee"),
                      family = "Wong",
                      role = "aut"),
               person(given = "Yarong",
                      family = "Yang",
                      role = "aut"))
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?
Maintainer: ‘Mizanur Khondoker <mizanur.khondoker@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mizanur",
                    family = "Khondoker",
                    role = c("aut", "cre"),
                    email = "mizanur.khondoker@gmail.com")
as necessary.
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’
Package has ‘vignettes’ subdirectory 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: ‘Bruno Remillard <bruno.remillard@hec.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Bruno",
                    family = "Remillard",
                    role = c("aut", "cre"),
                    email = "bruno.remillard@hec.ca")
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?
checkRd: (-1) drawdesign.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:44: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but 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’
Maintainer: ‘Nicholas Hamilton <n.hamilton@unsw.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Nicholas",
                    family = "Hamilton",
                    role = c("aut", "cre"),
                    email = "n.hamilton@unsw.edu.au")
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) gnu_style.Rd:24: Lost braces
    24 | [GNU Command Line Standards]{http://www.gnu.org/prep/standards/standards.html}
       |                             ^
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optigrab)
  > 
  > test_check("optigrab")
  Saving _problems/test-opt_expand-98.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 106 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-opt_expand.r:98:1'): (code run outside of `test_that()`) ───────
  Error in `is_true()`: could not find function "is_true"
  Backtrace:
      ▆
   1. └─testthat::expect_that(is.character(expanded), is_true()) at test-opt_expand.r:98:1
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 106 ]
  Error:
  ! Test failures.
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Monica Lopez Raton <monica.lopez.raton@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Monica",
                      family = "Lopez-Raton",
                      role = "aut"),
               person(given = c("Maria", "Xose"),
                      family = "Rodriguez-Alvarez",
                      role = "aut"),
               person(given = c("Monica", "Lopez"),
                      family = "Raton",
                      role = "cre",
                      email = "monica.lopez.raton@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: ‘rgl’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multiwave_diagram
> ### Title: Print Summary Diagram of Multiwave Object
> ### Aliases: multiwave_diagram
> 
> ### ** Examples
> 
> MySurvey <- multiwave(phases = 2, waves = c(1, 3))
> multiwave_diagram(MySurvey)
Error: Please install DiagrammeR: install.packages('DiagrammeR').
         Otherwise, try 'summary()'
Execution halted
Running ‘testthat.R’ [34s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optimall)
  > 
  > test_check("optimall")
  Saving _problems/test-multiwave_diagram-38.R
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 262 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • {shinytest} is not installed. (1): 'test-optimall_shiny.R:4:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-multiwave_diagram.R:38:3'): multiwave_diagram works ────────────
  Error: Please install DiagrammeR: install.packages('DiagrammeR').
           Otherwise, try 'summary()'
  Backtrace:
      ▆
   1. └─optimall::multiwave_diagram(MySurvey) at test-multiwave_diagram.R:38:3
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 262 ]
  Error:
  ! Test failures.
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Adam Kapelner <kapelner@qc.cuny.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Adam",
                      family = "Kapelner",
                      role = c("aut", "cre"),
                      email = "kapelner@qc.cuny.edu"),
               person(given = "Michael",
                      family = "Sklar",
                      role = "aut"),
               person(given = c("Abba", "M."),
                      family = "Krieger",
                      role = "aut"),
               person(given = "David",
                      family = "Azriel",
                      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.

The Description field contains
  M. Krieger, Michael Sklar and David Azriel (2020) <arXiv:1905.03337>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘GreedyExperimentalDesign’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Xiao Lin <xlin3@mdanderson.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xiao",
                      family = "Lin",
                      role = c("aut", "cre"),
                      email = "xlin3@mdanderson.org"),
               person(given = "Xuelin",
                      family = "Huang",
                      role = "aut",
                      email = "xlhuang@mdanderson.org"))
as necessary.
Maintainer: ‘Enrique del Castillo <exd13@psu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Enrique", "del"),
                      family = "Castillo",
                      role = c("aut", "cre"),
                      email = "exd13@psu.edu"),
               person(given = "Peng",
                      family = "Chen",
                      role = "aut"),
               person(given = "Adam",
                      family = "Meyers",
                      role = "aut"),
               person(given = "John",
                      family = "Hunt",
                      role = "aut"),
               person(given = "James",
                      family = "Rapkin",
                      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: ‘Vithor Rosa Franco <vithorfranco@gmail.com>’

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

The Description field contains
  Ruder (2016) <arXiv:1609.04747v2>. Currently, the Steepest 2-Groups
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Kai Husmann <kai.husmann@uni-goettingen.de>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Packages required but not available: 'oeli', 'TestFunctions'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Florian Gerber <flora.fauna.gerber@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 package required 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: ‘Edgar Bueno <edgar.bueno@stat.su.se>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Edgar",
                    family = "Bueno",
                    role = c("aut", "cre"),
                    email = "edgar.bueno@stat.su.se")
as necessary.
Maintainer: ‘Mitchell Lyons <mitchell.lyons@gmail.com>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘find_optimal.Rd’:
    \keyword{optimal,}
    \keyword{partition,}
  File ‘get_characteristic.Rd’:
    \keyword{characteristic,}
    \keyword{diagnostic,}
  File ‘merge_clusters.Rd’:
    \keyword{iterative,}
    \keyword{merging,}
    \keyword{reallocation,}
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Antoine Champion <antoine.champion@outlook.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Antoine",
                    family = "Champion",
                    role = c("aut", "cre"),
                    email = "antoine.champion@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?
Maintainer: ‘Doug Kelkhoff <doug.kelkhoff@gmail.com>’

Found the following (possibly) invalid URLs:
  URL: https://matrix.to/#/#r-pkg-options:matrix.org
    From: README.md
    Message: Invalid URL: '#' not allowed in fragment
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?
Maintainer: ‘John T. Buynak <jbuynak94@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("John", "T."),
                    family = "Buynak",
                    role = c("aut", "cre"),
                    email = "jbuynak94@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: 'kinship2', 'optiSolve'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Robin Wellmann <r.wellmann@uni-hohenheim.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Robin",
                    family = "Wellmann",
                    role = c("aut", "cre"),
                    email = "r.wellmann@uni-hohenheim.de")
as necessary.
Package required but not available: ‘shapes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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:
  'roxygen2', 'knitr', 'rmarkdown', 'rrelaxiv'

VignetteBuilder package required for checking but 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:
  '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: ‘Prakash <prakash2@uwalumni.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(family = "Prakash",
                    role = c("aut", "cre"),
                    email = "prakash2@uwalumni.com",
                    comment = "PKS Prakash")
as necessary.
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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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', 'roxygen2', '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:
  'gt', 'knitr', 'rmarkdown', 'rstanarm', 'sparklyr', 'tidypredict'

VignetteBuilder package required 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: ‘Gero Szepannek <gero.szepannek@web.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Gero",
                    family = "Szepannek",
                    role = c("aut", "cre"),
                    email = "gero.szepannek@web.de")
as necessary.
Maintainer: ‘Rudradev Sengupta <rudradev.sengupta@uhasselt.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Adetayo",
                      family = "Kasim",
                      role = "aut"),
               person(given = "Martin",
                      family = "Otava",
                      role = "aut"),
               person(given = "Tobias",
                      family = "Verbeke",
                      role = "aut"),
               person(given = "Rudradev",
                      family = "Sengupta",
                      role = "cre",
                      email = "rudradev.sengupta@uhasselt.be"))
as necessary.
Packages required but not available: 'bookdown', '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', 'quarto', 'knitr', 'gt', 'modelsummary', 'Hmisc'

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?
Maintainer: ‘Emily V. Dressler <EmilyVDressler@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Emily", "V."),
                      family = "Dressler",
                      role = c("aut", "cre"),
                      email = "emilyvdressler@gmail.com"),
               person(given = c("PhD", "Zhengyan"),
                      family = "Huang",
                      role = "aut"))
as necessary.
Package required but not available: ‘rms’

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

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: ‘Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Carlos", "Alberto", "Cardozo"),
                    family = "Delgado",
                    role = c("aut", "cre"),
                    email = "cardozorpackages@gmail.com")
as necessary.
Maintainer: ‘Christian Sims <christian_j_sims@yahoo.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Christian",
                    family = "Sims",
                    role = c("aut", "cre"),
                    email = "christian_j_sims@yahoo.com")
as necessary.
Maintainer: ‘Kaspar Rufibach <kaspar.rufibach@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kaspar",
                    family = "Rufibach",
                    role = c("aut", "cre"),
                    email = "kaspar.rufibach@gmail.com")
as necessary.
checkRd: (-1) internal.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:62-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:70: Lost braces in \itemize; meant \describe ?
Maintainer: ‘Philippe Lambert <p.lambert@uliege.be>’

The Description field contains
  <doi:10.1177/1471082X231181173> ; Preprint: <arXiv:2210.01668>).
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘James A. Fordyce <jfordyce@utk.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "James",
                      family = "Fordyce",
                      role = "aut"),
               person(given = c("James", "A."),
                      family = "Fordyce",
                      role = "cre",
                      email = "jfordyce@utk.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: ‘Marco Corneli <marcogenni@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Marco",
                      family = "Corneli",
                      role = c("aut", "cre"),
                      email = "marcogenni@gmail.com"),
               person(given = "Charles",
                      family = "Bouveyron",
                      role = "aut"),
               person(given = "Pierre",
                      family = "Latouche",
                      role = "aut"))
as necessary.
Maintainer: ‘Ken Ryan <kjryan@mail.wvu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ken",
                    family = "Ryan",
                    role = c("aut", "cre"),
                    email = "kjryan@mail.wvu.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.
Packages required but not available:
  'config', 'DT', 'golem', 'rhandsontable', 'rms'

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: ‘Kaspar Rufibach <kaspar.rufibach@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Fadoua",
                      family = "Balabdaoui",
                      role = "aut"),
               person(given = "Kaspar",
                      family = "Rufibach",
                      role = c("aut", "cre"),
                      email = "kaspar.rufibach@gmail.com"),
               person(given = "Filippo",
                      family = "Santambrogio",
                      role = "aut"))
as necessary.
checkRd: (-1) minK.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:15: Lost braces in \itemize; meant \describe ?
Maintainer: ‘Ran Gao <rgao8@uic.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Anup",
                      family = "Amatya",
                      role = "aut"),
               person(given = "Hakan",
                      family = "Demirtas",
                      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', '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: ‘Gabriel Okasa <okasa.gabriel@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gabriel",
                      family = "Okasa",
                      role = c("aut", "cre"),
                      email = "okasa.gabriel@gmail.com"),
               person(given = "Michael",
                      family = "Lechner",
                      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.

The Description field contains
  Lechner & Okasa (2019) <arXiv:1907.02436>. The Ordered Forest flexibly
  2017) <arXiv:1508.04409>.
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) orf.Rd:74: Lost braces
    74 | matrix of covariates \code{X} and a vector of outcomes 'code{Y} to the \code{orf}
       |                                                             ^
Package has ‘vignettes’ subdirectory 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: ‘Yi Tang <yi.tang.uk@me.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yi",
                    family = "Tang",
                    role = c("aut", "cre"),
                    email = "yi.tang.uk@me.com")
as necessary.
Maintainer: ‘Tianqing Liu <tianqingliu@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Tianqing",
                      family = "Liu",
                      role = c("aut", "cre"),
                      email = "tianqingliu@gmail.com"),
               person(given = "Nan",
                      family = "Lin",
                      role = "aut"),
               person(given = "Ningzhong",
                      family = "Shi",
                      role = "aut"),
               person(given = "Baoxue",
                      family = "Zhang",
                      role = "aut"))
as necessary.
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
Maintainer: ‘Duncan Murdoch <murdoch.duncan@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Duncan",
                    family = "Murdoch",
                    role = c("aut", "cre"),
                    email = "murdoch.duncan@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: '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?
Package required but not available: ‘orloca’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Manuel Munoz-Marquez <manuel.munoz@uca.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Manuel",
                    family = "Munoz-Marquez",
                    role = c("aut", "cre"),
                    email = "manuel.munoz@uca.es")
as necessary.
Packages required but not available: 'knitr', 'rmarkdown'

Package suggested but not available for checking: ‘orloca.es’

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: ‘rms’

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: ‘Brandon Whitcher <bwhitcher@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: ‘Brandon Whitcher <bwhitcher@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: ‘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.
checkRd: (-1) hillEquation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:84-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:88-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:91-93: Lost braces in \itemize; \value handles \item{}{} directly
Maintainer: ‘Michael D. Sumner <mdsumner@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', '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: ‘Zhu Wang <zwang145@uthsc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Zhu",
                    family = "Wang",
                    role = c("aut", "cre"),
                    email = "https://orcid.org/0000-0002-0773-0052")
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: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Andrew Redd <andrew.redd@hsc.utah.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Andrew",
                    family = "Redd",
                    role = c("aut", "cre"),
                    email = "andrew.redd@hsc.utah.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: ‘Frederick Novomestky <fnovomes@poly.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Frederick",
                    family = "Novomestky",
                    role = c("aut", "cre"),
                    email = "fnovomes@poly.edu")
as necessary.
checkRd: (-1) polynomial.derivatives.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.derivatives.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.derivatives.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:21: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: 'rmarkdown', 'xlsx', '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:
  'ePCR', '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:
    ‘fitS4.R’ ‘helpers.R’
checkRd: (-1) oscar.Rd:44: Lost braces; missing escapes or markup?
    44 | \item{print}{Level of verbosity in Fortran (may not be visible on all terminals); should be an integer between {range, range}, Default: 3}
       |                                                                                                                ^
checkRd: (-1) oscar.control.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{start}{Starting point generation method, see vignettes for details; should be an integer between {range,range}, Default: 2}
       |                                                                                                        ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Steffen Kriewald <kriewald@pik-potsdam.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Steffen",
                      family = "Kriewald",
                      role = c("aut", "cre"),
                      email = "kriewald@pik-potsdam.de"),
               person(given = "Till",
                      family = "Fluschnik",
                      role = "aut"),
               person(given = "Dominik",
                      family = "Reusser",
                      role = "aut"),
               person(given = "Diego",
                      family = "Rybski",
                      role = "aut"))
as necessary.
Maintainer: ‘Olga Savchuk <olga.y.savchuk@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Olga",
                    family = "Savchuk",
                    role = c("aut", "cre"),
                    email = "olga.y.savchuk@gmail.com")
as necessary.

The Description field contains
  functions, <arXiv:1703.05157>.
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: ‘Sebastien Haneuse <shaneuse@hsph.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Sebastien",
                      family = "Haneuse",
                      role = c("aut", "cre"),
                      email = "shaneuse@hsph.harvard.edu"),
               person(given = "Takumi",
                      family = "Saegusa",
                      role = "aut"),
               person(given = "Nilanjan",
                      family = "Chaterjee",
                      role = "aut"),
               person(given = "Norman",
                      family = "Breslow",
                      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: ‘Xavier Domingo-Almenara <xavier.domingo@urv.cat>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Xavier",
                    family = "Domingo-Almenara",
                    role = c("aut", "cre"),
                    email = "xavier.domingo@urv.cat")
as necessary.
Maintainer: ‘Aaron Wolen <aaron@wolen.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', 'lintr', 'covr', 'spelling', 'vcr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Use brio to write text to files in tests so \n is used for line endings on
  > # Windows. This produces files with identical sizes on all platforms allowing
  > # vcr to match requests that include file sizes in the body.
  > library(brio)
  
  Attaching package: 'brio'
  
  The following objects are masked from 'package:base':
  
      readLines, writeLines
  
  > library(testthat)
  > library(osfr)
  > 
  > test_check("osfr")
  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("osfr")
    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: ‘Brodie Gaslam <brodie.gaslam@yahoo.com>’

Found the following (possibly) invalid file URI:
  URI: ./Introduction.html
    From: inst/doc/nse-fun.html
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: ‘rmarkdown’

Packages suggested but not available for checking: 'kableExtra', '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', '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: ‘OpenStreetMap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Xiaoyao Yin <yinxy1992@sina.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Xiaoyao",
                    family = "Yin",
                    role = c("aut", "cre"),
                    email = "yinxy1992@sina.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', '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?
Maintainer: ‘Adrian Staempfli <adrian.staempfli@ost.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Adrian",
                      family = "Staempfli",
                      role = c("aut", "cre"),
                      email = "adrian.staempfli@ost.ch"),
               person(given = "Christoph",
                      family = "Strauss",
                      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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘link2GI’

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: ‘Zardad Khan <zardadkhan@awkum.edu.pk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zardad",
                      family = "Khan",
                      role = c("aut", "cre"),
                      email = "zardadkhan@awkum.edu.pk"),
               person(given = "Asma",
                      family = "Gul",
                      role = "aut"),
               person(given = "Aris",
                      family = "Perperoglou",
                      role = "aut"),
               person(given = "Osama",
                      family = "Mahmoud",
                      role = "aut"),
               person(given = "Werner",
                      family = "Adler",
                      role = "aut"),
               person(family = "Miftahuddin",
                      role = "aut"),
               person(given = "Berthold",
                      family = "Lausen",
                      role = "aut"))
as necessary.
Maintainer: ‘Marcus Young <M.A.Young@soton.ac.uk>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) otp_create_surface.Rd:33: Lost braces; missing escapes or markup?
    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                ^
checkRd: (-1) otp_create_surface.Rd:33: Lost braces; missing escapes or markup?
    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                                ^
Packages required but not available: 'missMDA', 'FactoMineR'

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: ‘Pietro Coretto <pcoretto@unisa.it>’

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: ‘Junwen Xia <xiajunwen@ruc.edu.cn>’

The Description field contains
  available (Xia, J., Zhan, Z., Zhang, J. (2022) <arXiv:2210.05538>).
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Packages required but not available:
  'knitr', 'rmarkdown', 'spelling', 'yaml'

Packages suggested but not available for checking: 'bookdown', 'quarto'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Sizhong Yang <yanglzu@163.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sizhong",
                    family = "Yang",
                    role = c("aut", "cre"),
                    email = "yanglzu@163.com")
as necessary.
Maintainer: ‘Alexandra Linz <amlinz16@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alexandra",
                    family = "Linz",
                    role = c("aut", "cre"),
                    email = "amlinz16@gmail.com")
as necessary.
Maintainer: ‘Finlay Campbell <finlaycampbell93@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘visNetwork’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Finlay Campbell <finlaycampbell93@gmail.com>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘zika_girardot_2015.Rd’:
    https://doi.org/10.2807/1560-7917.ES.2016.21.28.30283
Maintainer: ‘Rafael Pilliard Hellwig <rafael.taph@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', 'covr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) fmat.Rd:15: Lost braces; missing escapes or markup?
    15 | \item outcome: codes {I, P, R, NC, O, UH, UO, eUH, eUO, NE}
       |                      ^
checkRd: (-1) fmat.Rd:24: Lost braces; missing escapes or markup?
    24 | The input parameters given by the user are {I, P, R, NC, O, UH, UO} and
       |                                            ^
checkRd: (-1) fmat.Rd:25: Lost braces; missing escapes or markup?
    25 | the parameter 'e'. The parameter e is multiplied by {UH, UO} internally so as to
       |                                                     ^
checkRd: (-1) fmat.Rd:26: Lost braces; missing escapes or markup?
    26 | produce {eUH, eUO}.
       |         ^
checkRd: (-1) middleearth.Rd:14: Lost braces; missing escapes or markup?
    14 | \item \strong{code:} one of the outcome codes {I, P, R, NC, O, UH, UO, UH, UO, NE}
       |                                               ^
Package has ‘vignettes’ subdirectory 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: 'airt', 'EstCRM'

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: ‘Andres Missiego Manjon <andres.missiego@edu.uah.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Andres", "Missiego"),
                      family = "Manjon",
                      role = c("aut", "cre"),
                      email = "andres.missiego@edu.uah.es"),
               person(given = c("Juan", "Jose", "Cuadrado"),
                      family = "Gallego",
                      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: ‘Antony Unwin <unwin@math.uni-augsburg.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Antony",
                    family = "Unwin",
                    role = c("aut", "cre"),
                    email = "unwin@math.uni-augsburg.de")
as necessary.
Packages required but not available: 'rlist', 'HDoutliers', 'memisc'

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: ‘Lukasz Komsta <lukasz.komsta@umlub.pl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Lukasz",
                    family = "Komsta",
                    role = c("aut", "cre"),
                    email = "lukasz.komsta@umlub.pl")
as necessary.
Package required but not available: ‘SLBDD’

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', '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'

VignetteBuilder package required 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: ‘Jeremy Beaulieu <jmbeauli@uark.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Jeremy", "M."),
                      family = "Beaulieu",
                      role = "aut",
                      email = "jmbeauli@uark.edu"),
               person(given = "Brian",
                      family = "O'Meara",
                      role = "aut",
                      email = "bomeara@utk.edu"),
               person(given = "Jeremy",
                      family = "Beaulieu",
                      role = "cre",
                      email = "jmbeauli@uark.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: ‘shinyjqui’

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', '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', '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?
Package required but not available: ‘devtools’

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'

VignetteBuilder package required 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:
    ‘owid.R’
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(owmr)
  owmr 0.8.2
     another crazy way to talk to OpenWeatherMap's API
     Documentation: type ?owmr or https://crazycapivara.github.io/owmr/
     Issues, notes and bleeding edge: https://github.com/crazycapivara/owmr/
  
  It is recommended that you store your api key in an environment variable called OWM_API_KEY.
  
  > 
  > test_check("owmr")
  Saving _problems/test_current_mocks-30.R
  Saving _problems/test_forecast-29.R
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 28 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_current_mocks.R:8:3'): current weather data ────────────────────
  <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_current_mocks.R:8:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  ── Error ('test_forecast.R:8:3'): forecast data ────────────────────────────────
  <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_forecast.R:8:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 28 ]
  Error:
  ! Test failures.
  Execution halted
Packages required but not available: 'keyring', 'geometa'

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’
checkRd: (-1) ox.Rd:34: height/width attributes should be in pixels
checkRd: (-1) vectorized-ox.Rd:39: 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?
Maintainer: ‘E. Andres Houseman <eahouseman@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("E.", "Andres"),
                      family = "Houseman",
                      role = c("aut", "cre"),
                      email = "eahouseman@gmail.com"),
               person(family = "Sc.D.",
                      role = "aut"),
               person(given = c("Kevin", "C."),
                      family = "Johnson",
                      role = "aut"))
as necessary.
Package required but not available: ‘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.
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?
Packages required but not available: 'diffr', 'htmlwidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'formattable', 'htmlTable', 'reactable', 'shinybusy'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_github_url_to_desc
> ### Title: Add a github URL to File 'DESCRIPTION'
> ### Aliases: add_github_url_to_desc
> ### Keywords: internal
> 
> ### ** Examples
> 
> path <- file.path(tempdir(), "myPackage")
> usethis::create_package(path, open = FALSE)
Error in loadNamespace(x) : there is no package called ‘usethis’
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:
  'ggiraph', 'knitr', 'rmarkdown'

VignetteBuilder package required 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: 'usethis', 'roxygen2', 'htmlwidgets'

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

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: ‘Marion Brandolini-Bunlon <marion.brandolini-bunlon@inra.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Marion",
                      family = "Brandolini-Bunlon",
                      role = c("aut", "cre"),
                      email = "marion.brandolini-bunlon@inra.fr"),
               person(given = "Stephanie",
                      family = "Bougeard",
                      role = "aut"),
               person(given = "Melanie",
                      family = "Petera",
                      role = "aut"),
               person(given = "Estelle",
                      family = "Pujos-Guillot",
                      role = "aut"))
as necessary.
Package required but not available: ‘FactoMineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Tyler Rinker <tyler.rinker@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Matthew Hutchinson <matthewhutchinson15@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Juan", "Antonio"),
                      family = "Balbuena",
                      role = "aut",
                      email = "j.a.balbuena@uv.es"),
               person(given = "Timothee",
                      family = "Poisot",
                      role = "aut",
                      email = "tim@poisotlab.io"),
               person(given = "Matthew",
                      family = "Hutchinson",
                      role = c("aut", "cre"),
                      email = "matthewhutchinson15@gmail.com"),
               person(given = c("Fernando", "Cagua;", "see", "PLoS", "ONE", "Balbuena", "et", "al", "2013"),
                      family = "<https://doi.org/10.1371/journal.pone.0061048>",
                      role = "aut",
                      email = "https://doi.org/10.1371/journal.pone.0061048"))
as necessary.
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
Maintainer: ‘Ye Henry Li <hlowl2@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Ye", "Henry"),
                      family = "Li",
                      role = c("aut", "cre"),
                      email = "hlowl2@gmail.com"),
               person(given = "Dangna",
                      family = "Li",
                      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’
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:
  'covr', 'DiagrammeR', 'gt', 'knitr', 'rmarkdown', 'roxygen2',
  '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', 'yaml'

Packages suggested but not available for checking:
  'DiagrammeR', 'gt', 'knitr', 'pkgdown', 'rmarkdown', 'usethis'

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: 'apsimx', 'tmap'

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

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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘exams’

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’

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

Packages suggested but not available for checking:
  'xaringan', 'revealjs', 'covr'

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

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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘sccore’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Marina Evangelou <m.evangelou@ic.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Marina",
                    family = "Evangelou",
                    role = c("aut", "cre"),
                    email = "m.evangelou@ic.ac.uk")
as necessary.
Maintainer: ‘Steve Haroz <painbow@steveharoz.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Steve",
                    family = "Haroz",
                    role = c("aut", "cre"),
                    email = "painbow@steveharoz.com")
as necessary.
Maintainer: ‘Daniel Greene <dg333@cam.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Daniel",
                    family = "Greene",
                    role = c("aut", "cre"),
                    email = "dg333@cam.ac.uk")
as necessary.
Maintainer: ‘Stephane Champely <champely@univ-lyon1.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Stephane",
                    family = "Champely",
                    role = c("aut", "cre"),
                    email = "champely@univ-lyon1.fr")
as necessary.
Package required but not available: ‘htmlwidgets’

Package suggested but not available for checking: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Catherine Hurley <catherine.hurley@mu.ie>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "C.B.",
                      family = "Hurley",
                      role = "aut"),
               person(given = "R.W.",
                      family = "Oldford",
                      role = "aut"),
               person(given = "Catherine",
                      family = "Hurley",
                      role = "cre",
                      email = "catherine.hurley@mu.ie"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'scagnostics'

VignetteBuilder package required for checking but not installed: ‘knitr’
'library' or 'require' calls not declared from:
  ‘gclus’ ‘irr’ ‘seriation’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘spocc’

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.
Packages required but not available: 'DT', 'rpivotTable'

Package suggested but not available for checking: ‘shinytest2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DT', 'PakPC2023', 'rpivotTable'

Package suggested but not available for checking: ‘shinytest2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) MICS2014Ch.Rd:296: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Ch.Rd:297: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HH.Rd:214: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HH.Rd:215: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HL.Rd:109: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HL.Rd:110: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Wm.Rd:336: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Wm.Rd:337: Lost braces in \enumerate; meant \describe ?
Maintainer: ‘Muhammad Yaseen <myaseen208@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Muhammad",
                      family = "Yaseen",
                      role = c("aut", "cre"),
                      email = "myaseen208@gmail.com"),
               person(given = "Muhammad",
                      family = "Usman",
                      role = "ctb"))
as necessary.
checkRd: (-1) PakPMICS2018bh.Rd:88: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018bh.Rd:89: Lost braces in \enumerate; meant \describe ?
Maintainer: ‘Muhammad Yaseen <myaseen208@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Muhammad",
                      family = "Yaseen",
                      role = c("aut", "cre"),
                      email = "myaseen208@gmail.com"),
               person(given = "Muhammad",
                      family = "Usman",
                      role = "ctb"))
as necessary.
checkRd: (-1) PakPMICS2018fs.Rd:308: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018fs.Rd:309: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018hh.Rd:362: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018hh.Rd:363: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mm.Rd:69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mm.Rd:70: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mn.Rd:243: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mn.Rd:244: Lost braces in \enumerate; meant \describe ?
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pak.Rcheck/00install.out’ for details.
Packages required but not available: 'knitr', 'rmarkdown'

Package suggested but not available for checking: ‘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’
Package has ‘vignettes’ subdirectory 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', 'CorShrink'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Tim Lucas <timcdlucas@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Tim",
                      family = "Lucas",
                      role = c("aut", "cre"),
                      email = "timcdlucas@gmail.com"),
               person(given = "Anjali",
                      family = "Goswami",
                      role = "aut"))
as necessary.
Running examples in ‘paleomorph-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotSpecimens
> ### Title: Plot an array of specimen landmark data in an interactive 3D
> ###   frame
> ### Aliases: plotSpecimens
> 
> ### ** Examples
> 
> A <- array(rep(rnorm(3 * 20, sd = 30), by = 6) + rnorm(6 * 20 * 3), 
+        dim = c(20, 3, 6))
> plotSpecimens(A)
Error: Package rgl needed for this function to work. Please install it with install.packages('rgl').
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?
Maintainer: ‘David W. Bapst <dwbapst@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("David", "W."),
                      family = "Bapst",
                      role = c("aut", "cre"),
                      email = "dwbapst@gmail.com"),
               person(given = c("Peter", "J."),
                      family = "Wagner",
                      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: ‘Emil Hvitfeldt <emilhhvitfeldt@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("See", "AUTHORS"),
                      family = "file.",
                      role = "aut"),
               person(given = "Emil",
                      family = "Hvitfeldt",
                      role = "cre",
                      email = "emilhhvitfeldt@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'pkgdown', 'knitr', 'rmarkdown', 'gt', '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: ‘Tim Lucas <timcdlucas@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tim",
                    family = "Lucas",
                    role = c("aut", "cre"),
                    email = "timcdlucas@gmail.com")
as necessary.
Maintainer: ‘Allison Horst <ahorst@ucsb.edu>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Heidi Seibold <heidi@seibold.co>’

The Description field contains
  found in Seibold, Hothorn, Zeileis (2016) <arXiv:1612.07498>. 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', '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', '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?
Maintainer: ‘Xiaoyan Wang<xywang@ucla.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xiaoyan",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "xywang@ucla.edu"),
               person(given = "Gang",
                      family = "Li",
                      role = "aut"))
as necessary.

The Description field contains
  to Gang Li and Xiaoyan Wang (2016) <arXiv:1611.03063> for more details.
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: '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: ‘pec’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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:
  '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: ‘Joseph G Kreke <jkreke2@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Joseph", "G"),
                      family = "Kreke",
                      role = c("aut", "cre"),
                      email = "jkreke2@gmail.com"),
               person(given = "PhD;",
                      family = "Harris",
                      role = "aut"),
               person(given = c("Inc.", "Sangeet"),
                      family = "Khemlani",
                      role = "aut"),
               person(given = c("PhD;", "Naval", "Research", "Laboratory.", "Greg"),
                      family = "Trafton",
                      role = "aut"),
               person(given = c("PhD;", "Naval", "Research"),
                      family = "Laboratory.",
                      role = "aut"))
as necessary.
Packages required but not available: 'DT', 'detourr', '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', 'tables', 'memisc', 'rms'

VignetteBuilder package required 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/pandocfilters.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jing Peng <jing.peng@uconn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jing",
                    family = "Peng",
                    role = c("aut", "cre"),
                    email = "jing.peng@uconn.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', '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?
Maintainer: ‘Jacob A. Long <jacob.long@sc.edu>’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [43s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(panelr)
  Loading required package: lme4
  Loading required package: Matrix
  
  Attaching package: 'panelr'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("panelr")
  Saving _problems/test-utils-298.R
  Failed with error:  'there is no package called 'skimr''
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 290 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-utils.R:298:3'): extractors work ─────────────────────────────
  Expected `predict(mod)` to run silently.
  Actual noise: warnings.
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 290 ]
  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'

VignetteBuilder package required 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', 'modelsummary'

Packages suggested but not available for checking:
  'covr', 'gt', '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: ‘matlib’

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.
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', '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("pangaear")
  Loading required package: pangaear
  Error in `source_dir()`:
  ! Failed to evaluate './helper-pangaear.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("pangaear")
    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-pangaear.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?
Cannot process vignettes
Packages suggested but not available for checking:
  '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?
Maintainer: ‘Cathrine Ulla Jensen <cuj@ifro.ku.dk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Toke", "Emil"),
                      family = "Panduro",
                      role = "aut",
                      email = "tepp@ifro.ku.dk"),
               person(given = c("Cathrine", "Ulla"),
                      family = "Jensen",
                      role = c("aut", "cre"),
                      email = "cuj@ifro.ku.dk"))
as necessary.
checkRd: (-1) hvidovre.Rd:11: Lost braces
    11 |     \item{\code{roof_tile}}{a numeric vector, roof_tile}{dummy, roof made out of tiles =1}
       |                                                         ^
checkRd: (-1) hvidovre.Rd:25: Lost braces
    25 |     \item{\code{railways}}{a numeric vector, railways}{distance to nearest railway in meters}
       |                                                       ^
checkRd: (-1) hvidovre.Rd:26: Lost braces
    26 |     \item{\code{nature_SLD}}{a numeric vector, nature_SLD}{distance to nearest nature area in meters}
       |                                                           ^
Packages required but not available:
  'colourpicker', 'config', 'configr', 'golem', 'htmlwidgets',
  'leaflet', 'leaflet.extras', 'leafpm'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jing hua Zhao <jinghuazhao@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Original", "by", "Joseph", "L."),
                      family = "Schafer",
                      role = "aut"),
               person(given = c("Jing", "hua"),
                      family = "Zhao",
                      role = "cre",
                      email = "jinghuazhao@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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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:
  'bookdown', 'knitr', 'rmarkdown', 'rmdfiltr', 'yaml'

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

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/papeR_with_latex.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?
Maintainer: ‘Marek Hlavac <mhlavac@alumni.princeton.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Marek",
                    family = "Hlavac",
                    role = c("aut", "cre"),
                    email = "mhlavac@alumni.princeton.edu")
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: '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:
  '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?
Maintainer: ‘Erin Conlon <econlon@umass.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alexey",
                      family = "Miroshnikov",
                      role = "aut"),
               person(given = "Erin",
                      family = "Conlon",
                      role = c("aut", "cre"),
                      email = "econlon@umass.edu"))
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: ‘Thuc Duy Le <Thuc.Le@unisa.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Thuc", "Duy"),
                      family = "Le",
                      role = c("aut", "cre"),
                      email = "thuc.le@unisa.edu.au"),
               person(given = "Tao",
                      family = "Hoang",
                      role = "aut"),
               person(given = "Shu",
                      family = "Hu",
                      role = "aut"),
               person(given = "Liang",
                      family = "Zhang",
                      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: ‘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:
  'discovr', 'EGAnet', 'epiR', 'factoextra', 'FactoMineR', 'gam', 'gt',
  'Hmisc', 'knitr', 'mclogit', 'mediation', 'rmarkdown', 'rms',
  '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:
  'lintr', '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?
Packages required but not available: 'pedtools', 'pedprobr'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘kinship2’

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?
Maintainer: ‘Samuel Wilson <samwilson303@gmail.com>’

The Description field contains
  al. <arXiv:1206.2944>.  The package allows the user to run scoring
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: ‘htmlwidgets’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) returns.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{...}{Other options including {type} which refers to the
       |                                      ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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 = "Alex",
                      family = "Krasnitz",
                      role = "aut"),
               person(given = "Guoli",
                      family = "Sun",
                      role = c("aut", "cre"),
                      email = "guolisun87@gmail.com"))
as necessary.
Malformed Description field: should contain one or more complete sentences.
Packages required but not available:
  'DiagrammeR', 'lintr', 'pak', 'rmarkdown'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) PPS.fit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forbes400.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forbes400.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:11: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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', 'leafsync'

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.
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?
Maintainer: ‘Alexios Galanos <alexios@4dscape.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 package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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:
  'kableExtra', 'knitr', 'rmarkdown'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: find_pattern
> ### Title: Find a pattern in deparsed items
> ### Aliases: find_pattern
> 
> ### ** Examples
> 
> latex <- kableExtra::kbl(mtcars[1:2, 1:2], format = "latex", caption = "Sample table")
Error in loadNamespace(x) : there is no package called ‘kableExtra’
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: ‘RSelenium’

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

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

Package suggested but not available for checking: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Sacha Epskamp <mail@sachaepskamp.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sacha",
                    family = "Epskamp",
                    role = c("aut", "cre"),
                    email = "mail@sachaepskamp.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'keras', 'knitr', 'rmarkdown', 'sparklyr', 'tensorflow'

VignetteBuilder package required 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: ‘Marcela Nunez Lemus <marcela.nunez.lemus@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Marcela", "Nunez"),
                      family = "Lemus",
                      role = c("aut", "cre"),
                      email = "marcela.nunez.lemus@gmail.com"),
               person(given = c("Christian", "E."),
                      family = "Galarza",
                      role = "aut"),
               person(given = c("Larissa", "Avila"),
                      family = "Matos",
                      role = "aut"),
               person(given = c("Victor", "H"),
                      family = "Lachos",
                      role = "aut"))
as necessary.
Maintainer: ‘Annette Molinaro <annette.molinaro@ucsf.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Annette",
                      family = "Molinaro",
                      role = c("aut", "cre"),
                      email = "annette.molinaro@ucsf.edu"),
               person(given = "Adam",
                      family = "Olshen",
                      role = "aut",
                      email = "olshena@biostat.ucsf.edu"),
               person(given = "Karen",
                      family = "Lostritto",
                      role = "aut",
                      email = "karen.lostritto@yale.edu"),
               person(given = "Gregory",
                      family = "Ryslik",
                      role = "aut",
                      email = "gregory.ryslik@yale.edu"),
               person(given = "Steve",
                      family = "Weston",
                      role = "aut",
                      email = "stephen.weston@yale.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?
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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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:
    ‘evolve.Rd’ ‘genesis.Rd’ ‘simulate.Rd’ ‘wield.Rd’
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: ‘Adam Clark <adam.tclark@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Adam",
                    family = "Clark",
                    role = c("aut", "cre"),
                    email = "adam.tclark@gmail.com")
as necessary.
Maintainer: ‘David Weisman <David.Weisman@acm.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "David",
                      family = "Weisman",
                      role = c("aut", "cre"),
                      email = "david.weisman@acm.org"),
               person(given = "Dan",
                      family = "Simovici",
                      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: ‘Norm Matloff <normmatloff@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Norm",
                      family = "Matloff",
                      role = c("cre", "aut"),
                      email = "normmatloff@gmail.com"),
               person(given = "Clark",
                      family = "Fitzgerald",
                      role = "aut",
                      email = "clarkfitzg@gmail.com"),
               person(given = c("with", "contributions", "by", "Alex"),
                      family = "Rumbaugh",
                      email = "aprumbaugh@ucdavis.edu"),
               person(given = "Hadley",
                      family = "Wickham",
                      email = "h.wickham@gmail.com"))
as necessary.
Found the following files/directories:
  ‘co2’ ‘co2.1’ ‘co2.2’ ‘co2s.1’ ‘co2s.2’ ‘ctm.1’ ‘ctm.2’ ‘m’ ‘m.1’
  ‘m.2’ ‘test’ ‘test.1’ ‘test.2’ ‘testa.1’ ‘testa.2’ ‘xfile.1’
  ‘xfile.2’
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?
Note: skipping ‘constparty.Rnw’ due to unavailable dependencies: 'RWeka'
Cannot process vignettes
Packages suggested but not available for checking: 'quarto', 'leaflet'

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?
Maintainer: ‘Donghwan Kim <donhkim9714@korea.ac.kr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Donghwan",
                    family = "Kim",
                    role = c("aut", "cre"),
                    email = "donhkim9714@korea.ac.kr")
as necessary.
Maintainer: ‘Yukun Zhang <yukzhang@ucalgary.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yukun",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "yukzhang@ucalgary.ca"),
               person(given = "Milad",
                      family = "Yavari",
                      role = "aut"),
               person(given = "Bob",
                      family = "Haennel",
                      role = "aut"),
               person(given = "Haocheng",
                      family = "Li",
                      role = c("aut", "ctb")))
as necessary.
Maintainer: ‘Zhiqiu Hu <zhiqiu.hu@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Zhiqiu", "Hu;", "Shizhong", "Xu;", "Zhiquan", "Wang;", "Rongcai"),
                      family = "Yang",
                      role = "aut"),
               person(given = "Zhiqiu",
                      family = "Hu",
                      role = "cre",
                      email = "zhiqiu.hu@gmail.com"))
as necessary.
checkRd: (-1) PAS-package.Rd:30: Lost braces
    30 |     {\code{bin model}}{\cr Zhiqiu Hu, Zhiquan Wang, and Shizhong Xu (2012) An infinitesimal model for quantitative trait genomic value prediction. PloS ONE 7: e41336.}
       |                       ^
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: ‘Marco Chak Yan YU <marcocyyu@gmail.com>’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(passport)
  > 
  > test_check("passport")
  Saving _problems/test_parse_country-49.R
  [ FAIL 1 | WARN 4 | SKIP 1 | PASS 37 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test_parse_country.R:91:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_parse_country.R:43:5'): parsing country names with simulated geocoding APIs works ──
  `with_mock(...)` threw an error with unexpected message.
  Expected match: "jsonlite"
  Actual message: "`with_mock()` was deprecated in testthat 3.2.0 and is now defunct.\nℹ Please use `with_mocked_bindings()` instead."
  Backtrace:
      ▆
   1. ├─testthat::expect_error(...) at test_parse_country.R:43:5
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─testthat::with_mock(...)
   7.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   8.     └─lifecycle:::deprecate_stop0(msg)
   9.       └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 4 | SKIP 1 | PASS 37 ]
  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', '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', '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: ‘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:
  '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: ‘RmdConcord’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Emmanuel Charpentier <emm.charpentier@free.fr>’

Found the following (possibly) invalid file URI:
  URI: emm.charpentier@free.fr
    From: man/patchSynctex-package.Rd
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', '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?
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', 'DiagrammeR'

Packages suggested but not available for checking:
  'devtools', 'usethis', 'knitr', 'rmarkdown', 'roxygen2', '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', 'config', 'yaml'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as_config
> ### Title: Prepare list to be saved as config .yaml file
> ### Aliases: as_config as_config.path_chain as_config.list
> 
> ### ** Examples
> 
> library(magrittr)
> # Initializing sample directory
> tmp <- create_temp_dir("files")
> create_sample_dir(tmp, override = TRUE)
[1] TRUE
> full_path_chain(tmp, "kRoot", naming_k) %>%
+    list(kDirs = .) %>%
+    list(default = .) %>%
+    yaml::write_yaml(temp_path("config.yaml"))
Error in loadNamespace(x) : there is no package called ‘yaml’
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: 'rmarkdown', 'ggkegg', 'knitr'

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.
Package required but not available: ‘sparklyr’

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.
Maintainer: ‘Steven Andrew Culpepper <sculpepp@illinois.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', 'anomalize', '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?
Package required but not available: ‘clusterProfiler’

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

Packages suggested but not available for checking:
  'Eunomia', 'knitr', 'OhdsiShinyAppBuilder', 'ResultModelManager',
  'rmarkdown', 'survminer'

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', 'DT', 'gt', 'Hmisc', '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: 'clinUtils', '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: ‘Seong Hyun Hwang <krshh1412@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Seong", "Hyun"),
                      family = "Hwang",
                      role = c("aut", "cre"),
                      email = "krshh1412@gmail.com"),
               person(given = c("Rachel", "Myoung"),
                      family = "Moon",
                      role = "aut"))
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?
Packages required but not available: 'Morpho', 'geomorph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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: ‘WGCNA’

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', 'matchingMarkets'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'alphashape3d', '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?
Maintainer: ‘Dyfan Jones <dyfan.r.jones@gmail.com>’

Found the following (possibly) invalid URLs:
  URL: https://docs.aws.amazon.com/connect/latest/adminguide/historical-metrics-definitions.html##average-non-talk-time-historical
    From: man/connect_get_metric_data_v2.Rd
    Message: Invalid URL: '#' not allowed in fragment
Maintainer: ‘Dyfan Jones <dyfan.r.jones@gmail.com>’

Found the following (possibly) invalid URLs:
  URL: https://docs.aws.amazon.com/kms/latest/developerguide/concepts.html##aws-managed-cmk
    From: man/kms_describe_key.Rd
    Message: Invalid URL: '#' not allowed in fragment
Maintainer: ‘Thomas Hoffmann <tjhoffm@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Thomas",
                      family = "Hoffmann",
                      role = c("aut", "cre"),
                      email = "tjhoffm@gmail.com"),
               person(given = c("with", "contributions", "from", "Christoph"),
                      family = "Lange",
                      role = "aut",
                      email = "clange@hsph.harvard.edu"))
as necessary.
Maintainer: ‘Rampal S. Etienne <r.s.etienne@rug.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Rampal", "S."),
                    family = "Etienne",
                    role = c("aut", "cre"),
                    email = "r.s.etienne@rug.nl")
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) pbd_loglik.Rd:31: Lost braces
    31 |     \code{pars2[1]} {set the conditioning on non-extinction of the clade (1) or not (0) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:32: Lost braces
    32 |     \code{pars2[2]} {sets whether the likelihood is for the branching times (0) or the phylogeny (1) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:33: Lost braces
    33 |     \code{pars2[3]} {sets whether the first element of the branching times is the stem (1) or the crown (2) age \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:34: Lost braces
    34 |     \code{pars2[4]} {sets whether the parameters and likelihood should be shown on screen (1) or not (0) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:35: Lost braces
    35 |     \code{pars2[5]} {sets which method should be used in the ode-solver. Default is 'lsoda'. See package deSolve for details. \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:36: Lost braces
    36 |     \code{pars2[6]}{Sets the lower bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}
       |                    ^
checkRd: (-1) pbd_loglik.Rd:37: Lost braces
    37 |     \code{pars2[7]}{Sets the upper bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}  
       |                    ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Przemyslaw Biecek <przemyslaw.biecek@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Przemyslaw",
                    family = "Biecek",
                    role = c("aut", "cre"),
                    email = "przemyslaw.biecek@gmail.com")
as necessary.
Maintainer: ‘Lu Tian <lutian@stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xiaodong",
                      family = "Luo",
                      role = "aut"),
               person(given = "Bo",
                      family = "Huang",
                      role = "aut"),
               person(given = "Lu",
                      family = "Tian",
                      role = c("aut", "cre"),
                      email = "lutian@stanford.edu",
                      comment = c(ORCID = "0000-0002-5893-0169")))
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: ‘Brenton Kenkel <brenton.kenkel@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Fortran", "code", "by", "Alan", "Genz.", "R", "code", "by", "Brenton"),
                      family = "Kenkel",
                      role = "aut"),
               person(given = c("based", "on", "Adelchi", "Azzalini's", "'mnormt'"),
                      family = "package.",
                      role = "aut"),
               person(given = "Brenton",
                      family = "Kenkel",
                      role = "cre",
                      email = "brenton.kenkel@gmail.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: ‘Kevin kuang <kvn.kuang@mail.utoronto.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Kevin",
                      family = "Kuang",
                      role = c("aut", "cre"),
                      email = "kvn.kuang@mail.utoronto.ca",
                      comment = "aut"),
               person(given = "Quyu",
                      family = "Kong",
                      role = "aut",
                      comment = "ctb"),
               person(given = "Francesco",
                      family = "Napolitano",
                      role = "aut",
                      comment = "ctb"))
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', '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: ‘Andreas Schulz <ades-s@web.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Andreas",
                    family = "Schulz",
                    role = c("aut", "cre"),
                    email = "ades-s@web.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?
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.
':::' calls which should be '::':
  ‘PBSmodelling:::.findSquare’ ‘PBSmodelling:::.getHiddenEnv’
  ‘PBSmodelling:::.makeCleanVec’ ‘PBSmodelling:::.readList.P’
  ‘PBSmodelling:::.trimWhiteSpace’
  See the note in ?`:::` about the use of this operator.
Maintainer: ‘swang1 <swang1@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Shuangcai",
                      family = "Wang",
                      role = "aut"),
               person(family = "swang1",
                      role = "cre",
                      email = "swang1@gmail.com"))
as necessary.
Malformed Description field: should contain one or more complete sentences.
Maintainer: ‘Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alexander",
                    family = "Robitzsch",
                    role = c("aut", "cre"),
                    email = "robitzsch@ipn.uni-kiel.de",
                    comment = c(ORCID = "0000-0002-8226-3132"))
as necessary.
Maintainer: ‘Manuela Ott <manuela.c.ott@gmail.com>’

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 ‘twoby2Calibrate.Rd’:
    https://doi.org/10.1080/01621459.2018.1469992
    https://doi.org/10.1111/insr.12307
checkRd: (-1) twoby2Calibrate.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:85-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:87-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:97-100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:101-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:104-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:108-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:111-116: Lost braces in \itemize; meant \describe ?
Maintainer: ‘Elia Degiorgi <degioe@usi.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Elia",
                      family = "Degiorgi",
                      role = c("aut", "cre"),
                      email = "degioe@usi.ch"),
               person(given = "Federico",
                      family = "Milan",
                      role = "aut"),
               person(given = "Davide",
                      family = "Zaramella",
                      role = "aut"),
               person(given = "Valerija",
                      family = "Stoeva",
                      role = "aut"))
as necessary.
Maintainer: ‘Pedro Fonseca <pedro.teles.fonseca@outlook.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: ‘Derek W. Brown <derek9@gwmail.gwu.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: ‘Marie Chavent <Marie.Chavent@u-bordeaux.fr>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘MFAmix.Rd’:
    \keyword{multivariate, mixed type data, data struc [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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘gMOIP’

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown', '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: ‘pcds’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Maxime Turgeon <maxime.turgeon@mail.mcgill.ca>’

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/pcev.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', 'covr', 'qgraph'

VignetteBuilder package required 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: ‘Yi-Hui Zhou <yihui_zhou@ncsu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yi-Hui",
                    family = "Zhou",
                    role = c("aut", "cre"),
                    email = "yihui_zhou@ncsu.edu")
as necessary.
Maintainer: ‘Pariya Behrouzi <pariya.behrouzi@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Willem",
                      family = "Kruijer",
                      role = "aut"),
               person(given = "Pariya",
                      family = "Behrouzi",
                      role = c("aut", "cre"),
                      email = "pariya.behrouzi@gmail.com"),
               person(given = c("Maria", "Xose"),
                      family = "Rodriguez-Alvarez",
                      role = "aut"))
as necessary.
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:
  'tidyverse', 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘B N Mandal <mandal.stat@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("B", "N"),
                      family = "Mandal",
                      role = c("aut", "cre"),
                      email = "mandal.stat@gmail.com"),
               person(given = "Jun",
                      family = "Ma",
                      role = "aut",
                      email = "jun.ma@mq.edu.au"))
as necessary.
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.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Rob Tibshirani <tibs@stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jerome",
                      family = "Friedman",
                      role = "aut"),
               person(given = "Kenneth",
                      family = "Tay",
                      role = "aut"),
               person(given = "Robert",
                      family = "Tibshirani",
                      role = "aut"),
               person(given = "Rob",
                      family = "Tibshirani",
                      role = "cre",
                      email = "tibs@stanford.edu"))
as necessary.

The Description field contains
  regression' <arXiv:1810.04651>.
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: '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: ‘Andrew Ying <aying9339@gmail.com>’

The Description field contains
  arXiv e-prints, arXiv-2009 <arXiv:2009.10982>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Krzysztof Bartoszek <krzbar@protonmail.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Krzysztof",
                      family = "Bartoszek",
                      role = c("aut", "cre"),
                      email = "krzbar@protonmail.ch"),
               person(given = "Pietro",
                      family = "Lio'",
                      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.
checkRd: (-1) PCM_ABC.Rd:106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:108-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:114: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:205-207: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:208-211: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:212-216: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:221-224: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:225-228: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:229-231: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:232: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:233: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:234: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:235: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:236: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:237: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:238: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:239: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:240: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:67: Lost braces in \itemize; meant \describe ?
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?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggtree', '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: ‘S. Varet <suzanne.varet@universite-paris-saclay.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "S.",
                    family = "Varet",
                    role = c("aut", "cre"),
                    email = "suzanne.varet@universite-paris-saclay.fr")
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', 'Hmisc'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pCODE)
  > library(deSolve)
  > library(fda)
  Loading required package: splines
  Loading required package: fds
  Loading required package: rainbow
  Loading required package: MASS
  Loading required package: pcaPP
  Loading required package: RCurl
  
  Attaching package: 'fda'
  
  The following object is masked from 'package:graphics':
  
      matplot
  
  The following object is masked from 'package:datasets':
  
      gait
  
  > library(MASS)
  > library(pracma)
  
  Attaching package: 'pracma'
  
  The following object is masked from 'package:deSolve':
  
      rk4
  
  > library(rmarkdown)
  Error in library(rmarkdown) : there is no package called 'rmarkdown'
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Kristof Meers <kristof.meers+cran@kuleuven.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Marlies",
                      family = "Vervloet",
                      role = c("aut", "cre")),
               person(given = "Henk",
                      family = "Kiers",
                      role = "aut"),
               person(given = "Eva",
                      family = "Ceulemans",
                      role = "ctb"),
               person(given = "Kristof",
                      family = "Meers",
                      role = "cre",
                      email = "kristof.meers+cran@kuleuven.be"))
as necessary.
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:    ‘Lawrence G. Chillrud [aut, cre, cph] (<https://orcid.org/0000-0003-0727-0161>), Jaime Benavides [aut] (<https://orcid.org/0000-0002-1851-5155>), Elizabeth A. Gibson [aut] (<https://orcid.org/0000-0001-5119-5133>), Junhui Zhang [aut] (<https://orcid.org/0009-0008-5922-1058>), Jingkai Yan [aut] (<https://orcid.org/0000-0002-2094-2092>), John N. Wright [aut], Jeff Goldsmith [aut], Marianthi-Anna Kioumourtzoglou [aut] (<https://orcid.org/0000-0001-5710-4992>), Columbia University [fnd] (00hj8s172)’
  Authors@R: ‘Lawrence G. Chillrud [aut, cre, cph] (ORCID: <https://orcid.org/0000-0003-0727-0161>), Jaime Benavides [aut] (ORCID: <https://orcid.org/0000-0002-1851-5155>), Elizabeth A. Gibson [aut] (ORCID: <https://orcid.org/0000-0001-5119-5133>), Junhui Zhang [aut] (ORCID: <https://orcid.org/0009-0008-5922-1058>), Jingkai Yan [aut] (ORCID: <https://orcid.org/0000-0002-2094-2092>), John N. Wright [aut], Jeff Goldsmith [aut], Marianthi-Anna Kioumourtzoglou [aut] (ORCID: <https://orcid.org/0000-0001-5710-4992>), Columbia University [fnd] (ROR: <https://ror.org/00hj8s172>)’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) getPCRAData.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getPCRAData.Rd:29: Lost braces in \itemize; meant \describe ?
'::' or ':::' imports not declared from:
  ‘MASS’ ‘tensr’
'library' or 'require' calls not declared from:
  ‘MASS’ ‘facmodCS’ ‘fit.models’ ‘sandwich’
Packages required but not available: 'fda.usc', 'qpcR'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Delia Bailey <delia.bailey@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Delia",
                      family = "Bailey",
                      role = c("aut", "cre"),
                      email = "delia.bailey@gmail.com"),
               person(given = c("Jonathan", "N."),
                      family = "Katz",
                      role = "aut",
                      email = "jkatz@caltech.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.
Problems with news in ‘NEWS.md’:
No news entries found.
Maintainer: ‘Jason Wilson <jason.wilson@biola.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jason",
                    family = "Wilson",
                    role = c("aut", "cre"),
                    email = "jason.wilson@biola.edu")
as necessary.
Maintainer: ‘Aleksei Krasikov <krasikov.as@phystech.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Aleksei",
                    family = "Krasikov",
                    role = c("aut", "cre"),
                    email = "krasikov.as@phystech.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:
  'NST', 'mixOmics', 'plotly', 'Hmisc', 'ggtree', 'ggtreeExtra',
  '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', 'leaflet', 'rmarkdown', 'tmap', '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?
Cannot process vignettes
Packages suggested but not available for checking:
  'fUnitRoots', 'knitr', 'rmarkdown'

VignetteBuilder package required 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) pcvpcr.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
checkRd: (-1) pcvpls.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
Package required but not available: ‘FactoMineR’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Andreas M. Brandmaier <brandmaier@mpib-berlin.mpg.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Andreas", "M."),
                    family = "Brandmaier",
                    role = c("aut", "cre"),
                    email = "brandmaier@mpib-berlin.mpg.de")
as necessary.

Found the following (possibly) invalid file URI:
  URI: openclipart.org
    From: man/complex.shapes.Rd
Package required but not available: ‘plotly’

Package suggested but not available for checking: ‘modeest’

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: ‘Menardi Giovanna <menardi@stat.unipd.it>’

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: ‘Jenny Farmer <jfarmer@carolina.rr.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jenny",
                      family = "Farmer",
                      role = c("aut", "cre"),
                      email = "jfarmer@carolina.rr.com"),
               person(given = "Donald",
                      family = "Jacobs",
                      role = "aut",
                      email = "djacobs1@uncc.ecu"))
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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Jeffrey Wong <jeff.ct.wong@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jeffrey",
                    family = "Wong",
                    role = c("aut", "cre"),
                    email = "jeff.ct.wong@gmail.com")
as necessary.
Maintainer: ‘J.F. Palomeque-Gonzalez <jfpalomeque.gonzalez@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "J.F.",
                      family = "Palomeque-Gonzalez",
                      role = c("aut", "cre"),
                      email = "jfpalomeque.gonzalez@gmail.com"),
               person(given = "M.",
                      family = "San-Juan",
                      role = "aut"))
as necessary.
Maintainer: ‘Zhenbang Wang <bruce1edward@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Javier",
                      family = "Cabrera",
                      role = "aut",
                      email = "xavier.cabrera@gmail.com"),
               person(given = "Fei",
                      family = "Wang",
                      role = "aut",
                      email = "cherry8177@gmail.com"),
               person(given = "Zhenbang",
                      family = "Wang",
                      role = "cre",
                      email = "bruce1edward@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: ‘Luca Belmonte <luca.belmonte@unimore.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Luca",
                      family = "Belmonte",
                      role = c("aut", "cre"),
                      email = "luca.belmonte@unimore.it"),
               person(given = c("Sheref", "S."),
                      family = "Mansy",
                      role = "aut",
                      email = "sheref.mansy@unitn.it"))
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘PdPDB.Rd’:
    \keyword{PDB,}
    \keyword{alignment,}
    \keyword{metal,}
    \keyword{metalloproteins,}
    \keyword{patterns,}
Cannot process vignettes
Packages suggested but not available for checking:
  'adabag', 'covr', 'keras', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
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: ‘Steven E. Pav <shabbychef@gmail.com>’

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/PDQutils.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Adam J. Rothman <arothman@umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Adam", "J."),
                    family = "Rothman",
                    role = c("aut", "cre"),
                    email = "arothman@umn.edu")
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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘monobin’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Yuanhui Xiao <xiao_yuanhui@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yuanhui",
                    family = "Xiao",
                    role = c("aut", "cre"),
                    email = "xiao_yuanhui@hotmail.com")
as necessary.
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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/Examples.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Toby Dylan Hocking <toby.hocking@r-project.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Toby", "Dylan"),
                      family = "Hocking",
                      role = c("aut", "cre"),
                      email = "toby.hocking@r-project.org"),
               person(given = "Guillem",
                      family = "Rigaill",
                      role = "aut"))
as necessary.
Maintainer: ‘John Hughes <drjphughesjr@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "John",
                    family = "Hughes",
                    role = c("aut", "cre"),
                    email = "drjphughesjr@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.
Maintainer: ‘Juha Karvanen <juha.karvanen@iki.fi>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Juha",
                    family = "Karvanen",
                    role = c("aut", "cre"),
                    email = "juha.karvanen@iki.fi")
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: 'deaR', 'rminer'

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: 'rms', 'riskRegression'

Package suggested but not available for checking: ‘Hmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'qwraps2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'qwraps2', 'rmarkdown'

VignetteBuilder package required 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:
  'pedtools', 'forrel', 'pedprobr', 'ribd'

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

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

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

VignetteBuilder package required 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) variogramGuess.Rd:94: Lost braces
    94 | Method \code{"b"} was proposed by \doi{10.1016/0098-3004(95)00095-X}{Jian et al. (1996)} and
       |                                                                     ^
checkRd: (-1) variogramGuess.Rd:98: Lost braces
    98 | \doi{10.1016/j.cageo.2008.10.011}{Hiemstra et al. (2009)}.
       |                                  ^
checkRd: (-1) variogramGuess.Rd:100: Lost braces
   100 | Method \code{"d"} was developed by \doi{10.1007/s11004-012-9434-1}{Desassis & Renard (2012)}.
       |                                                                   ^
Package required but not available: ‘pedtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'echarts4r', 'htmlwidgets'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forrel', 'pedprobr', 'pedtools', 'ribd', 'verbalisr', 'dvir',
  'ibdfindr', 'ibdsim2', 'paramlink2', 'pedFamilias', 'pedbuildr',
  'segregatr'

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: ‘kinship2’

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.
Package required but not available: ‘kinship2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Qingyang Zhang <qz008@uark.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Qingyang",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "qz008@uark.edu"),
               person(given = "Yanchuan",
                      family = "Li",
                      role = "aut"))
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘PEGroupTesting-package.Rd’:
    \keyword{Group testing, maximum likelihood estimat [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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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', 'htmlwidgets'

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:
  'rmarkdown', 'knitr', 'webexercises'

VignetteBuilder package required 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 Guerrier <stef.guerrier@gmail.com>’

The Description field contains
  methods proposed in Guerrier et al. (2023) <arXiv:2012.10745>.
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: ‘loa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Daniele Cuntrera <daniele.cuntrera@unipa.it>’

The Description field contains
  Muggeo, V. M. (2022) <arXiv:2212.08582>.
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', '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: ‘riskRegression’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Christian Schellhase <cschellhase@wiwi.uni-bielefeld.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Christian",
                    family = "Schellhase",
                    role = c("aut", "cre"),
                    email = "cschellhase@wiwi.uni-bielefeld.de")
as necessary.
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
Maintainer: ‘Andreas Groll <groll@statistik.tu-dortmund.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Andreas",
                    family = "Groll",
                    role = c("aut", "cre"),
                    email = "groll@statistik.tu-dortmund.de")
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘pencoxfrail.rd’:
    \keyword{Cox frailty model; LASSO; Penalization; T [TRUNCATED]
'library' or 'require' call not declared from: ‘mgcv’
Maintainer: ‘Christian Schellhase <christian.schellhase@gmx.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Christian",
                    family = "Schellhase",
                    role = c("aut", "cre"),
                    email = "christian.schellhase@gmx.net")
as necessary.
checkRd: (-1) my.bspline.Rd:21: Escaped LaTeX specials: \$ \$ \$ \$ \$ \$
checkRd: (-1) my.bspline.Rd:27: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) pendensity.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:57: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:82: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:96: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:100: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:105: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
Package required but not available: ‘kinship2’

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.
Maintainer: ‘Elena Geminiani <geminianielena@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', '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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Yan Liu <yanliuresearch@gmail.com>’

The Description field contains
  (2019) <arXiv:1912.11703>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Holger Reulen <hreulen@uni-goettingen.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Holger",
                    family = "Reulen",
                    role = c("aut", "cre"),
                    email = "hreulen@uni-goettingen.de")
as necessary.
Specified C++11: support will be removed soon
Package required but not available: ‘devtools’

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?
Maintainer: ‘Levi Waldron <lwaldron.research@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Levi",
                    family = "Waldron",
                    role = c("aut", "cre"),
                    email = "lwaldron.research@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: '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: ‘Seyma Kalay <seymakalay@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Seyma",
                    family = "Kalay",
                    role = c("aut", "cre"),
                    email = "seymakalay@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?
Package required but not available: ‘DT’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Fabio Demarqui <fndemarqui@est.ufmg.br>’

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: ‘Nathan Sheffield <nathan@code.databio.org>’

The BugReports field in DESCRIPTION has
  https://github.com/pepkit/pepr
which should likely be
  https://github.com/pepkit/pepr/issues
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.
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/Paper_Analysis.Rnw’
   ‘inst/doc/PepSAVIms_Introduction.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jorge Cimentada <cimentadaj@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:
  'spelling', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [3s/4s]
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?
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?
Package required but not available: ‘Hmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Julien Idé <julien.ide.fr@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Julien",
                    family = "Idé",
                    role = c("aut", "cre"),
                    email = "julien.ide.fr@gmail.com")
as necessary.
Packages required but not available: 'DT', 'reactable', 'yaml'

Packages suggested but not available for checking:
  'canvasXpress', 'colourpicker', 'knitr', 'rmarkdown', '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: 'DT', 'yaml'

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

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', 'colourpicker', 'config', 'golem', '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: ‘Marie-Pierre Sylvestre <marie-pierre.sylvestre@umontreal.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Marie-Pierre",
                      family = "Sylvestre",
                      role = c("aut", "cre"),
                      email = "marie-pierre.sylvestre@umontreal.ca"),
               person(given = "Thad",
                      family = "Edens",
                      role = "aut"),
               person(given = "Todd",
                      family = "MacKenzie",
                      role = "aut"),
               person(given = "Michal",
                      family = "Abrahamowicz",
                      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: ‘Laura Vicente-Gonzalez <laura20vg@usal.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Laura",
                      family = "Vicente-Gonzalez",
                      role = c("aut", "cre"),
                      email = "laura20vg@usal.es"),
               person(given = c("Jose", "Luis"),
                      family = "Vicente-Villardon",
                      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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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/permPATHmanual.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?
Maintainer: ‘Michael P. Fay <mfay@niaid.nih.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Michael",
                      family = "Fay",
                      role = "aut"),
               person(given = c("Michael", "P."),
                      family = "Fay",
                      role = "cre",
                      email = "mfay@niaid.nih.gov"))
as necessary.
Maintainer: ‘Alfonso Benitez-Paez <alfbenpa@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alfonso",
                    family = "Benitez-Paez",
                    role = c("aut", "cre"),
                    email = "alfbenpa@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’
Maintainer: ‘Osama Abdalla <osama.abdalla@mail.utoronto.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Osama",
                    family = "Abdalla",
                    role = c("aut", "cre"),
                    email = "osama.abdalla@mail.utoronto.ca")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Gabriel Kaiser <quantresearch.gk@gmail.com>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘perplexR-package.Rd’:
    \keyword{annotate;}
Maintainer: ‘Roozbeh Safshekan <rse@mit.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Roozbeh",
                      family = "Safshekan",
                      role = c("aut", "cre"),
                      email = "rse@mit.edu"),
               person(given = "Rich",
                      family = "Nielsen",
                      role = "aut"))
as necessary.
Maintainer: ‘Jared Huling <jaredhuling@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘personalized’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jared Huling <jaredhuling@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
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 required but not available: 'devtools', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Renfei Mao <renfeimao@gmail.com>’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Kenneth B. Hoehn <perspectev@gmail.com>’

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

The Description field contains
  http://evolve.zoo.ox.ac.uk/Evolve/Perspectev.html.
Please enclose URLs in angle brackets (<...>).
Packages required but not available: 'rmarkdown', 'rms', 'survminer'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘KM Gates <gateskm@email.unc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "KM",
                      family = "Gates",
                      role = c("aut", "cre"),
                      email = "gateskm@email.unc.edu"),
               person(given = "Zachary",
                      family = "Fisher",
                      role = "aut"),
               person(given = "Cara",
                      family = "Arizmendi",
                      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?
Cannot process vignettes
Packages suggested but not available for checking:
  'gt', '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: ‘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 = "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?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
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'

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: ‘Aaron Schlegel <aaron@aaronschlegel.me>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Aaron",
                    family = "Schlegel",
                    role = c("aut", "cre"),
                    email = "aaron@aaronschlegel.me")
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: 'visNetwork', 'DiagrammeR'

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

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/pez-intro.Rnw’
   ‘inst/doc/pez-pglmm-overview.Rnw’
(Is a VignetteBuilder field missing?)

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

Package suggested but not available for checking: ‘rmarkdown’

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

Package in Depends/Imports which should probably only be in LinkingTo: ‘RcppArmadillo’

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: ‘Washington Junger <wjunger@ims.uerj.br>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Washington",
                    family = "Junger",
                    role = c("aut", "cre"),
                    email = "wjunger@ims.uerj.br")
as necessary.
Maintainer: ‘Daniel F. Schmidt <daniel.schmidt@monash.edu>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘pgdraw-package.Rd’:
    \keyword{distribution,}
Maintainer: ‘Gul Inan <ginan@metu.edu.tr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gul",
                      family = "Inan",
                      role = c("aut", "cre"),
                      email = "ginan@metu.edu.tr",
                      comment = "Lecturer, Middle East Technical University"),
               person(given = "Jianhui",
                      family = "Zhou",
                      role = "aut",
                      comment = "Associate Professor, University of Virginia"),
               person(given = "Lan",
                      family = "Wang",
                      role = "aut",
                      comment = c(ROR = "Professor", "University of Minnesota")))
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘PGEE-package.Rd’:
    \keyword{high-dimensional covariates, longitudinal [TRUNCATED]
Packages required but not available: 'rgl', 'Directional'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRD.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRDUS.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) DTV.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
Maintainer: ‘Yang Feng <yangfengstat@gmail.com>’

The Description field contains
  projection as introduced in Fan, Feng and Xia (2019)<arXiv:1501.01617>.
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’
Author field differs from that derived from Authors@R
  Author:    ‘J. Aravind [aut, cre] (<https://orcid.org/0000-0002-4791-442X>), J. Radhamani [aut], Kalyani Srinivasan [aut], B. Ananda Subhash [aut], Rishi Kumar Tyagi [aut], ICAR-NBGPR [cph] (www.nbpgr.ernet.in), Maurice Aubrey [ctb] (Double Metaphone), Kevin Atkinson [ctb] (Double Metaphone), Lawrence Philips [ctb] (Double Metaphone)’
  Authors@R: ‘J. Aravind [aut, cre] (ORCID: <https://orcid.org/0000-0002-4791-442X>), J. Radhamani [aut], Kalyani Srinivasan [aut], B. Ananda Subhash [aut], Rishi Kumar Tyagi [aut], ICAR-NBGPR [cph] (url: www.nbpgr.ernet.in), Maurice Aubrey [ctb] (Double Metaphone), Kevin Atkinson [ctb] (Double Metaphone), Lawrence Philips [ctb] (Double Metaphone)’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Gangcai Xie <gcxiester@gmail.com>’

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

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: ‘Philip Barrett <pobarrett@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Philip",
                    family = "Barrett",
                    role = c("aut", "cre"),
                    email = "pobarrett@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’
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: ‘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: ‘Yalin Zhu <yalin.zhu@outlook.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yalin",
                      family = "Zhu",
                      role = c("aut", "cre"),
                      email = "yalin.zhu@outlook.com"),
               person(given = "Rui",
                      family = "Qin",
                      role = "aut"))
as necessary.
Found the following files/directories:
  ‘animation.gif’
Maintainer: ‘Yalin Zhu <yalin.zhu@outlook.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yalin",
                      family = "Zhu",
                      role = c("aut", "cre"),
                      email = "yalin.zhu@outlook.com"),
               person(given = "Rui",
                      family = "Qin",
                      role = "aut"))
as necessary.
Package required but not available: ‘factoextra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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', 'devtools', '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:
  'gt', 'knitr', 'rmarkdown', 'kableExtra', '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: ‘altair’

Package suggested but not available for checking: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Andrew G Chapple <achapp@lsuhsc.edu>’

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Andrew", "G"),
                    family = "Chapple",
                    role = c("aut", "cre"),
                    email = "achapp@lsuhsc.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: ‘Lu Zhang <luzhangstat@gmail.com>’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jun Yin <vivien.jyin@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jun",
                      family = "Yin",
                      role = c("aut", "cre"),
                      email = "vivien.jyin@gmail.com"),
               person(given = "Yu",
                      family = "Du",
                      role = "aut"),
               person(given = "Sumithra",
                      family = "Mandrekar",
                      role = "aut"))
as necessary.
Packages required but not available: 'plotly', 'zeitgebr'

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: ‘Zhili Qiao <zlqiao@iastate.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Zhili",
                    family = "Qiao",
                    role = c("aut", "cre"),
                    email = "zlqiao@iastate.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?
Maintainer: ‘Jesse Hemerik <jesse.hemerik@wur.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jesse",
                      family = "Hemerik",
                      role = c("aut", "cre"),
                      email = "jesse.hemerik@wur.nl"),
               person(given = "Livio",
                      family = "Finos",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'randomForestSRC', 'knitr', 'rmarkdown'

VignetteBuilder package required 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:
  'collapsibleTree', 'config', 'DT', 'golem', 'plotly'

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

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?
Maintainer: ‘Daniel Doktor <daniel.doktor@ufz.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Maximilian",
                      family = "Lange",
                      role = "aut"),
               person(given = "Daniel",
                      family = "Doktor",
                      role = c("aut", "cre"),
                      email = "daniel.doktor@ufz.de"))
as necessary.
Maintainer: ‘Maximilian Lange <maximilian.lange@ufz.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Maximilian",
                    family = "Lange",
                    role = c("aut", "cre"),
                    email = "maximilian.lange@ufz.de")
as necessary.
Maintainer: ‘Koen Hufkens <koen.hufkens@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:
  'covr', 'knitr', 'rmarkdown', 'leaflet', 'plotly', 'DT'

VignetteBuilder package required 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: ‘Bijan Seyednasrollah <bijan.s.nasr@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Bijan",
                      family = "Seyednasrollah",
                      role = c("aut", "cre"),
                      email = "bijan.s.nasr@gmail.com"),
               person(given = c("Jennifer", "J."),
                      family = "Swenson",
                      role = "aut"),
               person(given = "Jean-Christophe",
                      family = "Domec",
                      role = "aut"),
               person(given = c("James", "S."),
                      family = "Clark",
                      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’
Package has ‘vignettes’ subdirectory 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
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: ‘Maximilian Lange <maximilian.lange@ufz.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Joerg",
                      family = "Schaber",
                      role = "aut"),
               person(given = "Maximilian",
                      family = "Lange",
                      role = "cre",
                      email = "maximilian.lange@ufz.de"))
as necessary.
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:29: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:31: Escaped LaTeX specials: \_ \_
checkRd: (-1) maxConnectedSet.Rd:35: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:37: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:39: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:41: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:45: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:47: Escaped LaTeX specials: \_ \_
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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:
  'gt', 'knitr', 'DiagrammeR', 'reactable', 'reactablefmtr',
  'sortable', 'DT', 'plotly', 'usethis', 'rmarkdown', 'visOmopResults',
  'rsconnect'

VignetteBuilder package required 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: ‘Hannah Meyer <hannah.v.meyer@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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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.
Maintainer: ‘Janez Komelj <jkomelj@siol.net>’

The Description field contains
  <doi:10.4236/ajcm.2023.134026> (or reprint <arXiv:2312.00011> with
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Ursula Neumann <ursula.neumann@uni-marburg.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Nikolas",
                      family = "Rothe",
                      role = "aut"),
               person(given = "Ursula",
                      family = "Neumann",
                      role = c("aut", "cre"),
                      email = "ursula.neumann@uni-marburg.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?
Package required but not available: ‘yaml’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘John E. Kolassa <kolassa@stat.rutgers.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("John", "E."),
                      family = "Kolassa",
                      role = c("aut", "cre"),
                      email = "kolassa@stat.rutgers.edu"),
               person(given = "Juan",
                      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’
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: ‘smallstuff’

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: 'FactoMineR', '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.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'qwraps2', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', '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: ‘rmarkdown’

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

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', '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: ‘Daniel R. McCloy <drmccloy@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Daniel", "R."),
                    family = "McCloy",
                    role = c("aut", "cre"),
                    email = "drmccloy@uw.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.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘indo.Rd’:
    http://dx.doi.org/10.1121/1.4870068
  File ‘normVowels.Rd’:
    http://dx.doi.org/10.1016/0378-5955(90)90170-T
    http://dx.doi.org/10.1121/1.1912396
    http://dx.doi.org/10.1121/1.399849
  File ‘repulsiveForce.Rd’:
    http://dx.doi.org/10.1177/0023830914559234
    http://dx.doi.org/10.1145/378456.378457
Maintainer: ‘Santiago Barreda <sbarreda@ucdavis.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Santiago",
                    family = "Barreda",
                    role = c("aut", "cre"),
                    email = "sbarreda@ucdavis.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:
  'fda.usc', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'roxygen2', '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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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 ‘photon-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: with_photon
> ### Title: Local photon instances
> ### Aliases: with_photon
> 
> ### ** Examples
> 
> # Get a public instance
> pub_photon <- new_photon()
> 
> # Mount a custom instance
> new_photon(url = "https://localhost:8001/")
<photon>
  Type   : remote
  Server : https://localhost:8001/
> 
> # Geocode with the public instance only once
> with_photon(pub_photon, geocode("Rutland"))
Error in `httr2::req_perform()`:
! HTTP 502 Bad Gateway.
Backtrace:
     ▆
  1. ├─photon::with_photon(pub_photon, geocode("Rutland"))
  2. │ └─base::force(code)
  3. └─photon::geocode("Rutland")
  4.   └─base::.mapply(iter, MoreArgs = options, FUN = geocode_impl)
  5.     └─photon (local) `<fn>`(q = dots[[1L]][[1L]], i = dots[[2L]][[1L]], env = `<env>`)
  6.       └─photon:::query_photon(...)
  7.         └─httr2::req_perform(req)
  8.           └─httr2:::handle_resp(req, resp, error_call = error_call)
  9.             └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 10.               ├─rlang::catch_cnd(...)
 11.               │ ├─rlang::eval_bare(...)
 12.               │ ├─base::tryCatch(...)
 13.               │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.               │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.               │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 16.               │ └─base::force(expr)
 17.               └─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: '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:
    ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’
    ‘constants.R’ ‘enviro-par.R’ ‘fit_aq_response.R’
    ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’
    ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’
    ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’
    ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'tidyverse', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'gt', '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:
  '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: ‘Jennifer Pohle <jennifer.pohle@uni-bielefeld.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jennifer",
                    family = "Pohle",
                    role = c("aut", "cre"),
                    email = "jennifer.pohle@uni-bielefeld.de")
as necessary.

The Description field contains
  hidden semi-Markov models. <arXiv:2101.09197>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Caterina Pisani <caterina.pisani@unisi.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Caterina",
                    family = "Pisani",
                    role = c("aut", "cre"),
                    email = "caterina.pisani@unisi.it")
as necessary.
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?
checkRd: (-1) 11_d.init.method.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:21-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:24-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:27-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:31-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:29: Lost braces in \itemize; meant \describe ?
Maintainer: ‘John R. Stevens <john.r.stevens@usu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("J.", "Conrad"),
                      family = "Stack",
                      role = "aut"),
               person(given = c("John", "R."),
                      family = "Stevens",
                      role = "cre",
                      email = "john.r.stevens@usu.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: ‘Pedro Tarroso <ptarroso@cibio.up.pt>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Pedro",
                      family = "Tarroso",
                      role = c("aut", "cre"),
                      email = "ptarroso@cibio.up.pt"),
               person(given = "Guillermo",
                      family = "Velo-Anton",
                      role = "aut"),
               person(given = "Silvia",
                      family = "Carvalho",
                      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: ‘Francois Michonneau <francois.michonneau@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("R", "Hackathon", "et"),
                      family = "al.",
                      role = "aut",
                      comment = "alphabetically: Ben Bolker, Marguerite Butler,\n    Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut\n    Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara,\n    Emmanuel Paradis, Jim Regetz, Derrick Zwickl"),
               person(given = "Francois",
                      family = "Michonneau",
                      role = "cre",
                      email = "francois.michonneau@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: ‘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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Shaun Wilkinson <shaunpwilkinson@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 package required 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: ‘Ramon Diaz-Uriarte <rdiaz02@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ramon",
                      family = "Diaz-Uriarte",
                      role = c("aut", "cre"),
                      email = "rdiaz@cnio.es"),
               person(given = "Theodore",
                      family = "Garland",
                      role = "aut"),
               person(family = "Jr",
                      role = "aut",
                      email = "theodore.garland@ucr.edu"))
as necessary.
checkRd: (-1) GarlandJanis.IC.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.IC.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:7: Escaped LaTeX specials: \&
Maintainer: ‘Xia Hua <xia.hua@anu.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xia",
                      family = "Hua",
                      role = c("aut", "cre"),
                      email = "xia.hua@anu.edu.au"),
               person(given = "Lindell",
                      family = "Bromham",
                      role = "aut",
                      email = "lindell.bromham@anu.edu.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'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'rJava'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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:
  'semPlot', 'knitr', 'rmarkdown'

Package which this enhances but not available for checking: ‘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?
Maintainer: ‘Julia Fukuyama <julia.fukuyama@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Julia",
                    family = "Fukuyama",
                    role = c("aut", "cre"),
                    email = "julia.fukuyama@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: ‘Francois Keck <francois.keck@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Francois",
                    family = "Keck",
                    role = c("aut", "cre"),
                    email = "francois.keck@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', '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: ‘Daniel Beer <dlbeer@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Daniel",
                      family = "Beer",
                      role = c("aut", "cre"),
                      email = "dlbeer@gmail.com"),
               person(given = "Anusha",
                      family = "Beer",
                      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: ‘Alan Grafen <alan.grafen@sjc.ox.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alan",
                    family = "Grafen",
                    role = c("aut", "cre"),
                    email = "alan.grafen@sjc.ox.ac.uk")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'INLA', '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: ‘J. Dustin Tracy <tracy@chapman.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("J.", "Dustin"),
                      family = "Tracy",
                      role = c("aut", "cre"),
                      email = "tracy@chapman.edu"),
               person(given = "Zhiyi",
                      family = "Xu",
                      role = "aut"),
               person(given = "Sari",
                      family = "Acra",
                      role = "aut"),
               person(given = c("Kong", "Y."),
                      family = "Chen",
                      role = "aut"),
               person(given = c("Maciej", "S."),
                      family = "Buchowski",
                      role = "aut"),
               person(given = "Thomas",
                      family = "Donnelly",
                      role = "aut"))
as necessary.
checkRd: (-1) pa-internal.Rd:11: Lost braces
    11 | code{l2df}: convert list to data.frame
       |     ^
checkRd: (-1) pa-internal.Rd:14: Lost braces
    14 | code{convertTZ}: force a new timezone on datetime
       |     ^
checkRd: (-1) pa-internal.Rd:16: Lost braces
    16 | code{createTime}: create datetime variable
       |     ^
checkRd: (-1) pa-internal.Rd:18: Lost braces
    18 | code{addDayIndex}: create ID_day variable from timestamp
       |     ^
Running examples in ‘PhysicalActivity-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: deliveryPred
> ### Title: Wrapper Function for Accelerometry data Preprocessing, Feature
> ###   Extraction, and Delivery Prediction
> ### Aliases: deliveryPred
> 
> ### ** Examples
> 
> data(deliveryData)
> 
> predictions <- deliveryPred(df = deliveryData, model = "GLM")
Warning in deliveryPreprocess(df = df) :
  .id unspecified - dummy ID created
Error: deliveryPrediction requires the rms package, please install it.
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
dataCollapser 5.836  0.032   7.005
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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’

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’
Running ‘test-making-price-indexes.R’ [0s/0s]
  Running ‘testthat.R’ [6s/6s]
Running the tests in ‘tests/test-making-price-indexes.R’ failed.
Complete output:
  > ## ----include = FALSE----------------------------------------------------------
  > knitr::opts_chunk$set(
  +   collapse = TRUE,
  +   comment = "#>"
  + )
  Error in loadNamespace(x) : there is no package called 'knitr'
  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?
Maintainer: ‘Steven W. Kembel <steve.kembel@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Steven", "W."),
                      family = "Kembel",
                      role = c("aut", "cre"),
                      email = "steve.kembel@gmail.com"),
               person(given = c("David", "D."),
                      family = "Ackerly",
                      role = "aut",
                      email = "dackerly@berkeley.edu"),
               person(given = c("Simon", "P."),
                      family = "Blomberg",
                      role = "aut",
                      email = "s.blomberg1@uq.edu.au"),
               person(given = c("Will", "K."),
                      family = "Cornwell",
                      role = "aut",
                      email = "cornwell@zoology.ubc.ca"),
               person(given = c("Peter", "D."),
                      family = "Cowan",
                      role = "aut",
                      email = "pdc@berkeley.edu"),
               person(given = c("Matthew", "R."),
                      family = "Helmus",
                      role = "aut",
                      email = "mrhelmus@wisc.edu"),
               person(given = "Helene",
                      family = "Morlon",
                      role = "aut",
                      email = "morlon.helene@gmail.com"),
               person(given = c("Campbell", "O."),
                      family = "Webb",
                      role = "aut",
                      email = "cwebb@oeb.harvard.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.
checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) sample2matrix.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sample2matrix.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sample2matrix.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
Maintainer: ‘Chun Pan <chunpan2003@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Chun",
                    family = "Pan",
                    role = c("aut", "cre"),
                    email = "chunpan2003@hotmail.com")
as necessary.
Maintainer: ‘Matt Deppe <deppemj@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Matt",
                    family = "Deppe",
                    role = c("aut", "cre"),
                    email = "deppemj@gmail.com")
as necessary.
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’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘exr-read.R’ ‘exr-types-read.R’ ‘exr-write.R’ ‘utils.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) tradeOffTable.Rd:28: height/width attributes should be in pixels
Maintainer: ‘Andrew G. Chapple <agc6@rice.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Andrew", "G."),
                    family = "Chapple",
                    role = c("aut", "cre"),
                    email = "agc6@rice.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: ‘univariateML’

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

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: ‘ggiraph’

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?
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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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
Package required but not available: ‘knitr’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Marco Blume <marco.blume@pinnaclesports.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Marco",
                      family = "Blume",
                      role = c("aut", "cre"),
                      email = "marco.blume@pinnaclesports.com"),
               person(given = "Michael",
                      family = "Yan",
                      role = "aut"))
as necessary.
Running examples in ‘pinnacle.data-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: USA_Election_2016
> ### Title: USA_Election_2016
> ### Aliases: USA_Election_2016
> ### Keywords: datasets
> 
> ### ** Examples
> 
> if (require("odds.converter")) {
+ library(tidyverse)
+ # What is Hilary Clinton's the highest implied winning probability at Pinnacle?
+ 
+ USA_Election_2016[which.min(USA_Election_2016$MoneyUS1),"EnteredDateTime"]
+ odds.converter::odds.us2prob(min(USA_Election_2016$MoneyUS1))
+ }
Loading required package: odds.converter
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
Maintainer: ‘Danilo Freire <danilofreire@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:
  'devtools', 'kableExtra', '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?
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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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’

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

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: '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: ‘reactable’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Author field differs from that derived from Authors@R
  Author:    ‘Brenton M. Wiernik [cre, aut] (<https://orcid.org/0000-0001-9560-6336>, @bmwiernik)’
  Authors@R: ‘Brenton M. Wiernik [cre, aut] (ORCID: <https://orcid.org/0000-0001-9560-6336>, Twitter: @bmwiernik)’

  Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘aliases.Rd’ ‘bind.Rd’
Maintainer: ‘Michael Sweeting <mjs212@medschl.cam.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Michael",
                    family = "Sweeting",
                    role = c("aut", "cre"),
                    email = "mjs212@medschl.cam.ac.uk")
as necessary.
Maintainer: ‘Sahil Seth <me@sahilseth.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Houston", "R"),
                      family = "Users",
                      role = "aut"),
               person(given = "Neeraj",
                      family = "Tandon",
                      role = "aut"),
               person(given = "Ed",
                      family = "Goodwin",
                      role = "aut"),
               person(given = c("Ju", "Yeong"),
                      family = "Kim",
                      role = "aut"),
               person(given = "Sahil",
                      family = "Seth",
                      role = c("aut", "cre"),
                      email = "me@sahilseth.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'visNetwork'

VignetteBuilder package required 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: ‘Alex Ioannides <alex.ioannides@yahoo.co.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alex",
                    family = "Ioannides",
                    role = c("aut", "cre"),
                    email = "alex.ioannides@yahoo.co.uk")
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?
Maintainer: ‘Kun Ren <ken@renkun.me>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kun",
                    family = "Ren",
                    role = c("aut", "cre"),
                    email = "ken@renkun.me")
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: ‘Lars Van Cutsem <lars.vancutsem@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Lars",
                    family = "Van Cutsem",
                    role = c("aut", "cre"),
                    email = "lars.vancutsem@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?
Maintainer: ‘Leonardo Egidi <legidi@units.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Leonardo",
                      family = "Egidi",
                      role = c("aut", "cre"),
                      email = "legidi@units.it"),
               person(given = "Roberta",
                      family = "Pappadà",
                      role = "aut"),
               person(given = "Francesco",
                      family = "Pauli",
                      role = "aut"),
               person(given = "Nicola",
                      family = "Torelli",
                      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', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = identical(Sys.getenv("TRAVIS"), "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?
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:
    ‘extract_col.Rd’ ‘na2empty.Rd’ ‘omit_na_cols.Rd’ ‘omit_na_rows.Rd’
    ‘pivot.R’ ‘pivot.Rd’ ‘utils.R’ ‘validate_col.Rd’
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:
  'listviewer', 'basictabler', 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Martin Stingl <martin.stingl@dfv.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Martin",
                    family = "Stingl",
                    role = c("aut", "cre"),
                    email = "martin.stingl@dfv.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', '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 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: ‘htmlwidgets’

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.
Packages required but not available:
  'DiagrammeR', 'DT', 'yaml', 'rhandsontable'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Eun-Kyung Lee <lee.eunk@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Eun-Kyung",
                      family = "Lee",
                      role = c("aut", "cre"),
                      email = "lee.eunk@gmail.com"),
               person(given = "Hye-sun",
                      family = "Cho",
                      role = "aut"))
as necessary.
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.
Package required but not available: ‘visNetwork’

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: ‘pkgdown’

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: 'downlit', 'rmarkdown', 'yaml'

Packages suggested but not available for checking:
  'covr', 'diffviewer', 'gt', 'htmlwidgets', 'knitr', 'quarto',
  'rsconnect', 'rticles'

VignetteBuilder packages required for checking but not installed:
  'knitr', '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: ‘networkD3’

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: ‘DiagrammeR’

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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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:
  'covr', 'DT', 'knitr', 'rmarkdown', 'visNetwork'

Package suggested but not available for checking: ‘pkgdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Meta-Lina Spohn <metalina.spohn@stat.math.ethz.ch>’

The Description field contains
  Michel et al. (2021) <arXiv:2109.10150>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Francois Deslandes <francois.deslandes@inra.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jade",
                      family = "Giguelay",
                      role = "aut"),
               person(given = "Francois",
                      family = "Deslandes",
                      role = "cre",
                      email = "francois.deslandes@inra.fr"))
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'

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

Package in Depends/Imports which should probably only be in LinkingTo: ‘BH’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Thomas Jaki <jaki.thomas@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Thomas",
                      family = "Jaki",
                      role = c("aut", "cre"),
                      email = "jaki.thomas@gmail.com"),
               person(given = c("Martin", "J."),
                      family = "Wolfsegger",
                      role = "aut",
                      email = "wolfseggerm@gmx.at"))
as necessary.
Maintainer: ‘Kyun-Seop Bae <k@acr.kr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Kyun-Seop",
                      family = "Bae",
                      role = c("aut", "cre"),
                      email = "k@acr.kr"),
               person(given = c("Jee", "Eun"),
                      family = "Lee",
                      role = "aut"))
as necessary.
Maintainer: ‘Nan-Hung Hsieh <d99622005@ntu.edu.tw>’

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’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Davi Castro-Tavares <davi.tavares@leibniz-zmt.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.
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?
Cannot process vignettes
Packages suggested but not available for checking:
  'BiocStyle', 'PLMIX', 'bookdown', 'covr', '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: ‘htmlwidgets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Erick Marroquin <ericksuhel@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Erick",
                    family = "Marroquin",
                    role = c("aut", "cre"),
                    email = "ericksuhel@gmail.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?
Maintainer: ‘Dan Kelley <Dan.Kelley@Dal.Ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dan",
                      family = "Kelley",
                      role = c("aut", "cre"),
                      email = "Dan.Kelley@Dal.Ca"),
               person(given = "Frank",
                      family = "Schmitt",
                      role = "aut",
                      email = "frankschmitt@gmx.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:
  'highcharter', 'knitr', 'reactable', 'reactablefmtr', 'rmarkdown',
  'tidyverse', 'sparkline', 'DT', 'DiagrammeR', 'networkD3'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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'

VignetteBuilder package required 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: ‘Yves Rozenholc <yves.rozenholc@parisdescartes.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yves",
                      family = "Rozenholc",
                      role = c("aut", "cre"),
                      email = "yves.rozenholc@parisdescartes.fr"),
               person(given = "Nicolas",
                      family = "Pécuchet",
                      role = "aut"),
               person(given = "Pierre",
                      family = "Laurent-Puig",
                      role = "aut"))
as necessary.
Packages required but not available: 'VariantAnnotation', 'rtracklayer'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'htmlwidgets', '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 package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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’
checkRd: (-1) one_design.Rd:125-126: Lost braces
   125 | function serves for the purpose of spot-testing for any pre-specified {n,
       |                                                                       ^
Package has ‘vignettes’ subdirectory 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: 'ggtree', 'knitr', 'Seurat'

Package suggested but not available for checking: ‘tidyverse’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 = c("aut", "cre"),
                      email = "alec_stephenson@hotmail.com"),
               person(given = "Jeff",
                      family = "Sonas.",
                      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:
    ‘plot_season_form.R’
Maintainer: ‘JungJun Lee <ljjoj@korea.ac.kr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "JungJun",
                      family = "Lee",
                      role = c("aut", "cre"),
                      email = "ljjoj@korea.ac.kr"),
               person(given = "Jae-Hwan",
                      family = "Jhong",
                      role = "aut"),
               person(given = "Young-Rae",
                      family = "Cho",
                      role = "aut"),
               person(given = "SungHwan",
                      family = "Kim",
                      role = "aut"),
               person(given = "Ja-yong",
                      family = "Koo",
                      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: ‘Jason Sinnwell <sinnwell.jason@mayo.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Daniel", "J"),
                      family = "Schaid",
                      role = "aut"),
               person(given = "Jason",
                      family = "Sinnwell",
                      role = "cre",
                      email = "sinnwell.jason@mayo.edu"))
as necessary.
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  getXX_XYc.cpp:26:25: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = int; typename arma_scalar_only<T>::result = int]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  getXX_XYc.cpp:52:25: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pleiotest.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-15 (Debian 15.2.0-9) 15.2.0’
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: ‘keras’

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: ‘Dhammapal Bharne <dhammapalb@uohyd.ac.in>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dhammapal",
                      family = "Bharne",
                      role = c("aut", "cre"),
                      email = "dhammapalb@uohyd.ac.in"),
               person(given = "Vaibhav",
                      family = "Vindal",
                      role = "aut"))
as necessary.
Maintainer: ‘Robert B. Gramacy <rbg@vt.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Robert", "B."),
                    family = "Gramacy",
                    role = c("aut", "cre"),
                    email = "rbg@vt.edu")
as necessary.

The Description field contains
  (PL) following Gramacy & Polson (2011) <arXiv:0909.5262>.  The
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
'library' or 'require' call not declared from: ‘MASS’
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/logst.Rnw’
   ‘inst/doc/pl-description.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
✖ Package EBImage is required. Please install it from <https://bioconductor.org/packages/EBImage>
! To use `viewer = 'mapview'`, install the following packages: mapview, mapedit, leaflet, and leafem

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Jonathan P. Weeks <weeksjp@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Jonathan", "P."),
                    family = "Weeks",
                    role = c("aut", "cre"),
                    email = "weeksjp@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.
Maintainer: ‘Zhi Wei <zhiwei04@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Zhi", "Wei", "&", "Wenguang"),
                      family = "Sun",
                      role = "aut"),
               person(given = "Zhi",
                      family = "Wei",
                      role = "cre",
                      email = "zhiwei04@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: ‘radarchart’

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:
  'factoextra', '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: ‘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.
Maintainer: ‘Euloge Clovis Kenne Pagui <kenne@stat.unipd.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Euloge", "Clovis", "Kenne"),
                      family = "Pagui",
                      role = c("aut", "cre"),
                      email = "kenne@stat.unipd.it"),
               person(given = "Antonio",
                      family = "Canale",
                      role = "aut"),
               person(given = "Alan",
                      family = "Genz",
                      role = "ctb"),
               person(given = "Adelchi",
                      family = "Azzalini",
                      role = "ctb"))
as necessary.
checkRd: (-1) delta2a.Rd:21: Lost braces; missing escapes or markup?
    21 | delta_k = log(a_k - a_{k+1})
       |                       ^
checkRd: (-1) ordprob.mple.Rd:29: Lost braces
    29 | logical. If code{TRUE} all the q variable are assumed to have the same mean.
       |                 ^
Maintainer: ‘Takahiko Koizumi <takahiko.koizumi@riken.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Takahiko",
                      family = "Koizumi",
                      role = c("aut", "cre"),
                      email = "takahiko.koizumi@riken.jp"),
               person(given = "Kenta",
                      family = "Suzuki",
                      role = "aut"),
               person(given = "Yasunori",
                      family = "Ichihashi",
                      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?
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?
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?
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’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Olivia Cheronet <cheronetolivia@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Olivia",
                    family = "Cheronet",
                    role = c("aut", "cre"),
                    email = "cheronetolivia@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', 'ChemoSpec'

VignetteBuilder package required for checking but 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’
checkRd: (-1) add_bars.Rd:15: Lost braces
    15 | When \\code{y0} is not specified, the lowest value of the y-axis is used.}
       |            ^
checkRd: (-1) add_bars.Rd:24: Lost braces
    24 | \\code{\\link[graphics]{par}}.}
       |       ^
checkRd: (-1) add_bars.Rd:24: Lost braces
    24 | \\code{\\link[graphics]{par}}.}
       |                        ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Running examples in ‘plotGMM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_GMM
> ### Title: Plots Mixture Components from Gaussian Mixture Models
> ### Aliases: plot_GMM
> 
> ### ** Examples
> 
> set.seed(235)
> mixmdl <- mixtools::normalmixEM(faithful$waiting, k = 2)
Error in loadNamespace(x) : there is no package called ‘mixtools’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Cannot process vignettes
Packages suggested but not available for checking: '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?
Package required but not available: ‘Hmisc’

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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’

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

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

VignetteBuilder package required 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’

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: ‘Stephen Milborrow <milbo@sonic.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Stephen",
                    family = "Milborrow",
                    role = c("aut", "cre"),
                    email = "milbo@sonic.net")
as necessary.
Maintainer: ‘Joaquin Bienvenido Ordieres Mere <j.ordieres@upm.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Javier", "Celigueta"),
                      family = "Mu<b1>oz",
                      role = "aut",
                      email = "b1"),
               person(given = c("Joaquin", "Bienvenido", "Ordieres"),
                      family = "Mere",
                      role = "cre",
                      email = "j.ordieres@upm.es"))
as necessary.
Maintainer: ‘Yao Geng <gengyao0103521@qq.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xiaoyu",
                      family = "Zhang",
                      role = "aut"),
               person(given = "Yao",
                      family = "Geng",
                      role = "cre",
                      email = "gengyao0103521@qq.com"))
as necessary.
checkRd: (-1) domain_data.Rd:29: Lost braces
    29 | code{\link{help}}
       |     ^
checkRd: (-1) length_data.Rd:32: Lost braces
    32 | code{\link{help}}
       |     ^
checkRd: (-1) plotdomain.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotmutagensis.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotprotein-package.Rd:20: Lost braces
    20 | code{\link{help}}
       |     ^
checkRd: (-1) plotprotein.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotsite.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) site_data.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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'

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: ‘January Weiner <january.weiner@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "January",
                    family = "Weiner",
                    role = c("aut", "cre"),
                    email = "january.weiner@gmail.com")
as necessary.
Maintainer: ‘Felipe Queiroz <ffelipeq@outlook.com>’

The Description field contains
  are described in Queiroz and Ferrari (2022) <arXiv:2202.01697>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Ana Lopez-Cheda <ana.lopez.cheda@udc.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("German", "Aneiros"),
                      family = "Perez",
                      role = "aut"),
               person(given = "Ana",
                      family = "Lopez-Cheda",
                      role = c("aut", "cre"),
                      email = "ana.lopez.cheda@udc.es"))
as necessary.
Maintainer: ‘Ghislain Durif <gd.dev@libertymail.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Anne-Laure",
                      family = "Boulesteix",
                      role = "aut",
                      email = "boulesteix@ibe.med.uni-muenchen.de"),
               person(given = "Ghislain",
                      family = "Durif",
                      role = c("aut", "cre"),
                      email = "gd.dev@libertymail.net"),
               person(given = "Sophie",
                      family = "Lambert-Lacroix",
                      role = "aut",
                      email = "sophie.lambert-lacroix@univ-grenoble-alpes.fr"),
               person(given = "Julie",
                      family = "Peyre",
                      role = "aut",
                      email = "Julie.Peyre@univ-grenoble-alpes.fr"),
               person(given = "Korbinian",
                      family = "Strimmer.",
                      role = "aut",
                      email = "k.strimmer@imperial.ac.uk"))
as necessary.
Maintainer: ‘Shunyao Wu <wushunyao@qdu.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Shunyao",
                      family = "Wu",
                      role = c("aut", "cre"),
                      email = "wushunyao@qdu.edu.cn"),
               person(given = "Qi",
                      family = "Zhang",
                      role = "aut"),
               person(given = "Zhiruo",
                      family = "Li",
                      role = "aut"),
               person(given = "Hua",
                      family = "Liang",
                      role = "aut"))
as necessary.
Specified C++11: support will be removed soon
Package required but not available: ‘mixOmics’

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

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?
Packages suggested but not available for checking: 'FactoMineR', 'knitr'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/plspm_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:
  '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?
Packages required but not available: 'mixOmics', 'survAUC', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Martin Maechler <maechler@stat.math.ethz.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Eva", "Herrmann;", "R", "interface", "etc", "by", "Martin"),
                      family = "Maechler",
                      role = "aut",
                      email = "eherrmann@mathematik.tu-darmstadt.de",
                      comment = "C original"),
               person(given = "Martin",
                      family = "Maechler",
                      role = "cre",
                      email = "maechler@stat.math.ethz.ch"))
as necessary.
Package required but not available: ‘keyring’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fiery', 'roxygen2', 'yaml'

Packages suggested but not available for checking: 'htmlwidgets', 'quarto'

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: ‘analogsea’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [19s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(plumber)
  > 
  > test_check("plumber")
  Saving _problems/test-serializer-htmlwidgets-39.R
  Saving _problems/test-zzz-openapi-347.R
  [ FAIL 2 | WARN 0 | SKIP 19 | PASS 1899 ]
  
  ══ Skipped tests (19) ══════════════════════════════════════════════════════════
  • On CRAN (15): 'test-cookies.R:47:3', 'test-deprecated.R:60:3',
    'test-find-port.R:40:3', 'test-find-port.R:56:3', 'test-legacy.R:20:3',
    'test-options.R:22:3', 'test-plumber-print.R:2:3',
    'test-plumber-print.R:60:3', 'test-plumber.R:67:3',
    'test-serializer-device.R:26:1', 'test-serializer-htmlwidgets.R:18:3',
    'test-static.R:23:3', 'test-zzz-openapi.R:254:3',
    'test-zzz-plumb_api.R:10:3', 'test-zzz-plumb_api.R:65:3'
  • {rmarkdown} is not installed. (1): 'test-zzzz-include.R:22:3'
  • {yaml} is not installed (3): 'test-parse-body.R:46:3',
    'test-serializer-yaml.R:4:3', 'test-serializer-yaml.R:26:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-serializer-htmlwidgets.R:37:3'): Errors call error handler ─────
  Error: The htmlwidgets package is not available but is required in order to use the htmlwidgets serializer
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-serializer-htmlwidgets.R:37:3
   2. │ └─base::withCallingHandlers(...)
   3. └─plumber::serializer_htmlwidget()
  ── Error ('test-zzz-openapi.R:347:3'): Api spec can be set using a file path ───
  Error in `pr$setApiSpec(api = api)`: yaml must be installed to read yaml format
  Backtrace:
      ▆
   1. ├─pr() %>% pr_set_api_spec(test_path("files/openapi.yaml")) at test-zzz-openapi.R:347:3
   2. └─plumber::pr_set_api_spec(., test_path("files/openapi.yaml"))
   3.   └─pr$setApiSpec(api = api)
  
  [ FAIL 2 | WARN 0 | SKIP 19 | PASS 1899 ]
  Error:
  ! Test failures.
  Execution halted
Package required but not available: ‘knitr’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Michael Lawrence <michafla@gene.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Michael",
                      family = "Lawrence",
                      role = c("aut", "cre"),
                      email = "michafla@gene.com"),
               person(given = "Hadley",
                      family = "Wickham",
                      role = "aut"))
as necessary.
Packages required but not available: 'knitr', 'yaml'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plu_more.Rd:16: Lost braces; missing escapes or markup?
    16 | Additional arguments are replaced with "{n} more".
       |                                         ^
Maintainer: ‘Michael Doyle <michaeledoyle7@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Michael",
                    family = "Doyle",
                    role = c("aut", "cre"),
                    email = "michaeledoyle7@gmail.com")
as necessary.
Package required but not available: ‘baizer’

Package suggested but not available for checking: ‘covr’

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

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: 'rmarkdown', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Wei-Chen Chen <wccsnow@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', 'NSM3'

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) PMCMR-deprecated.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
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: ‘enviGCMS’

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?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘earned_value.R’ ‘planned_value.R’ ‘pmevR6.R’
Maintainer: ‘Johan Dahlin <uni@johandahlin.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Johan",
                    family = "Dahlin",
                    role = c("aut", "cre"),
                    email = "uni@johandahlin.com")
as necessary.
Package required but not available: ‘pmcalibration’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) pmledecon.Rd:113: Lost braces; missing escapes or markup?
   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                              ^
checkRd: (-1) pmledecon.Rd:113: Lost braces; missing escapes or markup?
   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                                                         ^
Cannot process vignettes
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  '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: ‘Dmitriy Bolotov <rpmmlsupport@softwareag.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Tridivesh",
                      family = "Jena",
                      role = "aut"),
               person(given = c("Wen", "Ching"),
                      family = "Lin",
                      role = "aut"),
               person(given = "Dmitriy",
                      family = "Bolotov",
                      role = c("aut", "cre"),
                      email = "rpmmlsupport@softwareag.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: ‘Paul H. Lee <honglee@graduate.hku.hk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Paul", "H."),
                      family = "Lee",
                      role = c("aut", "cre"),
                      email = "honglee@graduate.hku.hk"),
               person(given = c("Philip", "L.", "H."),
                      family = "Yu",
                      role = "aut"))
as necessary.
checkRd: (-1) ahp.Rd:16: Lost braces; missing escapes or markup?
    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                   ^
checkRd: (-1) ahp.Rd:16: Lost braces; missing escapes or markup?
    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                              ^
Maintainer: ‘Alexander Davis <ajdavis2@mdanderson.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alexander",
                    family = "Davis",
                    role = c("aut", "cre"),
                    email = "ajdavis2@mdanderson.org")
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:
  'config', 'flextable', 'golem', 'htmlwidgets', 'rhandsontable'

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
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  'nlmixr2', 'lixoftConnectors', 'knitr', 'rmarkdown'

VignetteBuilder 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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Packages required but not available: 'table1', 'knitr'

Packages suggested but not available for checking: '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'

VignetteBuilder package required 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', 'tidyverse'

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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: person(given = "Simon",
                    family = "Urbanek",
                    role = c("aut", "cre"),
                    email = "Simon.Urbanek@r-project.org")
as necessary.
Cannot process vignettes
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  '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: ‘Jake Lawlor <jakealawlor@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jake",
                    family = "Lawlor",
                    role = c("aut", "cre"),
                    email = "jakealawlor@gmail.com")
as necessary.
Maintainer: ‘Hector Haffenden <haffendenh@cardiff.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hector",
                    family = "Haffenden",
                    role = c("aut", "cre"),
                    email = "haffendenh@cardiff.ac.uk")
as necessary.
Package required but not available: ‘usethis’

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: ‘Dabao Zhang <zhangdb@purdue.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dabao",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "zhangdb@purdue.edu"),
               person(given = "Zhongli",
                      family = "Jiang",
                      role = "aut"),
               person(given = "Zeyu",
                      family = "Zhang",
                      role = "aut"),
               person(given = "Yu-ting",
                      family = "Chen",
                      role = "aut"))
as necessary.
Maintainer: ‘"Brewer, Ben (arb5mt)" <arb5mt@virginia.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Nolan", "A."),
                      family = "Wages",
                      role = "aut"),
               person(family = "\"Brewer",
                      role = "cre"),
               person(family = "Ben\"",
                      role = "cre",
                      email = "arb5mt@virginia.edu",
                      comment = "arb5mt"))
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: ‘Markus Boenn <markus.boenn.sf@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Markus",
                    family = "Boenn",
                    role = c("aut", "cre"),
                    email = "markus.boenn.sf@gmail.com",
                    comment = "State Office for Consumer Protection Saxony-Anhalt, Germany")
as necessary.
Package has ‘vignettes’ subdirectory 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: ‘Martina Mincheva <m.z.mincheva@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jianqing",
                      family = "Fan",
                      role = "aut"),
               person(given = "Yuan",
                      family = "Liao",
                      role = "aut"),
               person(given = "Martina",
                      family = "Mincheva",
                      role = c("aut", "cre"),
                      email = "m.z.mincheva@gmail.com"))
as necessary.
Maintainer: ‘Michaela Dvorzak <m.dvorzak@gmx.at>’

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: ‘Przemyslaw Biecek <przemyslaw.biecek@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Przemyslaw",
                    family = "Biecek",
                    role = c("aut", "cre"),
                    email = "przemyslaw.biecek@gmail.com")
as necessary.
Maintainer: ‘Daniela Witten <dwitten@u.washington.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Daniela",
                    family = "Witten",
                    role = c("aut", "cre"),
                    email = "dwitten@u.washington.edu")
as necessary.
Packages required but not available: 'blastula', 'gt', 'knitr', 'yaml'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Paul Evangelista <paul.evangelista@westpoint.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "\"Paul",
                      family = "Evangelista",
                      role = "aut",
                      email = "paul.evangelista@westpoint.edu"),
               person(given = "Dave",
                      family = "Beskow\"",
                      role = "aut",
                      email = "david.beskow@westpoint.edu"),
               person(given = "Paul",
                      family = "Evangelista",
                      role = "cre",
                      email = "paul.evangelista@westpoint.edu"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'INLA', 'knitr', 'kableExtra', 'rmarkdown', 'spocc', '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: ‘Patrick Schmidt <pschmidte@gmail.com>’

The Description field contains
  Katzfuss and Gneiting (2015) <arXiv:1506.01917> for more details on 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', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) estimate.functional.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{bw}{function describing bandwidth selection (see ?gmm for alternatives). Standard is that the bandwidth depends on the sample length $T$ by $m(T)=T^{1/5}$.}
       |                                                                                                                                                           ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Marieke van der Maaten-Theunissen <marieke.theunissen@tu-dresden.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Marieke",
                      family = "van der Maaten-Theunissen",
                      role = c("aut", "cph", "cre", "trl"),
                      email = "marieke.theunissen@tu-dresden.de"),
               person(given = "Ernst",
                      family = "van der Maaten",
                      role = c("aut", "trl")),
               person(given = "Gottfried",
                      family = "Jetsckhe",
                      role = c("aut", "trl")),
               person(given = "Mario",
                      family = "Trouillier",
                      role = c("aut", "trl")))
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: ‘Ran Gao <rgao8@uic.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gul",
                      family = "Inan",
                      role = "aut"),
               person(given = "Hakan",
                      family = "Demirtas",
                      role = "aut"),
               person(given = "Ran",
                      family = "Gao",
                      role = c("aut", "cre"),
                      email = "rgao8@uic.edu"))
as necessary.
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 = "Rachel",
                      family = "Nordgren",
                      role = "aut"),
               person(given = "Rawan",
                      family = "Allozi",
                      role = "aut"),
               person(given = "Ran",
                      family = "Gao",
                      role = c("aut", "cre"),
                      email = "rgao8@uic.edu"))
as necessary.
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 = "Yiran",
                      family = "Hu",
                      role = "aut"),
               person(given = "Rawan",
                      family = "Allozi",
                      role = "aut"),
               person(given = "Ran",
                      family = "Gao",
                      role = c("aut", "cre"),
                      email = "rgao8@uic.edu"))
as necessary.
Maintainer: ‘Ran Gao <rgao8@uic.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gul",
                      family = "Inan",
                      role = "aut"),
               person(given = "Hakan",
                      family = "Demirtas",
                      role = "aut"),
               person(given = "Ran",
                      family = "Gao",
                      role = c("aut", "cre"),
                      email = "rgao8@uic.edu"))
as necessary.
Maintainer: ‘David Kahle <david@kahle.io>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) pois.fe.robust.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pois.fe.robust.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pois.fe.robust.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
Maintainer: ‘David Cortes <david.cortes.rivera@gmail.com>’

The Description field contains
  bag-of-words-based topic modeling) (Cortes, (2018) <arXiv:1811.01908>),
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
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 = "Yaru",
                      family = "Shi",
                      role = "aut"),
               person(given = "Rawan",
                      family = "Allozi",
                      role = "aut"),
               person(given = "Ran",
                      family = "Gao",
                      role = c("aut", "cre"),
                      email = "rgao8@uic.edu"))
as necessary.
Maintainer: ‘Ran Gao <rgao8@uic.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Anup",
                      family = "Amatya",
                      role = "aut"),
               person(given = "Hakan",
                      family = "Demirtas",
                      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?
Maintainer: ‘Toby Kenney <tkenney@mathstat.dal.ca>’

The Description field contains
  Kenney, T. Huang, H. Gu (2019) <arXiv:1904.11745>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘David Pechel Cactcha <davidpechel@uy1.uninet.cm>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("David", "Pechel"),
                      family = "Cactcha",
                      role = c("aut", "cre"),
                      email = "davidpechel@uy1.uninet.cm"),
               person(given = c("Laure", "Pauline"),
                      family = "Fotso",
                      role = "aut"),
               person(given = c("Celestin", "C"),
                      family = "Kokonendji",
                      role = "aut"))
as necessary.
Packages required but not available: 'detourr', 'DT', 'plotly', 'quollr'

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

VignetteBuilder package required 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: ‘Drew Linzer <drew@votamatic.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Drew",
                      family = "Linzer",
                      role = c("aut", "cre"),
                      email = "drew@votamatic.org"),
               person(given = "Jeffrey",
                      family = "Lewis.",
                      role = "aut",
                      email = "jblewis@ucla.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.
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
Packages required but not available: 'quanteda', 'textstem'

Packages suggested but not available for checking:
  'rmarkdown', 'quanteda.textstats', 'keyATM'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Barry Edwards <barry.edwards@ucf.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Barry",
                      family = "Edwards",
                      role = c("aut", "cre"),
                      email = "barry.edwards@ucf.edu"),
               person(given = "Philip",
                      family = "Pollock",
                      role = "aut"))
as necessary.
Packages required but not available: 'Hmisc', 'weights'

Package suggested but not available for checking: ‘rgl’

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

Packages suggested but not available for checking: 'config', '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: 'NaileR', 'FactoMineR'

Package suggested but not available for checking: ‘SensoMineR’

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

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: ‘usethis’

Package suggested but not available for checking: ‘covr’

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:
    ‘hiperfrac.R’ ‘rice.R’
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: ‘SuperLearner’

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: 'DT', 'knitr'

Packages suggested but not available for checking:
  'rmarkdown', 'rhandsontable', '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: 'leaflet', 'DT', 'leaflet.extras'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Conrad Burden <conrad.burden@anu.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Conrad",
                    family = "Burden",
                    role = c("aut", "cre"),
                    email = "conrad.burden@anu.edu.au")
as necessary.

The Description field contains
  Conrad J. Burden (2014) <arXiv:1406.2780>.
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
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', 'DT'

VignetteBuilder package required 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: ‘Roeland E. Voorrips <roeland.voorrips@wur.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Roeland", "E."),
                    family = "Voorrips",
                    role = c("aut", "cre"),
                    email = "roeland.voorrips@wur.nl")
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?
Running examples in ‘polykde-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: index_ridge
> ### Title: Index a ridge curve, creating the Smoothed and Indexed Estimated
> ###   Ridge (SIER)
> ### Aliases: index_ridge
> 
> ### ** Examples
> 
> ## Test on (S^1)^2
> 
> # Sample
> set.seed(132121)
> r <- 2
> d <- rep(1, r)
> n <- 200
> ind_dj <- comp_ind_dj(d = d)
> Th <- matrix(runif(n = n * (r - 1), min = -pi / 2, max = pi / 2),
+              nrow = n, ncol = r - 1)
> Th[, r - 1] <- sort(Th[, r - 1])
> Th <- cbind(Th, sdetorus::toPiInt(
+   pi + Th[, r - 1] + runif(n = n, min = -pi / 4, max = pi / 4)))
> X <- angles_to_torus(Th)
> col_X_alp <- viridis::viridis(n, alpha = 0.25)
> col_X <- viridis::viridis(n)
> 
> # Euler
> h_rid <- rep(0.75, r)
> h_eu <- h_rid^2
> N <- 200
> eps <- 1e-6
> Y <- euler_ridge(x = X, X = X, d = d, h = h_rid, h_euler = h_eu,
+                  N = N, eps = eps, keep_paths = TRUE)
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
> 
> # Visualization
> i <- N # Between 1 and N
> plot(rbind(torus_to_angles(Y$paths[, , 1])), col = col_X_alp, pch = 19,
+      axes = FALSE, xlim = c(-pi, pi), ylim = c(-pi, pi),
+      xlab = "", ylab = "")
> points(rbind(torus_to_angles(Y$paths[, , i])), col = col_X, pch = 16,
+        cex = 0.75)
> sdetorus::torusAxis(1:2)
> for (k in seq_len(nrow(Y$paths))) {
+ 
+   xy <- torus_to_angles(t(Y$paths[k, , ]))
+   sdetorus::linesTorus(x = xy[, 1], y = xy[, 2], col = col_X_alp[k])
+ 
+ }
> 
> # SIER
> ind_rid <- index_ridge(endpoints = Y$ridge_y, X = X, d = d,
+                        probs_scores = seq(0, 1, l = 50))
Error in loadNamespace(x) : there is no package called ‘smacof’
Calls: index_ridge ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'knitr', 'MDSMap'

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

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Bill",
                      family = "Venables",
                      role = c("aut", "cre"),
                      email = "bill.venables@gmail.com"),
               person(given = c("with", "contribution", "by", "Kurt"),
                      family = "Hornik",
                      role = "aut"),
               person(given = "Georgi",
                      family = "Boshnakov",
                      role = "aut"),
               person(given = "Brian",
                      family = "Ripley.",
                      role = "aut"))
as necessary.
Cannot process vignettes
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VignetteBuilder 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: ‘Bill Venables <Bill.Venables@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?
Maintainer: ‘Alexander Zwart <Alec.Zwart@csiro.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alexander",
                    family = "Zwart",
                    role = c("aut", "cre"),
                    email = "alec.zwart@csiro.au")
as necessary.
checkRd: (-1) inputData.Rd:94: Lost braces
    94 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
checkRd: (-1) inputData.Rd:95: Lost braces
    95 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
checkRd: (-1) preprocessData.Rd:81: Lost braces
    81 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
checkRd: (-1) preprocessData.Rd:82: Lost braces
    82 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
checkRd: (-1) stat_quantile_prob.Rd:14: Lost braces; missing escapes or markup?
    14 | Number {25, 50, 75}
       |        ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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', 'knitr'

Packages suggested but not available for checking:
  'mappoly', 'polymapR', '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:
  'VariantAnnotation', 'knitr', 'rmarkdown', 'GenomicFeatures'

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: ‘Norm Matloff <matloff@cs.ucdavis.edu>’

The Description field contains
  Matloff, and Pete Mohanty (<arXiv:1806.06850>).
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: '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: ‘Peter Baker <p.baker1@uq.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.
checkRd: (-1) calculateDIC.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculateDIC.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polySegratioMM-package.Rd:70-72: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
Maintainer: ‘Peter Baker <p.baker1@uq.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Peter",
                    family = "Baker",
                    role = c("aut", "cre"),
                    email = "p.baker1@uq.edu.au")
as necessary.
Maintainer: ‘Sourav Chatterjee <souravc@stanford.edu>’

The Description field contains
  Vidyasagar (2022) <arxiv:2209.07028>. The method is fully
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Junghi Kim <junghikim0@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Junghi",
                      family = "Kim",
                      role = c("aut", "cre"),
                      email = "junghikim0@gmail.com"),
               person(given = "Wei",
                      family = "Pan",
                      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', 'visNetwork'

VignetteBuilder package required 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: ‘Cyril Piou <cyril.piou@cirad.fr>’

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 ‘Pomic-package.Rd’:
    http://dx.doi.org/10.1016/j.ecolmodel.2009.05.003
Maintainer: ‘Seyma Kalay <seymakalay@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Seyma",
                    family = "Kalay",
                    role = c("aut", "cre"),
                    email = "seymakalay@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’
checkRd: (-1) MLM_Model.Rd:31: Lost braces; missing escapes or markup?
    31 |   the weight vectors \bold{{w}^{i}} corresponds to class \eqn{i}{i}.
       |                                ^
checkRd: (-1) MLM_Model.Rd:33: Lost braces; missing escapes or markup?
    33 | We set \eqn{{\bold{{w}}^{h}} = 0} and the parameters to be learned are the weight vectors \bold{{w}^{i}}
       |                                                                                                     ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘qgraph’

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: ‘Gavin Douglas <gavinmdouglas@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 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: ‘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.
Maintainer: ‘Chris Salahub <chris.salahub@uwaterloo.ca>’

The Description field contains
  in Salahub and Olford (2023) <arXiv:2310.16600>. This package provides
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: ‘Lech Kujawski <lech.kujawski@ug.edu.pl>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘PooledMeanGroup-package.Rd’:
    \keyword{package, PMG, pooled mean group, dynamic  [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: ‘DiagrammeR’

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?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘getPrevalence.R’
Maintainer: ‘Stefano Nembrini <stefanonembrini@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Stefano",
                    family = "Nembrini",
                    role = c("aut", "cre"),
                    email = "stefanonembrini@gmail.com")
as necessary.
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', '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: ‘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.
Maintainer: ‘Chris Stubben <chris.stubben@hci.utah.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chris",
                      family = "Stubben",
                      role = c("aut", "cre"),
                      email = "chris.stubben@hci.utah.edu"),
               person(given = "Brook",
                      family = "Milligan",
                      role = "aut"),
               person(given = "Patrick",
                      family = "Nantel",
                      role = "aut"))
as necessary.
Package required but not available: ‘Seurat’

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: ‘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:
  'Hmisc', 'rhandsontable', '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:
  'covr', 'knitr', 'relsurv', '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: 'knitr', 'gap'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Aki Jarl Laruson <akijarl@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Aki", "Jarl", "Laruson;", "Floyd"),
                      family = "Reed",
                      role = "aut"),
               person(given = c("Aki", "Jarl"),
                      family = "Laruson",
                      role = "cre",
                      email = "akijarl@gmail.com"))
as necessary.
Maintainer: ‘Jiacheng Miao <jiacheng.miao@wisc.edu>’

The Description field contains
  (2023) <arXiv:2311.14220>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Alejandro Ochoa <alejandro.ochoa@duke.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects 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 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/algo.Rnw’
(Is a VignetteBuilder field missing?)

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: ‘"Mark C. Wheldon" <biostatmark@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Mark", "C."),
                      family = "Wheldon",
                      role = "aut"),
               person(given = c("\"Mark", "C."),
                      family = "Wheldon\"",
                      role = "cre",
                      email = "biostatmark@gmail.com"))
as necessary.
Packages required but not available: 'demography', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Guillaume Chapron <gchapron@carnivoreconservation.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Guillaume",
                    family = "Chapron",
                    role = c("aut", "cre"),
                    email = "gchapron@carnivoreconservation.org")
as necessary.
Maintainer: ‘Marios Batsaris <m.batsaris@aegean.gr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Marios",
                    family = "Batsaris",
                    role = c("aut", "cre"),
                    email = "m.batsaris@aegean.gr")
as necessary.
Package required but not available: ‘usethis’

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:
  'bookdown', '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: ‘qtl’

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: '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: ‘timetk’

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: ‘Esam Mahdi <emahdi2012@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Esam",
                    family = "Mahdi",
                    role = c("aut", "cre"),
                    email = "emahdi2012@gmail.com")
as necessary.
'::' or ':::' import not declared from: ‘RPESE’
'library' or 'require' calls not declared from:
  ‘TTR’ ‘doMC’
Cannot process vignettes
Packages suggested but not available for checking:
  'DT', 'knitr', 'prettydoc', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Problems with news in ‘NEWS.md’:
No news entries found.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'keras', 'tensorflow'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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'

VignetteBuilder package required 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: 'tutorial.helpers', 'usethis'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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.
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: ‘James Robinson <james.em.robinson@gmail.com>’

The Description field contains
  <arXiv:1806.11544>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
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  'covr', 'knitr', 'lintr', 'rmarkdown', 'roxygen2'

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
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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  'xlsx', 'cosinor2', 'accelerometry', 'ActCR', 'ActFrag',
  'kableExtra', 'GGIR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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DESCRIPTION file?
Maintainer: ‘Char Leung <charleung@hotmail.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Char",
                    family = "Leung",
                    role = c("aut", "cre"),
                    email = "charleung@hotmail.fr")
as necessary.
Maintainer: ‘Mikkel Freltoft Krogsholm <mikkel@56n.dk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Mikkel", "Freltoft"),
                    family = "Krogsholm",
                    role = c("aut", "cre"),
                    email = "mikkel@56n.dk")
as necessary.
Cannot process vignettes
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Cannot process vignettes
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Package required but not available: ‘yaml’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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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 = "Leif",
                      family = "Johnson",
                      role = "aut",
                      email = "ltjohnson@google.com"))
as necessary.
Packages required but not available: 'haplo.stats', 'gap', 'BIGDAWG'

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

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Cannot process vignettes
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  'usethis', '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
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Cannot process vignettes
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VignetteBuilder 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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Package required but not available: ‘yaml’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Eric Kawaguchi <erickawaguchi@ucla.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Qing",
                      family = "Yang",
                      role = "aut"),
               person(given = c("Wing", "K."),
                      family = "Fung",
                      role = "aut"),
               person(given = "Eric",
                      family = "Kawaguchi",
                      role = c("ctb", "cre"),
                      email = "erickawaguchi@ucla.edu"),
               person(given = "Gang",
                      family = "Li",
                      role = c("aut", "cre")))
as necessary.
Packages required but not available: 'Seurat', 'plotly', 'rayshader'

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Cannot process vignettes
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Charles Kooperberg <clk@fredhutch.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Charles",
                      family = "Kooperberg",
                      role = c("aut", "cre"),
                      email = "clk@fredhutch.org"),
               person(given = "Li",
                      family = "Hsu",
                      role = "aut",
                      email = "lih@fredhutch.org"))
as necessary.
checkRd: (-1) coalesce_xy.Rd:22: Lost braces; missing escapes or markup?
    22 | the \code{conflict} argument of {powerjoin}'s join functions. \code{coalesce_xy()} is
       |                                 ^
checkRd: (-1) power_left_join.Rd:67: Lost braces; missing escapes or markup?
    67 | \item{by}{As in {dplyr}, but extended so user can supply a formula or a list
       |                 ^
checkRd: (-1) power_left_join.Rd:79: Lost braces; missing escapes or markup?
    79 | \item{keep}{A boolean for compatibility with {dplyr}, or a value among "left",
       |                                              ^
checkRd: (-1) preprocess_inputs.Rd:37: Lost braces; missing escapes or markup?
    37 | only be used in the \code{x} and \code{y} arguments of {powerjoin} join functions. No
       |                                                        ^
Packages suggested but not available for checking: 'covr', 'knitr'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Weiliang Qiu <weiliang.qiu@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Weiliang",
                    family = "Qiu",
                    role = c("aut", "cre"),
                    email = "weiliang.qiu@gmail.com")
as necessary.
Cannot process vignettes
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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:
    ‘FSR.R’ ‘SR.R’ ‘helper_functions_model.R’ ‘plot.powerNLSEM.R’
    ‘smart_search.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Daniel E. Weeks <weeks@pitt.edu>’

No Authors@R field in DESCRIPTION.
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  Authors@R: person(given = c("Daniel", "E."),
                    family = "Weeks",
                    role = c("aut", "cre"),
                    email = "weeks@pitt.edu")
as necessary.
Package required but not available: ‘DT’

Package suggested but not available for checking: ‘rmarkdown’

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Cannot process vignettes
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  'knitr', 'rmarkdown', 'vcr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
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VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
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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:
    ‘save.R’
Running examples in ‘powRICLPM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.powRICLPM
> ### Title: Summarize Results from 'powRICLPM' Object
> ### Aliases: summary.powRICLPM
> 
> ### ** Examples
> 
> ## Don't show: 
> load(system.file("extdata", "out_preliminary.RData", package = "powRICLPM"))
> ## End(Don't show)
> # Get setup of powRICLPM analysis and convergence issues
> summary(out_preliminary)
powRICLPM (0.2.1) simulated power for 16 experimental conditions.
Error in loadNamespace(x) : there is no package called ‘knitr’
Calls: summary ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
plot.powRICLPM 4.939  0.167   5.845
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘weights’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Thorsten Pohlert <thorsten.pohlert@gmx.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thorsten",
                    family = "Pohlert",
                    role = c("aut", "cre"),
                    email = "thorsten.pohlert@gmx.de")
as necessary.
Maintainer: ‘David Hofmeyr <dhofmeyr@sun.ac.za>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "David",
                    family = "Hofmeyr",
                    role = c("aut", "cre"),
                    email = "n.pavlidis@lancaster.ac.uk")
as necessary.
Maintainer: ‘Zeynel Cebeci <zcebeci@cukurova.edu.tr>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
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  'factoextra', '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
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Maintainer: ‘Seongho Kim <biostatistician.kim@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Seongho",
                    family = "Kim",
                    role = c("aut", "cre"),
                    email = "biostatistician.kim@gmail.com")
as necessary.
Packages required but not available: 'htmlwidgets', 'leaflet', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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DESCRIPTION file?
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  'knitr', 'roxygen2', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
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Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ben Youngman <b.youngman@exeter.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ben",
                      family = "Youngman",
                      role = c("aut", "cre"),
                      email = "b.youngman@exeter.ac.uk"),
               person(given = "Theo",
                      family = "Economou",
                      role = "aut"))
as necessary.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'rmarkdown'

VignetteBuilder package required 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: ‘Di Shu <shudi1991@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Di",
                      family = "Shu",
                      role = c("aut", "cre"),
                      email = "shudi1991@gmail.com"),
               person(given = "Sengwee",
                      family = "Toh",
                      role = "aut",
                      email = "darren_toh@harvardpilgrim.org"))
as necessary.
Maintainer: ‘Taiane Schaedler Prass <taianeprass@gmail.com>’

The Description field contains
  <arXiv:2303.04754>) and has been found to outperform several other
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) ccp_ppm.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{model}{Determines of model fit is such that there are p_{it}s (model=1) or
       |                                                               ^
checkRd: (-1) curve_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
checkRd: (-1) gaussian_ppmx.Rd:143: Lost braces; missing escapes or markup?
   143 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
checkRd: (-1) gaussian_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
checkRd: (-1) ordinal_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
checkRd: (-1) ordinal_ppmx.Rd:147: Lost braces; missing escapes or markup?
   147 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each sujbects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
Package required but not available: ‘plotly’

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  'knitr', 'rmarkdown', 'devtools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jan Steinfeld <jan.d.steinfeld@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
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  'roxygen2', '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
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Package required but not available: ‘plotly’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jack G. Gambino <jack.gambino@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Jack", "G."),
                    family = "Gambino",
                    role = c("aut", "cre"),
                    email = "jack.gambino@gmail.com")
as necessary.
Maintainer: ‘Karla Mayra Perez <karla.mayra25@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Karla", "Mayra"),
                      family = "Perez",
                      role = c("aut", "cre"),
                      email = "karla.mayra25@gmail.com"),
               person(given = c("Luis", "E."),
                      family = "Nieto-Barajas",
                      role = "aut"))
as necessary.

The Description field contains
  (2019) <arXiv:1902.06020>).
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
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VignetteBuilder package required 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: ‘Eun-Kyung Lee <lee.eunk@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Eun-Kyung",
                    family = "Lee",
                    role = c("aut", "cre"),
                    email = "lee.eunk@gmail.com")
as necessary.
Maintainer: ‘Jessica J. Kraker <krakerjj@uwec.edu>’

The Description field contains
  mathematical derivations and applications can be found on arXiv:
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Guangbao Guo <ggb11111111@163.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Guangbao",
                      family = "Guo",
                      role = c("aut", "cre"),
                      email = "ggb11111111@163.com"),
               person(given = "Jiarui",
                      family = "Li",
                      role = "aut"))
as necessary.
Maintainer: ‘Jiaqiang Zhu <jiaqiang@umich.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Shiquan",
                      family = "Sun",
                      role = "aut"),
               person(given = "Jiaqiang",
                      family = "Zhu",
                      role = c("aut", "cre"),
                      email = "jiaqiang@umich.edu"),
               person(given = "Xiang",
                      family = "Zhou",
                      role = "aut"))
as necessary.
Specified C++11: support will be removed soon
Package required but not available: ‘knitr’

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  'EnsDb.Hsapiens.v75', 'ensembldb'

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: 'emuR', 'rPraat', 'wrassp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
2c2
< Package 'mclust' version 6.1.2
---
> Package 'mclust' version 6.1.1
Running ‘donttestexamples.R’ [2s/2s]
  Running ‘prabclustests.R’ [10s/13s]
  Comparing ‘prabclustests.Rout’ to ‘prabclustests.Rout.save’ ...4c4
< Package 'mclust' version 6.1.2
---
> Package 'mclust' version 6.1.1
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
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Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'ShapleyValue', 'NNS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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  'knitr', 'rmarkdown', 'kableExtra', 'roxygen2'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SampStop
> ### Title: Stopping rule for surveys
> ### Aliases: SampStop
> ### Keywords: methods survey
> 
> ### ** Examples
> 
> library(PracTools)
> library(kableExtra)
Error in library(kableExtra) : there is no package called ‘kableExtra’
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Gabor Csardi <csardi.gabor@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gabor",
                      family = "Csardi",
                      role = c("aut", "cre"),
                      email = "csardi.gabor@gmail.com"),
               person(given = "Sindre",
                      family = "Sorhus",
                      role = "aut"))
as necessary.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
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  'rJava', 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Chong Wu <wuxx0845@umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chong",
                      family = "Wu",
                      role = c("aut", "cre"),
                      email = "wuxx0845@umn.edu"),
               person(given = "Wei",
                      family = "Pan",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', '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:
  'covr', 'devtools', 'knitr', 'rmarkdown', 'roxygen2', '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?
Packages required but not available: 'Seurat', 'DR.SC'

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:
  'kableExtra', '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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: 'gam', 'randomForestSRC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Lorenz Walthert <lorenz.walthert@icloud.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Lorenz",
                    family = "Walthert",
                    role = c("aut", "cre"),
                    email = "lorenz.walthert@icloud.com")
as necessary.
Package required but not available: ‘yaml’

Packages suggested but not available for checking:
  'knitr', 'lintr', 'pkgdown', 'rmarkdown', 'roxygen2', 'spelling',
  'usethis'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) diagnose_expressions.Rd:39: Lost braces
    39 | \item wrapping a function argument in two curly braces (e.g. `{{arg}} > 0) means
       |                                                               ^
File ‘precondition/libs/precondition.so’:
  Found non-API calls to R: ‘PRENV’, ‘R_PromiseExpr’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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.
Packages required but not available: 'rgl', 'ggiraphExtra'

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: ‘Suman Kundu <suman_math@yahoo.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Suman",
                      family = "Kundu",
                      role = c("aut", "cre"),
                      email = "suman_math@yahoo.com"),
               person(given = c("Yurii", "S."),
                      family = "Aulchenko",
                      role = "aut"),
               person(given = c("A.", "Cecile", "J.W."),
                      family = "Janssens",
                      role = "aut"))
as necessary.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘David Stanley <dstanley@uoguelph.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "David",
                    family = "Stanley",
                    role = c("aut", "cre"),
                    email = "dstanley@uoguelph.ca")
as necessary.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Marcel Miché <marcel.miche.predictme@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Marcel",
                    family = "Miché",
                    role = c("aut", "cre"),
                    email = "marcel.miche.predictme@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:
  'spelling', 'covr', 'flextable', 'knitr', 'rmarkdown'

VignetteBuilder package required 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', 'golem', 'loadeR', 'config', 'traineR', 'echarts4r',
  'colourpicker'

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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Orestis Efthimiou <oremiou@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Orestis",
                    family = "Efthimiou",
                    role = c("aut", "cre"),
                    email = "oremiou@gmail.com")
as necessary.
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:
  '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:
  'devtools', '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: ‘Amin Adibi <adibi@alumni.ubc.ca>’

The Description field contains
  <arXiv:2003.00316>.
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:
  'rmarkdown', 'knitr', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) dev_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:14: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘TSPred’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) preference-package.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:58-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:61-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:26-27: Lost braces in \itemize; meant \describe ?
Maintainer: ‘John Lepird <jlepird@alum.mit.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "John",
                    family = "Lepird",
                    role = c("aut", "cre"),
                    email = "jlepird@alum.mit.edu")
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: ‘Denis Mollison <denis.mollison@gmail.com>’

The Description field contains
  (2023) <arXiv:2303.15310>, (see also the package manual
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?
Maintainer: ‘Chin Soon Lim <chinsoon12@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Chin", "Soon"),
                    family = "Lim",
                    role = c("aut", "cre"),
                    email = "chinsoon12@hotmail.com")
as necessary.

The BugReports field in DESCRIPTION has
  https://github.com/chinsoon12/PreKnitPostHTMLRender
which should likely be
  https://github.com/chinsoon12/PreKnitPostHTMLRender/issues
instead.
Packages required but not available: 'knitr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Silvia Liverani <liveranis@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("David", "I."),
                      family = "Hastie",
                      role = "aut"),
               person(given = "Silvia",
                      family = "Liverani",
                      role = c("aut", "cre"),
                      email = "liveranis@gmail.com"),
               person(given = c("Sylvia", "Richardson", "with", "contributions", "from", "Aurore", "J."),
                      family = "Lavigne",
                      role = "aut"),
               person(given = "Lucy",
                      family = "Leigh",
                      role = "aut"),
               person(given = "Lamiae",
                      family = "Azizi",
                      role = "aut"),
               person(given = "Xi",
                      family = "Liu",
                      role = "aut"),
               person(given = "Ruizhu",
                      family = "Huang",
                      role = "aut"),
               person(given = "Austin",
                      family = "Gratton",
                      role = "aut"),
               person(given = "Wei",
                      family = "Jing",
                      role = "aut"))
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?
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?
Maintainer: ‘Swamiji Pravedson <swamiji.pravedson@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Swamiji",
                    family = "Pravedson",
                    role = c("aut", "cre"),
                    email = "swamiji.pravedson@gmail.com")
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: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Josef Frank <josef.frank@gmx.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Josef",
                    family = "Frank",
                    role = c("aut", "cre"),
                    email = "josef.frank@gmx.ch")
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: ‘rmarkdown’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Elizabeth Freeman <elizabeth.a.freeman@usda.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Elizabeth",
                    family = "Freeman",
                    role = c("aut", "cre"),
                    email = "elizabeth.a.freeman@usda.gov")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Matthew A. Birk <matthewabirk@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Matthew", "A."),
                    family = "Birk",
                    role = c("aut", "cre"),
                    email = "matthewabirk@gmail.com")
as necessary.
Packages required but not available:
  'flextable', 'formattable', 'framecleaner'

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

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:
  'gt', 'Hmisc', 'knitr', 'rmarkdown', 'shinytest'

VignetteBuilder package required 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: ‘Gustavo Soutinho <gustavosoutinho@sapo.pt>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gustavo",
                      family = "Soutinho",
                      role = c("aut", "cre"),
                      email = "gustavosoutinho@sapo.pt"),
               person(given = "Luis",
                      family = "Meira-Machado",
                      role = "aut"),
               person(given = "Pedro",
                      family = "Oliveira",
                      role = "aut"))
as necessary.
Package required but not available: ‘Morpho’

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

Package suggested but not available for checking: ‘knitr’

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: 'kableExtra', 'knitr', 'plotly'

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: ‘Dewey Dunnington <dewey@fishandwhistle.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Dewey",
                    family = "Dunnington",
                    role = c("aut", "cre"),
                    email = "dewey@fishandwhistle.net")
as necessary.
Maintainer: ‘Jim Lemon <drjimlemon@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jim",
                      family = "Lemon",
                      role = c("aut", "cre"),
                      email = "drjimlemon@gmail.com"),
               person(given = "Philippe",
                      family = "Grosjean",
                      role = "aut",
                      email = "phgrosjean@sciviews.org"))
as necessary.
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
Maintainer: ‘Brecht Devleesschauwer <brechtdv@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', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘estimate_risk.Rd’
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.
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: ‘Ankur Chakravarthy <ankur.chakravarthy.10@ucl.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ankur",
                    family = "Chakravarthy",
                    role = c("aut", "cre"),
                    email = "ankur.chakravarthy.10@ucl.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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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:
  'bookdown', 'cmdstanr', '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?
Maintainer: ‘David Schruth <data@anthropoidea.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "David",
                      family = "Schruth",
                      role = "cre",
                      email = "data@anthropoidea.org"),
               person(given = "Marc",
                      family = "Myers",
                      role = "ctb"),
               person(given = "Noel",
                      family = "Rowe",
                      role = "aut"))
as necessary.
Maintainer: ‘Florian Privé <florian.prive.21@gmail.com>’

Found the following (possibly) invalid file URIs:
  URI: commits/master
    From: README.md
  URI: /commits/master
    From: README.md
Maintainer: ‘Ziwei Zhu <ziweiz@umich.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ziwei",
                      family = "Zhu",
                      role = c("aut", "cre"),
                      email = "ziweiz@umich.edu"),
               person(given = "Tengyao",
                      family = "Wang",
                      role = "aut"),
               person(given = c("Richard", "J."),
                      family = "Samworth",
                      role = "aut"))
as necessary.

The Description field contains
  component analysis with heterogeneous missingness. <arXiv:1906.12125>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Hank Stevens <hank.stevens@miamioh.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("M", "H", "H"),
                      family = "Stevens",
                      role = "aut"),
               person(given = "Hank",
                      family = "Stevens",
                      role = "cre",
                      email = "hank.stevens@miamioh.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.
checkRd: (-1) alogistic.Rd:20: Lost braces
    20 | The user does not put these directly into this function, but rather uses code{ode} in the \code{deSolve} package.
       |                                                                              ^
File ‘PRIMME/libs/PRIMME.so’:
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘primme/libprimme.a’

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

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

VignetteBuilder package required 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: ‘Robrecht Cannoodt <rcannood@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Author field differs from that derived from Authors@R
  Author:    ‘Trevor Hastie [aut], Andreas Weingessel [aut], Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>), Henrik Bengtsson [ctb] (HenrikBengtsson), Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood)’
  Authors@R: ‘Trevor Hastie [aut], Andreas Weingessel [aut], Kurt Hornik [aut] (ORCID: <https://orcid.org/0000-0003-4198-9911>), Henrik Bengtsson [ctb] (github: HenrikBengtsson), Robrecht Cannoodt [aut, cre] (ORCID: <https://orcid.org/0000-0003-3641-729X>, github: rcannood)’
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: ‘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’
Package has ‘vignettes’ subdirectory 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: ‘tmap’

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:
  'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) findbeta.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{lower.v}{logical, if TRUE the specified percentile.value is the upper limit for the mean (or the median or the mode) at the specified confidence level (percentile). If {FALSE} the specified percentile.value is the lower limit for the mean (or the median or the mode) at the specified confidence level (percentile). The default is FALSE.}
       |                                                                                                                                                                               ^
Package has ‘vignettes’ subdirectory 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', 'gurobi', 'roxygen2', 'rcbc', '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', 'gurobi', 'rcbc', 'cplexAPI', 'rmarkdown'

VignetteBuilder package required 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: ‘glmSparseNet’

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: ‘Roman Hornung <hornung@ibe.med.uni-muenchen.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Simon",
                      family = "Klau",
                      role = "aut"),
               person(given = "Roman",
                      family = "Hornung",
                      role = c("aut", "cre"),
                      email = "hornung@ibe.med.uni-muenchen.de"),
               person(given = "Alina",
                      family = "Bauer",
                      role = "aut"),
               person(given = "Jonas",
                      family = "Hagenberg",
                      role = "aut"))
as necessary.
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?
Cannot process vignettes
Packages suggested but not available for checking:
  'cmdstanr', 'iwmm', '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?
Packages required but not available: 'DiagrammeR', 'htmlwidgets', 'DT'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Tammo Krueger <tammokrueger@googlemail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Tammo",
                      family = "Krueger",
                      role = c("aut", "cre"),
                      email = "tammokrueger@googlemail.com"),
               person(given = "Nicole",
                      family = "Kraemer",
                      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?
Maintainer: ‘Danilo Freire <danilofreire@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: ‘Prithul Chaturvedi <prithulc@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Prithul",
                    family = "Chaturvedi",
                    role = c("aut", "cre"),
                    email = "prithulc@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: ‘Staal A. Vinterbo <Staal.Vinterbo@ntnu.no>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Staal", "A."),
                    family = "Vinterbo",
                    role = c("aut", "cre"),
                    email = "Staal.Vinterbo@ntnu.no")
as necessary.
Package has ‘vignettes’ subdirectory 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:
  '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?
Packages required but not available: 'Hmisc', '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.
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: ‘Jim Albert <albert@bgsu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jim",
                    family = "Albert",
                    role = c("aut", "cre"),
                    email = "albert@bgsu.edu")
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: ‘Alexander McLain <mclaina@mailbox.sc.edu>’

The Description field contains
  Zgodic, and Bondell (2022) <arXiv:2209.08139>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Tim Liao <tfliao@illinois.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tim",
                    family = "Liao",
                    role = c("aut", "cre"),
                    email = "tfliao@illinois.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: ‘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.
Packages required but not available: 'rmarkdown', 'rpivotTable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Giuliana Cortese <gcortese@stat.unipd.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Giuliana",
                    family = "Cortese",
                    role = c("aut", "cre"),
                    email = "gcortese@stat.unipd.it")
as necessary.
Maintainer: ‘Rishabh Gupta <rishabh.uk@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rishabh",
                      family = "Gupta",
                      role = c("aut", "cre"),
                      email = "rishabh.uk@gmail.com"),
               person(given = c("Nicholas", "J."),
                      family = "Matzke",
                      role = "aut"))
as necessary.
Package required but not available: ‘keras’

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’
Unexported objects imported by ':::' calls:
  ‘bupaR:::allowed_lifecycles’ ‘bupaR:::apply_grouped_fun’
  See the note in ?`:::` about the use of this operator.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'DiagrammeR', 'plotly', 'htmlwidgets'

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: ‘gert.janssenswillen@uhasselt.be <gert.janssenswillen@uhasselt.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gert",
                      family = "Janssenswillen",
                      role = "aut"),
               person(family = "gert.janssenswillen@uhasselt.be",
                      role = "cre",
                      email = "gert.janssenswillen@uhasselt.be"))
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
Packages required but not available: 'keras', 'tensorflow', '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: ‘Eric Coissac <eric.coissac@metabarcoding.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Eric",
                      family = "Coissac",
                      role = c("aut", "cre"),
                      email = "eric.coissac@metabarcoding.org"),
               person(given = "Christelle",
                      family = "Gonindard-Melodelima",
                      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: ‘Trevor Hastie <hastie@stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Trevor",
                      family = "Hastie",
                      role = c("aut", "cre"),
                      email = "hastie@stanford.edu"),
               person(given = "Rob",
                      family = "Tibshirani",
                      role = "aut"))
as necessary.
Package required but not available: ‘gam’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Gabriele Rovigatti <gabriele.rovigatti@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Gabriele",
                    family = "Rovigatti",
                    role = c("aut", "cre"),
                    email = "gabriele.rovigatti@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?
Running examples in ‘prodlim-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggprodlim
> ### Title: ggplot2::ggplot support for Kaplan-Meier and Aalen-Johansen
> ###   estimators
> ### Aliases: ggprodlim
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> # Kaplan-Meier and stratified Kaplan-Meier
> 
> set.seed(9)
> ds <- SimSurv(27)
> 
> km <- prodlim(Hist(time,event)~1,data = ds)
> ggprodlim(km)
Loading required namespace: pammtools
Failed with error:  ‘there is no package called ‘pammtools’’
Error in loadNamespace(x) : there is no package called ‘pammtools’
Calls: ggprodlim ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Maintainer: ‘Yann Desjeux <yann.desjeux@inra.fr>’

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

Found the following URLs which should use \doi (with the DOI name only):
  File ‘fareprim.Rd’:
    https://doi.org/10.1093/ajae/aas023
  File ‘fisher.Rd’:
    https://doi.org/10.1007/BF00158354
  File ‘hicksmoorsteen.Rd’:
    https://doi.org/10.1111/j.1467-9957.2010.02169.x
    https://doi.org/10.1111/j.1467-8489.2010.00512.x
  File ‘lowe.Rd’:
    https://doi.org/10.1093/ajae/aas023
  File ‘usagri.Rd’:
    https://doi.org/10.2307/1244458
    https://doi.org/10.1111/j.0002-9092.2004.00683.x
checkRd: (-1) paasche.Rd:91: Lost braces
    91 |     \code{OSME} \tab Output-oriented scale-mix efficiency score \emph{(code{orientation = "out"})}\cr
       |                                                                            ^
Packages required but not available: 'DR.SC', 'PRECAST', 'Seurat'

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) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
Maintainer: ‘Christopher David Desjardins <cddesjardins@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Okan",
                      family = "Bulut",
                      role = "aut",
                      email = "okanbulut84@gmail.com"),
               person(given = c("Christopher", "David"),
                      family = "Desjardins",
                      role = c("aut", "cre"),
                      email = "cddesjardins@gmail.com"))
as necessary.
checkRd: (-1) PS.Rd:9: Lost braces
     9 |                 \item{CD}{}{Character disorder scale score}
       |                            ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Luke Tierney <luke-tierney@uiowa.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Luke",
                      family = "Tierney",
                      role = c("aut", "cre"),
                      email = "luke-tierney@uiowa.edu"),
               person(given = "Riad",
                      family = "Jarjour",
                      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/proftools.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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: ‘plotly’

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.
Cannot process vignettes
Packages suggested but not available for checking:
  'tidyverse', 'knitr', 'rmarkdown', 'downloadthis', '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: ‘mclogit’

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

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:
  '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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'reactable', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) prolific_prescreener.Rd:254: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_prescreener.Rd:255: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:243: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:244: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Francesco Vidoli <fvidoli@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Giuliano",
                      family = "Resce",
                      role = "aut"),
               person(given = "Menelaos",
                      family = "Tasiou",
                      role = "aut"),
               person(given = "Francesco",
                      family = "Vidoli",
                      role = c("aut", "cre"),
                      email = "fvidoli@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.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘Austria.Rd’:
    https://doi.org/10.1016/j.jclepro.2019.02.115
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?
Maintainer: ‘Paul E. Promote <promotedev@alteryx.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Paul", "E."),
                    family = "Promote",
                    role = c("aut", "cre"),
                    email = "promotedev@alteryx.com")
as necessary.
Package required but not available: ‘prophet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘complete_chat.R’ ‘complete_prompt.R’ ‘format_prompt.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘build_url.R’
Maintainer: ‘Ralph Scherer <shearer.ra76@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ralph",
                    family = "Scherer",
                    role = c("aut", "cre"),
                    email = "shearer.ra76@gmail.com")
as necessary.
Maintainer: ‘Peter Langfelder <Peter.Langfelder@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("John", "Michael", "O"),
                      family = "Ranola",
                      role = "aut"),
               person(given = "Kenneth",
                      family = "Lange",
                      role = "aut"),
               person(given = "Steve",
                      family = "Horvath",
                      role = "aut"),
               person(given = "Peter",
                      family = "Langfelder",
                      role = c("aut", "cre"),
                      email = "peter.langfelder@gmail.com"))
as necessary.
Maintainer: ‘Maria Alvarez <maria.alvarez@uvigo.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Maria",
                      family = "Alvarez",
                      role = c("aut", "cre"),
                      email = "maria.alvarez@uvigo.es"),
               person(given = "Javier",
                      family = "Roca-Pardinas",
                      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: ‘Daan Seynaeve <daan.seynaeve@openanalytics.eu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Tobias",
                      family = "Verbeke",
                      role = "aut"),
               person(given = "Daan",
                      family = "Seynaeve",
                      role = c("aut", "cre"),
                      email = "daan.seynaeve@openanalytics.eu"),
               person(given = c("based", "on", "read.dcf", "by", "R", "Core", "Development"),
                      family = "Team",
                      role = "aut"))
as necessary.
Package required but not available: ‘dygraphs’

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: ‘Osama Mahmoud <ofamah@essex.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Osama",
                      family = "Mahmoud",
                      role = c("aut", "cre"),
                      email = "ofamah@essex.ac.uk"),
               person(given = "Andrew",
                      family = "Harrison",
                      role = "aut"),
               person(given = "Aris",
                      family = "Perperoglou",
                      role = "aut"),
               person(given = "Asma",
                      family = "Gul",
                      role = "aut"),
               person(given = "Zardad",
                      family = "Khan",
                      role = "aut"),
               person(given = "Berthold",
                      family = "Lausen",
                      role = "aut"))
as necessary.
Maintainer: ‘Travis Loux <travis.loux@slu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Travis",
                    family = "Loux",
                    role = c("aut", "cre"),
                    email = "travis.loux@slu.edu")
as necessary.
Maintainer: ‘Nadine Fischoff <nadine.khattak@gmail.com>’

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

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

VignetteBuilder package required 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’

Package suggested but not available for checking: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Xi (Rossi) LUO <xi.rossi.luo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Xi", "LUO", "with", "contributions", "from", "Dylan"),
                      family = "Small",
                      role = "aut",
                      comment = "Rossi"),
               person(given = "Vikaas",
                      family = "Sohal",
                      role = "aut"),
               person(given = "Xi",
                      family = "LUO",
                      role = "cre",
                      email = "xi.rossi.luo@gmail.com",
                      comment = "Rossi"))
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?
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:
  'DT', 'knitr', 'kableExtra', '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: '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', '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?
checkRd: (-1) struc_addSimData.Rd:15: Lost braces
    15 | \item{value}{code{data.frame} or code{data.table}}
       |                  ^
checkRd: (-1) struc_addSimData.Rd:15: Lost braces
    15 | \item{value}{code{data.frame} or code{data.table}}
       |                                      ^
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:
    ‘nba_data.R’ ‘nba_data.Rd’ ‘nfl_data.R’ ‘nhl_data.R’ ‘nhl_data.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Simon Liles <simon@quantknot.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Simon",
                    family = "Liles",
                    role = c("aut", "cre"),
                    email = "simon@quantknot.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?
No examples, no tests, no vignettes
Maintainer: ‘Arthur Leroy <arthur.leroy.pro@gmail.com>’

The Description field contains
  <arXiv:2307.08975>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘modeest’

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: ‘Jacob Bien <jbien@usc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jacob",
                      family = "Bien",
                      role = c("aut", "cre"),
                      email = "jbien@usc.edu"),
               person(given = "Rob",
                      family = "Tibshirani",
                      role = "aut"))
as necessary.
Maintainer: ‘Przemysław Biecek <przemyslaw.biecek@gmail.com>’

The Description field contains
  available at http://biecek.pl/BetaBit/Warsaw.  It's a part of Beta and
  http://biecek.pl/BetaBit.
Please enclose URLs in angle brackets (<...>).
Package required but not available: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Stephen Reid <sreid1652@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Stephen",
                    family = "Reid",
                    role = c("aut", "cre"),
                    email = "sreid1652@gmail.com")
as necessary.
checkRd: (-1) prototest.univariate.Rd:21: Lost braces
    21 | response variable. Vector of length emph{n}, assumed to be quantitative.
       |                                         ^
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?
Package required but not available: ‘plotly’

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'r3dmol', 'heatmaply'

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’
checkRd: (-1) pr_stem_sentences.Rd:20: Lost braces; missing escapes or markup?
    20 | Implementation of the {SnowballC} stemmer. Note that punctuation and capital letters 
       |                       ^
checkRd: (-1) pr_stem_words.Rd:20: Lost braces; missing escapes or markup?
    20 | Implementation of the {SnowballC} stemmer. Note that punctuation and capitals letters 
       |                       ^
checkRd: (-1) proust_sentiments.Rd:7: Lost braces; missing escapes or markup?
     7 | See the {rfeel} package now: http://github.com/ColinFay/rfeel}
       |         ^
checkRd: (-1) proust_sentiments.Rd:20: Lost braces; missing escapes or markup?
    20 | See the {rfeel} package now: http://github.com/ColinFay/rfeel
       |         ^
Package has ‘vignettes’ subdirectory 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', 'rdtLite', 'rdt', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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:
    ‘get_proverbs.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', 'rdtLite', 'rdt'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'rdt', 'rdtLite', 'rmarkdown'

VignetteBuilder package required 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: ‘EBImage’

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?
File ‘proxy/libs/proxy.so’:
  Found non-API calls to R: ‘OBJECT’, ‘Rf_NonNullStringMatch’,
    ‘SET_OBJECT’
These entry points may be removed soon:
‘Rf_NonNullStringMatch’, ‘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: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Yi Zhao <zhayi@umich.edu>’

The Description field contains
  <arXiv:2105.03993>.
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: ‘Dirk Eddelbuettel <edd@debian.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Dirk",
                    family = "Eddelbuettel",
                    role = c("aut", "cre"),
                    email = "edd@debian.org")
as necessary.
Package required but not available: ‘config’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘M. S. Islam <shahed-sta@sust.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("M.", "S."),
                    family = "Islam",
                    role = c("aut", "cre"),
                    email = "shahed-sta@sust.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', '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: ‘Morpho’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘pryr/libs/pryr.so’:
  Found non-API calls to R: ‘BODY’, ‘CLOENV’, ‘ENCLOS’, ‘EXTPTR_PROT’,
    ‘EXTPTR_TAG’, ‘FORMALS’, ‘FRAME’, ‘HASHTAB’, ‘NAMED’, ‘PRCODE’,
    ‘PRENV’, ‘PRVALUE’, ‘Rf_findVarInFrame3’
These entry points may be removed soon:
‘EXTPTR_PROT’, ‘EXTPTR_TAG’, ‘NAMED’, ‘FRAME’, ‘HASHTAB’, ‘BODY’, ‘FORMALS’, ‘CLOENV’, ‘ENCLOS’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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 ‘testthat.R’ [1s/1s]
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(PSAWR)
  > 
  > test_check("PSAWR")
  Error in `source_dir()`:
  ! Failed to evaluate './setup-PSAWR.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("PSAWR")
    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-PSAWR.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
Maintainer: ‘Kyu Ha Lee <klee@hsph.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Kyu", "Ha"),
                      family = "Lee",
                      role = c("aut", "cre"),
                      email = "klee@hsph.harvard.edu"),
               person(given = "Sounak",
                      family = "Chakraborty",
                      role = "aut"),
               person(given = "Harrison",
                      family = "Reeder",
                      role = "aut"),
               person(given = c("", "Jianguo"),
                      family = "Sun",
                      role = "aut",
                      comment = "Tony"))
as necessary.
Package required but not available: ‘riskRegression’

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:
  'cmdstanr', 'usethis', 'knitr', 'rmarkdown', 'table1', 'gt',
  'gtsummary'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: 'survminer', 'gtsummary'

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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) qpc.Rd:43: Lost braces
    43 | S{Sulewski, P. (2020). \emph{Normal Distribution with Plasticizing Component,} Communications in Statistics ? Theory and Method 51(11), 3806-3835.}
       |  ^
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/fftw.Rnw’
   ‘inst/doc/multivariate.Rnw’
   ‘inst/doc/normalization.Rnw’
   ‘inst/doc/psd_overview.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', '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: 'quanteda', 'quanteda.textstats'

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’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘pseudohouseholds.R’
Package has ‘vignettes’ subdirectory 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', 'printr', 'rmarkdown'

VignetteBuilder package required 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’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 = "Gualberto",
                      family = "Asencio-Cortes",
                      role = "aut"),
               person(given = "Francisco",
                      family = "Martinez-Alvarez",
                      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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) data1.Rd:14: Lost braces
    14 | The data set from {AbouRizk, S.M., Halpin, D.W., Wilson, J. R. (1994). \emph{Fitting beta distributions based on sample data.} Journal of Construction Engineering and Management 120(2), 288–305.}
       |                   ^
checkRd: (-1) data2.Rd:14: Lost braces; missing escapes or markup?
    14 | The data set presents the height of 99 five-year-old British boys in cm downloaded from {http://www.mas.ncl.ac.uk/njnsm/medfac/docs/intro.pdf.}
       |                                                                                         ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
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: ‘Oleg Sysoev <Oleg.Sysoev@liu.se>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Oleg",
                      family = "Sysoev",
                      role = c("aut", "cre"),
                      email = "oleg.sysoev@liu.se"),
               person(given = "Krzysztof",
                      family = "Bartoszek",
                      role = "aut"),
               person(given = c("Katarina", "Ekholm"),
                      family = "Selling",
                      role = "aut"),
               person(given = "Lotta",
                      family = "Ekstrom",
                      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', 'DiagrammeR', '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: 'rmarkdown', '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’
checkRd: (-1) table1.Rd:14: Lost braces
    14 | The first data set from {Sulewski, P. (2017) \emph{A new test for independence in 2x2 contingency tables,} Acta Universitatis Lodziensis. Folia Oeconomica, 4(330), 55–75}
       |                         ^
checkRd: (-1) table3.Rd:14: Lost braces
    14 | The third data set from {Sulewski, P. (2021). \emph{Logarithmic Minimum Test for Independence in Three Way Con-tingency Table of Small Sizes.} Journal of Statistical Computation and Simulation 91(13), 2780-2799}
       |                         ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘admiral’

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', '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: ‘Claus Bendtsen <papyrus.bendtsen@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Claus",
                      family = "Bendtsen.",
                      role = "aut",
                      email = "papyrus.bendtsen@gmail.com"),
               person(given = "Claus",
                      family = "Bendtsen",
                      role = "cre",
                      email = "papyrus.bendtsen@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: ‘Petr Savicky <savicky@cs.cas.cz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Petr",
                    family = "Savicky",
                    role = c("aut", "cre"),
                    email = "savicky@cs.cas.cz")
as necessary.
Maintainer: ‘Brian Ripley <Brian.Ripley@R-project.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("S", "original", "by", "Jim", "Ramsey.", "R", "port", "by", "Brian", "Ripley"),
                      family = "<Brian.Ripley@R-project.org>.",
                      role = "aut",
                      email = "Brian.Ripley@R-project.org"),
               person(given = "Brian",
                      family = "Ripley",
                      role = "cre",
                      email = "Brian.Ripley@R-project.org"))
as necessary.
Maintainer: ‘Andre M. de Roos <A.M.deRoos@uva.nl>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Lenard Dome <lenarddome@gmail.com>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘psp.Rd’:
    \keyword{computational modelling; parameter space  [TRUNCATED]
  File ‘pspGlobal.Rd’:
    \keyword{computational modelling; parameter space  [TRUNCATED]
  File ‘psp_global.Rd’:
    \keyword{computational modelling; parameter space; [TRUNCATED]
Packages required but not available: 'DT', 'epiR', 'plotly'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Haiyan Wang <hwang@ksu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Luann", "C."),
                      family = "Jung",
                      role = "aut"),
               person(given = "Haiyan",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "hwang@ksu.edu"),
               person(given = "Diego",
                      family = "Maldonado",
                      role = "aut"),
               person(given = "Sharad",
                      family = "Silwal",
                      role = "aut"),
               person(given = "Siti",
                      family = "Tolos",
                      role = "aut"),
               person(given = "Suojin",
                      family = "Wang",
                      role = "aut"))
as necessary.
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: ‘Michal Juraska <mjuraska@fredhutch.org>’

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 ‘riskCurve.Rd’:
    https://doi.org/10.1093/biostatistics/kxy074
  File ‘summary.riskCurve.Rd’:
    https://doi.org/10.1093/biostatistics/kxy074
  File ‘testConstancy.Rd’:
    https://doi.org/10.1093/biostatistics/kxy074
  File ‘testEquality.Rd’:
    https://doi.org/10.1093/biostatistics/kxy074
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 = "Qing",
                      family = "Fei",
                      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: ‘Blondeau Da Silva Stephane <blondeaudasilva@xlim.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Blondeau", "Da", "Silva"),
                      family = "Stephane.",
                      role = "aut"),
               person(given = c("Blondeau", "Da", "Silva"),
                      family = "Stephane",
                      role = "cre",
                      email = "blondeaudasilva@xlim.fr"))
as necessary.
Maintainer: ‘Pedro H. C. Sant'Anna <pedro.h.santanna@vanderbilt.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Pedro", "H.", "C."),
                      family = "Sant'Anna",
                      role = c("aut", "cre"),
                      email = "pedro.h.santanna@vanderbilt.edu"),
               person(given = "Xiaojun",
                      family = "Song",
                      role = "aut",
                      email = "sxj@gsm.pku.edu.cn"))
as necessary.
Package required but not available: ‘SuperLearner’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Huzhang Mao <huzhangmao@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Huzhang",
                      family = "Mao",
                      role = c("aut", "cre"),
                      email = "huzhangmao@gmail.com"),
               person(given = "Liang",
                      family = "Li",
                      role = "aut",
                      email = "LLi15@mdanderson.org"))
as necessary.
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: 'rmarkdown', 'knitr'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: metabulate_rmd_helper
> ### Title: Add metabulate equation commands and LaTeX dependencies
> ### Aliases: metabulate_rmd_helper
> 
> ### ** Examples
> 
> ## Include this line as 'asis' output in your RMarkdown document:
> metabulate_rmd_helper()
Error: Package 'knitr' is not installed. 'knitr' is required for 'metabulate_rmd_helper'.
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Thomas D. Fletcher <t.d.fletcher05@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Thomas", "D."),
                    family = "Fletcher",
                    role = c("aut", "cre"),
                    email = "t.d.fletcher05@gmail.com")
as necessary.
Package required but not available: ‘qgraph’

Packages suggested but not available for checking:
  'semPlot', 'graphicalVAR'

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’
checkRd: (-1) dprime.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
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/scoring.Rnw’
(Is a VignetteBuilder field missing?)

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’
Packages required but not available: 'bruceR', 'rgl', 'qgraph'

Package suggested but not available for checking: ‘sweater’

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: ‘Ken Knoblauch <ken.knoblauch@inserm.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Kenneth",
                      family = "Knoblauch",
                      role = "aut"),
               person(given = "Ken",
                      family = "Knoblauch",
                      role = "cre",
                      email = "ken.knoblauch@inserm.fr"))
as necessary.
Packages required but not available: 'yaml', 'yum'

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

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: 'flexdashboard', '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: ‘Didier G. Leibovici <GeotRYcs@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Didier", "G."),
                    family = "Leibovici",
                    role = c("aut", "cre"),
                    email = "doi:10.18637/jss.v034.i10",
                    comment = "2010")
as necessary.
Maintainer: ‘Adam Kapelner <kapelner@qc.cuny.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Adam",
                      family = "Kapelner",
                      role = c("aut", "cre"),
                      email = "kapelner@qc.cuny.edu"),
               person(given = c("Alina", "Levine", "&", "Justin"),
                      family = "Bleich",
                      role = "aut"))
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘PTE.Rd’:
    \keyword{medicine,}
checkRd: (-1) PTE_bootstrap_inference.Rd:39-42: Lost braces
    39 |                                                         continuous = function(Xytrain){ #defalt is OLS regression
       |                                                                                       ^
checkRd: (-1) PTE_bootstrap_inference.Rd:43-47: Lost braces
    43 |                                                         incidence = function(Xytrain){ #default is logistic regression
       |                                                                                      ^
checkRd: (-1) PTE_bootstrap_inference.Rd:48-52: Lost braces
    48 |                                                         survival = function(Xytrain){ #default is Weibull regression
       |                                                                                     ^
checkRd: (-1) PTE_bootstrap_inference.Rd:66-68: Lost braces
    66 |                                         function(mod, Xyleftout){
       |                                                                 ^
checkRd: (-1) PTE_bootstrap_inference.Rd:74-77: Lost braces
    74 |                                         function(results, indices_1_1, indices_0_0, indices_0_1, indices_1_0){
       |                                                                                                              ^
Maintainer: ‘Layla Parast <parast@austin.utexas.edu>’

The Description field contains
  available in Wang et al (2022) <arXiv:2209.08414>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Jose M. Maisog <bravas02@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Jose", "M."),
                      family = "Maisog",
                      role = c("aut", "cre"),
                      email = "bravas02@gmail.com"),
               person(given = "Yuan",
                      family = "Wang",
                      role = "aut"),
               person(given = "George",
                      family = "Luta",
                      role = "aut"),
               person(given = "Jianfei",
                      family = "Liu",
                      role = "aut"))
as necessary.
Maintainer: ‘Peter DeWitt <peter.dewitt@cuanschutz.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:
  'bookdown', 'DiagrammeR', 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Mirko Signorelli <msignorelli.rpackages@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: '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:
  '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: ‘Ron Wehrens <ron.wehrens@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.
checkRd: (-1) ptw-package.Rd:20-28: Lost braces
    20 | @Article{Bloemberg2010,
       |         ^
checkRd: (-1) ptw-package.Rd:30-38: Lost braces
    30 | Article{Wehrens2015,
       |        ^
Packages required but not available:
  'htmlTable', 'knitr', 'rmarkdown', 'rmzqc', 'yaml'

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: ‘rcdk’

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: ‘gtsummary’

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', 'kableExtra', 'DT'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'gt', 'knitr', 'kableExtra', 'pkgdown', 'rmarkdown',
  'roxygen2', 'rUM', 'table1', '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', '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?
Maintainer: ‘Jonas Moss <jonas.gjertsen@gmail.com>’

The Description field contains
  <arXiv:1911.12445>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) ma.Rd:62: Lost braces
    62 | \item{yi}{Numeric vector of length code{k} with observed effect size
       |                                        ^
checkRd: (-1) ma.Rd:65: Lost braces
    65 | \item{vi}{Numeric vector of length code{k} with sampling variances.}
       |                                        ^
Running examples in ‘Publish-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: splinePlot.lrm
> ### Title: Plot predictions of logistic regression
> ### Aliases: splinePlot.lrm
> 
> ### ** Examples
> 
> data(Diabetes)
> Diabetes$hypertension=  1*(Diabetes$bp.1s>140)
> library(rms)
Error in library(rms) : there is no package called ‘rms’
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:
  'bibliometrix', 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Felix Yanhui Fan <nolanfyh@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Felix", "Yanhui"),
                    family = "Fan",
                    role = c("aut", "cre"),
                    email = "nolanfyh@gmail.com")
as necessary.
checkRd: (-1) plotWordCloud.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{PubMed wordcloud using function 'wordcloud' of package {wordcloud}}
       |                                                               ^
checkRd: (-1) plotWordCloud.Rd:32: Lost braces; missing escapes or markup?
    32 | This function just call 'wordcloud' from package {wordcloud}. See package {wordcloud} for more details about the parameters.
       |                                                  ^
checkRd: (-1) plotWordCloud.Rd:32: Lost braces; missing escapes or markup?
    32 | This function just call 'wordcloud' from package {wordcloud}. See package {wordcloud} for more details about the parameters.
       |                                                                           ^
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: 'htmlwidgets', '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.
Maintainer: ‘Hyebin Song <hps5320@psu.edu>’

The Description field contains
  <arXiv:1711.08129>.
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: ‘Tong He <hetong007@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tong",
                    family = "He",
                    role = c("aut", "cre"),
                    email = "hetong007@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: ‘Zachary Kurtz <zdkurtz@gmail.com>’

The Description field contains
  Müller, Richard Bonneau, Zachary Kurtz (2016) <arXiv:1605.07072>.
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: ‘fda.usc’

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: ‘Luis J. Villanueva-Rivera <ljvillanueva@coquipr.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Luis", "J."),
                    family = "Villanueva-Rivera",
                    role = c("aut", "cre"),
                    email = "ljvillanueva@coquipr.com")
as necessary.

The Description field contains
  (http://ljvillanueva.github.io/pumilio/).
Please enclose URLs in angle brackets (<...>).
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: 'kableExtra', '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', 'itsadug', 'rmarkdown'

VignetteBuilder package required 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: ‘colordistance’

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:
    ‘source_pmc.R’ ‘source_pubmed.R’ ‘source_pubtations.R’
Maintainer: ‘Richèl J.C. Bilderbeek <richel@richelbilderbeek.nl>’

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

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

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 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: ‘Philip D. Waggoner <philip.waggoner@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Philip", "D."),
                    family = "Waggoner",
                    role = c("aut", "cre"),
                    email = "philip.waggoner@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 package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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?
Packages required but not available: 'kableExtra', 'tidyverse'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', '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', '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: ‘Vygantas Butkus <Vygantas.Butkus@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Vygantas",
                    family = "Butkus",
                    role = c("aut", "cre"),
                    email = "vygantas.butkus@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/pvar_intro.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/pvars_vignette.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ryota Suzuki <suzuki@ef-prime.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ryota",
                      family = "Suzuki",
                      role = c("aut", "cre"),
                      email = "suzuki@ef-prime.com"),
               person(given = "Yoshikazu",
                      family = "Terada",
                      role = "aut",
                      email = "terada@sigmath.es.osaka-u.ac.jp"),
               person(given = "Hidetoshi",
                      family = "Shimodaira",
                      role = "aut",
                      email = "shimo@i.kyoto-u.ac.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?
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:
    ‘da.Rd’ ‘da_object_oriented_functions.R’
    ‘higher_level_disprop_analysis.R’ ‘lower_level_disprop_analysis.R’
    ‘print.da.Rd’
Package has ‘vignettes’ subdirectory 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) pvlrt.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{no_zi_idx}{List of pairs {(i, j)} where zero inflation is not allowed. To
       |                                ^
checkRd: (-1) r_contin_table_zip.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{no_zi_idx}{List of pairs {(i, j)} where zero inflation is not allowed. To
       |                                ^
Maintainer: ‘Thiago Santos <thiago.santos@ufvjm.edu.br>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thiago",
                    family = "Santos",
                    role = c("aut", "cre"),
                    email = "thiago.santos@ufvjm.edu.br")
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: ‘Tianchen Xu <zjph602xutianchen@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tianchen",
                    family = "Xu",
                    role = c("aut", "cre"),
                    email = "zjph602xutianchen@gmail.com",
                    comment = c(ORCID = "0000-0002-0102-7630"))
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: ‘bibliometrix’

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 in Depends/Imports which should probably only be in LinkingTo: ‘RcppEigen’
'library' or 'require' calls not declared from:
  ‘Hmisc’ ‘car’ ‘dplyr’ ‘ggplot2’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Chris Aberson <chris.aberson@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Chris",
                    family = "Aberson",
                    role = c("aut", "cre"),
                    email = "chris.aberson@gmail.com")
as necessary.
Maintainer: ‘Pengcheng Lu <plu2@kumc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Pengcheng",
                      family = "Lu",
                      role = c("aut", "cre"),
                      email = "plu2@kumc.edu"),
               person(given = "Junhao",
                      family = "Liu",
                      role = "aut"),
               person(given = "Devin",
                      family = "Koestler",
                      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?
Package required but not available: ‘flextable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) aid_st2.Rd:6: 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'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Achim Zeileis <Achim.Zeileis@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.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘pwt8.0.Rd’:
    http://dx.doi.org/10.15141/S5159X
    http://dx.doi.org/10.1016/j.jdeveco.2012.10.001
  File ‘pwt8.1.Rd’:
    http://dx.doi.org/10.15141/S5NP4S
Maintainer: ‘Achim Zeileis <Achim.Zeileis@R-project.org>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘pwt9.0.Rd’:
    https://doi.org/10.15141/S5J01T
  File ‘pwt9.1.Rd’:
    https://doi.org/10.15141/S50T0R
Maintainer: ‘Achim Zeileis <Achim.Zeileis@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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘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: ‘htmlwidgets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Author field differs from that derived from Authors@R
  Author:    ‘Tyler Burleigh [aut] (https://twitter.com/tylerburleigh), Thomas J. Leeper [aut] (<https://orcid.org/0000-0003-4097-6326>), Solomon Messing [ctb], Sean Murphy [ctb], Jonathan Chang [ctb], Andrew Brown [ctb], Vineet Bansal [cre]’
  Authors@R: ‘Tyler Burleigh [aut] (twitter: https://twitter.com/tylerburleigh), Thomas J. Leeper [aut] (ORCID: <https://orcid.org/0000-0003-4097-6326>), Solomon Messing [ctb], Sean Murphy [ctb], Jonathan Chang [ctb], Andrew Brown [ctb], Vineet Bansal [cre]’
Maintainer: ‘Minato Nakazawa <minato-nakazawa@umin.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Minato",
                    family = "Nakazawa",
                    role = c("aut", "cre"),
                    email = "minato-nakazawa@umin.net")
as necessary.
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.
Packages required but not available: 'sparklyr', 'rsconnect'

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?
Package required but not available: ‘ggExtra’

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'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Alicja Wolny-Dominiak <alicja.wolny-dominiak@ue.katowice.pl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alicja",
                      family = "Wolny-Dominiak",
                      role = c("aut", "cre"),
                      email = "alicja.wolny-dominiak@ue.katowice.pl"),
               person(given = "Tomasz",
                      family = "Zadlo",
                      role = "aut"))
as necessary.
checkRd: (-1) srswrRe.Rd:10: Lost braces
    10 |   \item{listRanef}{{\emph{ranef(model)}} object where {\emph{model}} is an { \emph{lmer}} object.}
       |                                                                            ^
Maintainer: ‘Hong Zhang <hzhang@wpi.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hong",
                    family = "Zhang",
                    role = c("aut", "cre"),
                    email = "hzhang@wpi.edu")
as necessary.

The Description field contains
  <arXiv:2005.00905>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Ayush Agarwal<ayush.agarwal50@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ayush",
                      family = "Agarwal",
                      role = c("aut", "cre"),
                      email = "ayush.agarwal50@gmail.com"),
               person(given = "Dootika",
                      family = "Vats",
                      role = "ctb"))
as necessary.

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

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/qbld.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?
Maintainer: ‘Tom Pike <tpike@lincoln.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tom",
                    family = "Pike",
                    role = c("aut", "cre"),
                    email = "tpike@lincoln.ac.uk")
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:
    ‘qb_records.R’
Maintainer: ‘Ingo Rohlfing <i.rohlfing@uni-koeln.de>’

The BugReports field in DESCRIPTION has
  https://github.com/ingorohlfing/qcapower
which should likely be
  https://github.com/ingorohlfing/qcapower/issues
instead.
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.
Maintainer: ‘Jirka Lewandowski <jirka.lewandowski@wzb.eu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jirka",
                    family = "Lewandowski",
                    role = c("aut", "cre"),
                    email = "jirka.lewandowski@wzb.eu")
as necessary.
Package required but not available: ‘rJava’

Package suggested but not available for checking: ‘rCBA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Luca Scrucca <luca.scrucca@unipg.it>’

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: ‘Peter J. van der Most <p.j.van.der.most@umcg.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Peter", "J."),
                      family = "van der Most",
                      role = c("aut", "cre"),
                      email = "p.j.van.der.most@umcg.nl"),
               person(given = c("Leanne", "K."),
                      family = "Kupers",
                      role = "aut"),
               person(given = "Ilja",
                      family = "Nolte",
                      role = "aut"))
as necessary.
Maintainer: ‘Peter J. van der Most <p.j.van.der.most@umcg.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Peter", "J."),
                      family = "van der Most",
                      role = c("aut", "cre"),
                      email = "p.j.van.der.most@umcg.nl"),
               person(given = c("Ilja", "M."),
                      family = "Nolte",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Alireza Lorzadeh <alorzadeh@bcgsc.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alireza",
                    family = "Lorzadeh",
                    role = c("aut", "cre"),
                    email = "alorzadeh@bcgsc.ca")
as necessary.
Package required but not available: ‘fda.usc’

Packages suggested but not available for checking: 'rmarkdown', '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.
Maintainer: ‘Xuejun Ma <yinuoyumi@163.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xuejun",
                      family = "Ma",
                      role = c("aut", "cre"),
                      email = "yinuoyumi@163.com"),
               person(given = "Jingxiao",
                      family = "Zhang",
                      role = "aut"),
               person(given = "Jingke",
                      family = "Zhou",
                      role = "aut"))
as necessary.
Maintainer: ‘Tyler Rinker <tyler.rinker@gmail.com>’

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

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Packages required but not available: 'openNLP', 'venneuler'

Package suggested but not available for checking: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘David Jungreis <dbjungreis@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "David",
                      family = "Jungreis",
                      role = c("aut", "cre"),
                      email = "dbjungreis@gmail.com"),
               person(given = "Subhadeep",
                      family = "Mukhopadhyay",
                      role = "aut"))
as necessary.
Packages required but not available: 'rmarkdown', 'tufte', 'toweranNA'

Packages suggested but not available for checking:
  'knitr', 'keras', 'cdparcoord'

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: ‘pch’

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

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

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: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Indranil Ghosh <indranilg49@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Indranil",
                    family = "Ghosh",
                    role = c("aut", "cre"),
                    email = "indranilg49@gmail.com")
as necessary.

The Description field contains
  theoretic models (Flitney and Abbott 2002) <arXiv:quant-ph/0208069>.
  1998) <arXiv:quant-ph/9804010>, Prisoner's Dilemma (J. Orlin Grabbe
  2005) <arXiv:quant-ph/0506219>, Two Person Duel (Flitney and Abbott
  2004) <arXiv:quant-ph/0305058>, Battle of the Sexes (Nawaz and Toor
  2004) <arXiv:quant-ph/0110096>, Hawk and Dove Game (Nawaz and Toor
  2010) <arXiv:quant-ph/0108075>, Newcomb's Paradox (Piotrowski and
  Sladkowski 2002) <arXiv:quant-ph/0202074> and Monty Hall Problem
  (Flitney and Abbott 2002) <arXiv:quant-ph/0109035>.
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
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: ‘Wagner Santos de Lima <wagnersantos.ufs@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Emerson", "Luis", "de", "Santa", "Helena", "Wagner", "Santos", "de", "Lima"),
                      family = "<wagnersantos.ufs@hotmail.com>",
                      role = "aut",
                      email = "wagnersantos.ufs@hotmail.com"),
               person(given = c("Wagner", "Santos"),
                      family = "de Lima",
                      role = "cre",
                      email = "wagnersantos.ufs@hotmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', '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: '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?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'mapview', 'rmarkdown', 'spDataLarge'

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:
    ‘qgis_run_algorithm_p.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Sacha Epskamp <mail@sachaepskamp.com>’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘ManHsia Yang <ymh@tari.gov.tw>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "ManHsia",
                    family = "Yang",
                    role = c("aut", "cre"),
                    email = "ymh@tari.gov.tw")
as necessary.
Packages required but not available: 'rms', '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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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) qif.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘plotly’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘yaml’

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

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 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: ‘Liam Bressler <liam.bressler@yale.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Liam",
                    family = "Bressler",
                    role = c("aut", "cre"),
                    email = "liam.bressler@yale.edu")
as necessary.
Package required but not available: ‘qad’

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:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘Juan Gea <juangea@geax.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Juan", "Gea"),
                      family = "Rosat",
                      role = "aut"),
               person(given = c("Ramon", "Martínez", "Coscollà"),
                      family = ".",
                      role = "aut"),
               person(given = "Juan",
                      family = "Gea",
                      role = "cre",
                      email = "juangea@geax.net"))
as necessary.
Maintainer: ‘Wilson Jr. Aala <s98107020@gs.ncku.edu.tw>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Wilson", "Jr."),
                    family = "Aala",
                    role = c("aut", "cre"),
                    email = "s98107020@gs.ncku.edu.tw")
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: ‘rgl’

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

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

VignetteBuilder package required 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
Package required but not available: ‘knitr’

Packages suggested but not available for checking: '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: 'bsplus', 'DT', '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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Stephen Turner <vustephen@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Stephen",
                    family = "Turner",
                    role = c("aut", "cre"),
                    email = "vustephen@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:
  '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: ‘Wayne Oldford <rwoldford@uwaterloo.ca>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘qqtest.Rd’:
    https://doi.org/10.1080/00031305.2015.1090338
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) hideLocation.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{trueLoc}{A vector of one or more numbers in the set {1, 2, ..., nSubjects} whose locations are to be hidden.}
       |                                                           ^
checkRd: (-1) hideLocation.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{nSubjects}{An integer larger than 1 used to define the set {1, 2, ..., nSubjects}.}
       |                                                                  ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Robert Stine  <stine@upenn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Robert",
                    family = "Stine",
                    role = c("aut", "cre"),
                    email = "stine@upenn.edu")
as necessary.
Packages required but not available: 'htmlwidgets', 'leaflet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Xiaoyu Song <xs2148@cumc.columbia.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Xiaoyu",
                    family = "Song",
                    role = c("aut", "cre"),
                    email = "xs2148@cumc.columbia.edu")
as necessary.
Packages required but not available: 'knitr', 'rmarkdown'

Packages suggested but not available for checking:
  'prettydoc', 'DHARMa', 'kableExtra', 'bookdown'

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

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

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

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:
    ‘qr_vcard.R’
Maintainer: ‘Karl Gregory <gregorkb@stat.sc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Karl",
                    family = "Gregory",
                    role = c("aut", "cre"),
                    email = "gregorkb@stat.sc.edu")
as necessary.
Maintainer: ‘Bob Rudis <bob@rud.is>’

Found the following (possibly) invalid file URI:
  URI: CONDUCT.md
    From: README.md
Packages required but not available: 'Hmisc', 'rms', 'knitr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Yan Li <bluefatterplaydota@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yan",
                      family = "Li",
                      role = c("aut", "cre", "trl"),
                      email = "bluefatterplaydota@gmail.com"),
               person(given = "Matthew",
                      family = "Sperrin",
                      role = c("aut", "ctb")),
               person(given = "ClinRisk",
                      family = "Ltd.",
                      role = "cph"),
               person(given = c("Tjeerd", "Pieter"),
                      family = "van Staa",
                      role = c("aut", "ths")))
as necessary.
Specified C++11: support will be removed soon
Package required but not available: ‘reactable’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Christian E. Galarza <cgalarza88@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Christian", "E."),
                      family = "Galarza",
                      role = c("aut", "cre"),
                      email = "cgalarza88@gmail.com"),
               person(given = c("Victor", "H."),
                      family = "Lachos",
                      role = "aut",
                      email = "hlachos@ime.unicamp.br"))
as necessary.
Maintainer: ‘Maria de los Angeles Resa <maria@stat.columbia.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Maria", "de", "los", "Angeles"),
                      family = "Resa",
                      role = c("aut", "cre"),
                      email = "maria@stat.columbia.edu"),
               person(given = "Birol",
                      family = "Emir",
                      role = "aut"),
               person(given = "Javier",
                      family = "Cabrera",
                      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?
'::' or ':::' imports not declared from:
  ‘simsalapar’ ‘stabledist’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Max Kuhn <mxkuhn@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Max",
                    family = "Kuhn",
                    role = c("aut", "cre"),
                    email = "mxkuhn@gmail.com")
as necessary.
Malformed Description field: should contain one or more complete sentences.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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’
File ‘qs/libs/qs.so’:
  Found non-API calls to R: ‘CLOENV’, ‘ENCLOS’, ‘FRAME’, ‘HASHTAB’,
    ‘IS_S4_OBJECT’, ‘LEVELS’, ‘OBJECT’, ‘PRENV’, ‘Rf_allocSExp’,
    ‘SETLEVELS’, ‘SET_CLOENV’, ‘SET_ENCLOS’, ‘SET_FRAME’,
    ‘SET_HASHTAB’, ‘SET_OBJECT’, ‘SET_PRENV’, ‘SET_S4_OBJECT’,
    ‘SET_TRUELENGTH’
These entry points may be removed soon:
‘SET_FRAME’, ‘SET_HASHTAB’, ‘SET_ENCLOS’, ‘SET_S4_OBJECT’, ‘FRAME’, ‘HASHTAB’, ‘IS_S4_OBJECT’, ‘CLOENV’, ‘ENCLOS’, ‘OBJECT’, ‘SET_CLOENV’, ‘LEVELS’, ‘SETLEVELS’

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

See ‘Writing portable 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: ‘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.
Maintainer: ‘Robrecht Cannoodt <rcannood@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Author field differs from that derived from Authors@R
  Author:    ‘Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood), Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)’
  Authors@R: ‘Robrecht Cannoodt [aut, cre] (ORCID: <https://orcid.org/0000-0003-3641-729X>, github: rcannood), Wouter Saelens [aut] (ORCID: <https://orcid.org/0000-0002-7114-6248>, github: zouter)’
Package required but not available: ‘Hmisc’

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’
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.
Packages required but not available: 'qtl', 'qtl2'

Packages suggested but not available for checking: 'devtools', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qtl2’

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: ‘qtl2’

Packages suggested but not available for checking:
  'devtools', 'roxygen2', '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: 'qtl2', 'qtl2fst'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'qtl2ggplot'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Frederick J Boehm <frederick.boehm@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:
  'covr', 'knitr', 'rmarkdown', 'broman', 'devtools', 'qtl2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘qtl2pleio-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert_to_scan1_output
> ### Title: Convert 'scan_multi_oneqtl' output of 'qtl2::scan1' output
> ### Aliases: convert_to_scan1_output
> 
> ### ** Examples
> 
> # read data
> iron <- qtl2::read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
Error in loadNamespace(x) : there is no package called ‘qtl2’
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: ‘yaml’

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'qtl'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ch3a
> ### Title: Data with a phenotype error
> ### Aliases: ch3a
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(ch3a)
> 
> # phenotype problem
> pairs(ch3a$pheno)
> ch3a$pheno[ch3a$pheno[,4]==0,] # individual 159
    phe1 phe2 phe3 phe4 phe5
159   50   75   70    0   80
> 
> # individuals with similar genotypes
> library(qtl)
Error in library(qtl) : there is no package called ‘qtl’
Execution halted
Packages required but not available: 'qtl', 'htmlwidgets'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ivan D. Pavicevic <ivanp84@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Ivan", "D."),
                    family = "Pavicevic",
                    role = c("aut", "cre"),
                    email = "ivanp84@gmail.com")
as necessary.
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Yuanming Zhang<soyzhang@mail.hzau.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhang",
                      family = "Ya-Wen",
                      role = "aut"),
               person(given = "Wen",
                      family = "Yang-Jun",
                      role = "aut"),
               person(given = "Wang",
                      family = "Shi-Bo",
                      role = "aut"),
               person(given = "Zhang",
                      family = "Yuan-Ming",
                      role = "aut"),
               person(given = "Yuanming",
                      family = "Zhang",
                      role = "cre",
                      email = "soyzhang@mail.hzau.edu.cn"))
as necessary.
Packages required but not available: 'qtl', 'QTL.gCIMapping'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Yuanming Zhang<soyzhang@mail.hzau.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhou",
                      family = "Ya-Hui",
                      role = "aut"),
               person(given = "Zhang",
                      family = "Ya-Wen",
                      role = "aut"),
               person(given = "Wen",
                      family = "Yang-Jun",
                      role = "aut"),
               person(given = "Wang",
                      family = "Shi-Bo",
                      role = "aut"),
               person(given = "Zhang",
                      family = "Yuan-Ming",
                      role = "aut"),
               person(given = "Yuanming",
                      family = "Zhang",
                      role = "cre",
                      email = "soyzhang@mail.hzau.edu.cn"))
as necessary.
Package required but not available: ‘qtl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Brian S. Yandell <brian.yandell@wisc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Elias", "Chaibub"),
                      family = "Neto",
                      role = "aut",
                      email = "echaibub@hotmail.com"),
               person(given = c("Brian", "S"),
                      family = "Yandell",
                      role = "aut",
                      email = "brian.yandell@wisc.edu"),
               person(given = c("Brian", "S."),
                      family = "Yandell",
                      role = "cre",
                      email = "brian.yandell@wisc.edu"))
as necessary.
Package required but not available: ‘qtl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Brian S. Yandell <brian.yandell@wisc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Elias", "Chaibub"),
                      family = "Neto",
                      role = "aut",
                      email = "echaibub@hotmail.com"),
               person(given = c("Brian", "S."),
                      family = "yandell",
                      role = c("aut", "cre"),
                      email = "brian.yandell@wisc.edu"))
as necessary.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘Pscdbp.Rd’:
    http://dx.doi.org/10.1371/journal.pgen.0020130
    http://dx.doi.org/10.1214/09-AOAS288
  File ‘bic.Rd’:
    http://dx.doi.org/10.1214/09-AOAS288
  File ‘mcmc.Rd’:
    http://dx.doi.org/10.1214/09-AOAS288
    http://dx.doi.org/10.1007/s10994-008-5057-7
  File ‘parents.Rd’:
    http://dx.doi.org/10.1214/09-AOAS288
Package required but not available: ‘qtl’

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

Packages suggested but not available for checking:
  'rmarkdown', 'devtools', '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/qtl.Rcheck/00install.out’ for details.
Running examples in ‘QTLRel-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: qtl2rel
> ### Title: Convert data from R/qtl to QTLRel format
> ### Aliases: qtl2rel
> ### Keywords: manip
> 
> ### ** Examples
> 
> library(qtl)
Error in library(qtl) : there is no package called ‘qtl’
Execution halted
checkRd: (-1) IPWE_mean_IndCen.Rd:54-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{case}{string. One of {"a", "b", "c"}, corresponding to three models.}
       |                            ^
checkRd: (-1) simJLSDdata.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:32-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', '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:
  'DT', 'knitr', 'leaflet', 'rmarkdown', 'shinytest2'

VignetteBuilder package required 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: ‘Siva Rajesh Kasa <sivarajesh.kasa@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(family = "Kasa",
                      role = "aut"),
               person(given = c("Siva", "Rajesh"),
                      family = "Kasa",
                      role = "cre",
                      email = "sivarajesh.kasa@gmail.com"))
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: ‘Berwin A. Turlach <Berwin.Turlach@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("S", "original", "by", "Berwin", "A.", "Turlach", "R", "port", "by", "Andreas", "Weingessel", "<Andreas.Weingessel@ci.tuwien.ac.at>", "Fortran", "contributions", "from", "Cleve", "Moler"),
                      family = "dpodi/LINPACK)",
                      role = "aut",
                      email = "Andreas.Weingessel@ci.tuwien.ac.at",
                      comment = "a modified version of"),
               person(given = c("Berwin", "A."),
                      family = "Turlach",
                      role = "cre",
                      email = "Berwin.Turlach@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxygen2', 'rgl'

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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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) find_lcp.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:63-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:18-19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:23-25: Lost braces in \itemize; \value handles \item{}{} directly
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘qgraph’

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) als_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:13: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory 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:
  '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', 'rgl', '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:
  'covr', 'knitr', 'rmarkdown', 'vcr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(qualtRics)
  > 
  > test_check("qualtRics")
  Error in `source_dir()`:
  ! Failed to evaluate './helper-qualtRics.R'.
  Caused by error in `loadNamespace()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("qualtRics")
    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::loadNamespace(x) at ./helper-qualtRics.R:1:1
   15. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   16. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
   17. │ │   └─base (local) doWithOneRestart(return(expr), restart)
   18. │ └─base::stop(cond)
   19. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   20.   └─cli::cli_abort(...)
   21.     └─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:
  'knitr', 'rmarkdown', 'DT'

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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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’

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

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

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: ‘quanteda’

Packages suggested but not available for checking:
  'covr', 'knitr', 'quanteda.textplots', 'spelling', '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: ‘quanteda’

Packages suggested but not available for checking:
  'knitr', 'quanteda.textmodels', 'quanteda.textstats', 'rmarkdown',
  'spelling'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Joachim Zuckarelli <joachim@zuckarelli.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Joachim",
                    family = "Zuckarelli",
                    role = c("aut", "cre"),
                    email = "joachim@zuckarelli.de")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Cinzia Viroli <cinzia.viroli@unibo.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Marco",
                      family = "Berrettini",
                      role = "aut"),
               person(given = "Christian",
                      family = "Hennig",
                      role = "aut"),
               person(given = "Cinzia",
                      family = "Viroli",
                      role = c("aut", "cre"),
                      email = "cinzia.viroli@unibo.it"))
as necessary.
Package required but not available: ‘mixtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Zoe Ashwood <zashwood@law.stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zoe",
                      family = "Ashwood",
                      role = c("aut", "cre"),
                      email = "zashwood@law.stanford.edu"),
               person(given = "Becky",
                      family = "Elias",
                      role = "aut",
                      email = "Becky.Elias@kingcounty.gov"),
               person(given = c("Daniel", "E."),
                      family = "Ho",
                      role = "aut",
                      email = "dho@law.stanford.edu"))
as necessary.
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?
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.
Maintainer: ‘Teng Fei <tfei@emory.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Teng",
                      family = "Fei",
                      role = c("aut", "cre"),
                      email = "tfei@emory.edu"),
               person(given = "Tianwei",
                      family = "Yu",
                      role = "aut"))
as necessary.
Maintainer: ‘Thomas D. Fletcher <t.d.fletcher05@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Thomas", "D."),
                    family = "Fletcher",
                    role = c("aut", "cre"),
                    email = "t.d.fletcher05@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: ‘Ivan Fernandez-Val <ivanf@bu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Michael",
                      family = "Lipsitz",
                      role = "aut"),
               person(given = "Alexandre",
                      family = "Belloni",
                      role = "aut"),
               person(given = "Victor",
                      family = "Chernozhukov",
                      role = "aut"),
               person(given = "Ivan",
                      family = "Fernandez-Val",
                      role = c("aut", "cre"),
                      email = "ivanf@bu.edu"))
as necessary.
Maintainer: ‘Salonik Resch <resc0059@umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Salonik",
                    family = "Resch",
                    role = c("aut", "cre"),
                    email = "resc0059@umn.edu")
as necessary.

The Description field contains
  <arXiv:1411.4028>, and a variational quantum classifier (Schuld 2018)
  <arXiv:1804.00633>. Can be used with the gridsynth algorithm
  <arXiv:1212.6253> to perform decomposition into the Clifford+T set.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘dygraphs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) quarries.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:20-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:26-28: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking:
  'bookdown', '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: 'rmarkdown', 'yaml'

Packages suggested but not available for checking:
  'flextable', 'ggiraph', 'gt', 'heatmaply', 'kableExtra', 'knitr',
  'plotly', 'rsconnect', 'tidyverse'

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

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

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:
    ‘quax.Rd’
Maintainer: ‘Laura Anderlucci <laura.anderlucci@unibo.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Christian",
                      family = "Hennig",
                      role = "aut"),
               person(given = "Cinzia",
                      family = "Viroli",
                      role = "aut"),
               person(given = "Laura",
                      family = "Anderlucci",
                      role = c("aut", "cre"),
                      email = "laura.anderlucci@unibo.it"))
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 package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', '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: ‘Takahiko Koizumi <takahiko.koizumi@riken.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Takahiko",
                      family = "Koizumi",
                      role = c("aut", "cre"),
                      email = "takahiko.koizumi@riken.jp"),
               person(given = "Kenta",
                      family = "Suzuki",
                      role = "aut"),
               person(given = "Yasunori",
                      family = "Ichihashi",
                      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: ‘Pedro Canadilla <pedro.canadilla@gmail.com>’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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?
Maintainer: ‘Linares Daniel <danilinares@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?
Maintainer: ‘A. Luise Kuehn <luise.kuehn@uni-greifswald.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("A.", "Luise"),
                    family = "Kuehn",
                    role = c("aut", "cre"),
                    email = "luise.kuehn@uni-greifswald.de")
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?
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: ‘tidyjson’

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?
Packages required but not available: 'langevitour', '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’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Radford Neal <radfordneal@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Radford",
                    family = "Neal",
                    role = c("aut", "cre"),
                    email = "radfordneal@gmail.com")
as necessary.
File ‘quotedargs/libs/quotedargs.so’:
  Found non-API calls to R: ‘ENCLOS’, ‘LEVELS’, ‘PRCODE’, ‘PRENV’,
    ‘PRVALUE’, ‘Rf_allocSExp’, ‘SETLEVELS’, ‘SET_NAMED’, ‘SET_PRCODE’,
    ‘SET_PRENV’, ‘SET_PRVALUE’
These entry points may be removed soon:
‘SET_NAMED’, ‘ENCLOS’, ‘LEVELS’, ‘SETLEVELS’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Maintainer: ‘Andrew Heiss <andrew@andrewheiss.com>’

Found the following (possibly) invalid file URI:
  URI: CONDUCT.md
    From: README.md
Packages required but not available:
  'DT', 'kableExtra', 'knitr', 'rmarkdown'

Packages suggested but not available for checking: 'bookdown', 'prettydoc'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Vitor Marques <vmrodriguespro@gmail.com>’

The Description field contains
  <arXiv:quant-ph/9706062v2>; C. Godsil (2011) <arXiv:1103.2578v3>.
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: ‘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.
Package required but not available: ‘learnr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Thomas Obadia <thomas.obadia@pasteur.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Pierre-Yves",
                      family = "Boelle",
                      role = "aut"),
               person(given = "Thomas",
                      family = "Obadia",
                      role = c("aut", "cre"),
                      email = "thomas.obadia@pasteur.fr"))
as necessary.
checkRd: (-1) est.R0.ML.Rd:98: Lost braces
    98 | Supplementary Material S1 from \doi{10.1186/1472-6947-12-147}{Obadia et al., 2012}.
       |                                                              ^
checkRd: (-1) plot.R0.R.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from one estimation method.
       |                                                      ^
checkRd: (-1) plot.R0.sR.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from an
       |                                                      ^
Maintainer: ‘Denise Rava <drava@ucsd.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Denise",
                    family = "Rava",
                    role = c("aut", "cre"),
                    email = "drava@ucsd.edu")
as necessary.

The Description field contains
  selection process. Rava, D. and Xu, R. (2020) <arXiv:2003.09460>.
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/R2admb.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Andrea Fasulo <fasulo@istat.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Andrea", "Fasulo,Giulio", "Barcaroli,Stefano", "Falorsi,Alessio", "Guandalini,Daniela", "Pagliuca,Marco", "Dionisio"),
                      family = "Terribili",
                      role = "aut"),
               person(given = "Andrea",
                      family = "Fasulo",
                      role = "cre",
                      email = "fasulo@istat.it"))
as necessary.
Maintainer: ‘Obinna Obianom <idonshayo@gmail.com>’

The BugReports field in DESCRIPTION has
  https://github.com/oobianom/r2country
which should likely be
  https://github.com/oobianom/r2country/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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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', 'shinytest'

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: ‘Robin Van Oirbeek <robin.vanoirbeek@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Robin",
                    family = "Van Oirbeek",
                    role = c("aut", "cre"),
                    email = "robin.vanoirbeek@gmail.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: ‘memisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: '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', '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:
  '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: '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: ‘Obinna Obianom <idonshayo@gmail.com>’

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

The BugReports field in DESCRIPTION has
  https://github.com/oobianom/r2shortcode
which should likely be
  https://github.com/oobianom/r2shortcode/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?
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 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/r2spss-intro.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Unknown package ‘ast2ast’ in Rd xrefs
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?
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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', 'covr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Sam Wilks <sw463@cam.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sam",
                    family = "Wilks",
                    role = c("aut", "cre"),
                    email = "sw463@cam.ac.uk")
as necessary.
Package required but not available: ‘htmlwidgets’

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'

VignetteBuilder package required 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 Bock <thsteinbock@web.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thomas",
                    family = "Bock",
                    role = c("aut", "cre"),
                    email = "thsteinbock@web.de")
as necessary.
Package required but not available: ‘tutorial.helpers’

Packages suggested but not available for checking:
  'gt', 'learnr', 'reprex', 'rsconnect', 'tidyverse'

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

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: '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?
Maintainer: ‘Ian G. Taylor <Ian.Taylor@noaa.gov>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘kableExtra’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DT', 'mapgl', 'r5r'

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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) extract_class.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extract_class.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extract_class.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) post_RA_fits.Rd:61: Lost braces; missing escapes or markup?
    61 |     \item{\code{H(po_{bm_{n.bm}}, po_act)}:}{ last benchmark prior bm_{n.bm} inducing the fit \code{fits.bm[[n.bm]]} and actual prior}
       |                                                                       ^
Maintainer: ‘Andrew Taylor Burchill <andrew.burchill@asu.edu>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘brute_IDs.Rd’:
    https://doi.org/10.1016/j.anbehav.2019.05.013
  File ‘codes_to_colors.Rd’:
    https://doi.org/10.1016/j.anbehav.2019.05.013
  File ‘exampleGUI.Rd’:
    https://doi.org/10.1016/j.anbehav.2019.05.013
  File ‘how_many.Rd’:
    https://doi.org/10.1016/j.anbehav.2019.05.013
  File ‘how_robust.Rd’:
    https://doi.org/10.1016/j.anbehav.2019.05.013
  File ‘rabi.Rd’:
    https://doi.org/10.1016/j.anbehav.2019.05.013
  File ‘rs_IDs.Rd’:
    https://doi.org/10.1016/j.anbehav.2019.05.013
  File ‘simple_IDs.Rd’:
    https://doi.org/10.1016/j.anbehav.2019.05.013
  File ‘tweaked_IDs.Rd’:
    https://doi.org/10.1016/j.anbehav.2019.05.013
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ao_get_leaners_progress_by_course.R’
Packages required but not available:
  'config', 'DT', 'htmlwidgets', 'pins', '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?
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?
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking:
  'r3js', 'knitr', 'rmarkdown', 'plotly', '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'

VignetteBuilder package required 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?
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.
Packages required but not available: 'Hmisc', 'knitr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'roxygen2', 'usethis', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘José Matute <jmatuteflores@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 package required 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: ‘radiant.data’

Package suggested but not available for checking: ‘pkgdown’

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

Package suggested but not available for checking: ‘pkgdown’

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

Package suggested but not available for checking: ‘pkgdown’

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

Package suggested but not available for checking: ‘pkgdown’

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

Package suggested but not available for checking: ‘pkgdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'radiant.data', 'radiant.design', 'radiant.basics', 'radiant.model',
  'radiant.multivariate'

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: ‘Doug Nychka <nychka@mines.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Doug",
                      family = "Nychka",
                      role = c("aut", "cre"),
                      email = "nychka@mines.edu"),
               person(given = "Eric",
                      family = "Gilleland",
                      role = "aut"),
               person(given = "Liangying",
                      family = "Zhang",
                      role = "aut"),
               person(given = "Tim",
                      family = "Hoar",
                      role = "aut"),
               person(given = "Kate",
                      family = "Young",
                      role = "aut"))
as necessary.
Maintainer: ‘David Moriña Soler <david.morina@uab.cat>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "David",
                      family = "Moriña",
                      role = c("aut", "cre"),
                      email = "david.morina@uab.cat",
                      comment = "Barcelona Graduate School of Mathematics"),
               person(given = "Manuel",
                      family = "Higueras",
                      role = "aut",
                      comment = "Basque Center for Applied Mathematics"),
               person(given = "Pedro",
                      family = "Puig",
                      role = "aut",
                      comment = "Universitat Autònoma de Barcelona"))
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: ‘Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Mohamed", "El", "Fodil"),
                    family = "Ihaddaden",
                    role = c("aut", "cre"),
                    email = "ihaddaden.fodeil@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?
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’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Johannes Burkhardt <johannes.burkhardt@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Johannes",
                      family = "Burkhardt",
                      role = c("aut", "cre"),
                      email = "johannes.burkhardt@gmail.com"),
               person(given = "Matthias",
                      family = "Bannert",
                      role = "aut",
                      email = "matthias.bannert@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:
    ‘add_element.Rd’
Package has ‘vignettes’ subdirectory 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: ‘DiagrammeR’

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

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’
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.
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?
Package required but not available: ‘htmlwidgets’

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

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: 'quanteda', 'quanteda.textstats'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Dione Pereira Cardoso <cardoso.dione@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Dione", "Pereira"),
                      family = "Cardoso",
                      role = c("aut", "cre"),
                      email = "cardoso.dione@gmail.com"),
               person(given = c("Edilson", "Marcelino"),
                      family = "Silva",
                      role = "aut"),
               person(given = c("Paulo", "Cesar"),
                      family = "Ossani",
                      role = "aut"),
               person(given = c("Marx", "Leandro", "Naves"),
                      family = "Silva",
                      role = "ctb"),
               person(given = c("Joel", "Augusto"),
                      family = "Muniz",
                      role = "ctb"),
               person(given = c("Daniel", "Furtado"),
                      family = "Ferreira",
                      role = "ctb"),
               person(given = c("Junior", "Cesar"),
                      family = "Avanzi",
                      role = "ctb"))
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘RFactor.Rd’:
    \keyword{
        Erosivity index; R-Factor; Universal S [TRUNCATED]
  File ‘RainFallExample.Rd’:
    \keyword{
          Erosivity index; R-Factor; Universal [TRUNCATED]
  File ‘RainfallErosivityFactor.Rd’:
    \keyword{
        Erosivity index; R-Factor; Universal S [TRUNCATED]
Maintainer: ‘Jost von Hardenberg <j.vonhardenberg@isac.cnr.it>’

The BugReports field in DESCRIPTION has
  https://github.com/jhardenberg/rainfarmr
which should likely be
  https://github.com/jhardenberg/rainfarmr/issues
instead.
Maintainer: ‘Kory D. Johnson <korydjohnson@gmail.com>’

The Description field contains
  <arXiv:1510.06322>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Erica Ponzi <erica.ponzi@medisin.uio.no>’

The Description field contains
  <arXiv:2101.09110>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Phil Mike Jones <philmikejones@gmail.com>’

Found the following (possibly) invalid file URI:
  URI: CONDUCT.md
    From: README.md
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: ‘diffr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Chapman Siu <chpmn.siu@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Chapman",
                    family = "Siu",
                    role = c("aut", "cre"),
                    email = "chpmn.siu@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: ‘htmlwidgets’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Xinwei Ma <x1ma@ucsd.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Matias", "D."),
                      family = "Cattaneo",
                      role = "aut"),
               person(given = "Paul",
                      family = "Cheung",
                      role = "aut"),
               person(given = "Xinwei",
                      family = "Ma",
                      role = c("aut", "cre"),
                      email = "x1ma@ucsd.edu"),
               person(given = "Yusufcan",
                      family = "Masatlioglu",
                      role = "aut"),
               person(given = "Elchin",
                      family = "Suleymanov",
                      role = "aut"))
as necessary.

The Description field contains
  Cattaneo, Ma, Masatlioglu and Suleymanov (2020) <arXiv:1712.03448> and
  Cattaneo, Cheung, Ma, and Masatlioglu (2022) <arXiv:2110.10650>, which
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?
Maintainer: ‘Zhiyong Zhang <zzhang4@nd.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhiyong",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "zzhang4@nd.edu"),
               person(given = "Jack",
                      family = "McArdle",
                      role = "aut"),
               person(given = "Aki",
                      family = "Hamagami",
                      role = "aut"),
               person(given = c("&", "Kevin"),
                      family = "Grimm",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse', '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: ‘Zach Branson <zach@stat.cmu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Zach",
                    family = "Branson",
                    role = c("aut", "cre"),
                    email = "zach@stat.cmu.edu")
as necessary.

The Description field contains
  variable. See Branson (2021) <arXiv:1804.08760> for details.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Daniel F. Schmidt <daniel.schmidt@monash.edu>’

The Description field contains
  <arXiv:1809.05212>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘randcorr-package.Rd’:
    \keyword{matrix,}
Maintainer: ‘Scott Chamberlain <myrmecocystus@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: '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: ‘Lu Tian <lutian@stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Grace",
                      family = "Deng",
                      role = "aut"),
               person(given = "Lu",
                      family = "Tian",
                      role = c("aut", "cre"),
                      email = "lutian@stanford.edu"))
as necessary.
Package required but not available: ‘yaml’

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: ‘Ron Ammar <ron.ammar@gmail.com>’

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

VignetteBuilder package required 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: ‘DiagrammeR’

Package suggested but not available for checking: ‘pec’

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

VignetteBuilder package required 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 Langfelder <peter.langfelder@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Lin",
                      family = "Song",
                      role = "aut"),
               person(given = "Peter",
                      family = "Langfelder",
                      role = c("aut", "cre"),
                      email = "peter.langfelder@gmail.com"))
as necessary.
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'

VignetteBuilder package required 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 J. Lee <joseph.j.lee@post.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Joseph", "J."),
                      family = "Lee",
                      role = c("aut", "cre"),
                      email = "joseph.j.lee@post.harvard.edu"),
               person(given = "Tirthankar",
                      family = "Dasgupta",
                      role = "aut"))
as necessary.
Maintainer: ‘D. Labes <detlewlabes@gmx.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "D.",
                    family = "Labes",
                    role = c("aut", "cre"),
                    email = "detlewlabes@gmx.de")
as necessary.
Package required but not available: ‘gsDesign’

Package suggested 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 package required for checking but not installed: ‘knitr’
File ‘randomizr/libs/randomizr.so’:
  Found non-API call to R: ‘SETLENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Package has ‘vignettes’ subdirectory 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: ‘Dirk Eddelbuettel <edd@debian.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Dirk",
                    family = "Eddelbuettel",
                    role = c("aut", "cre"),
                    email = "edd@debian.org")
as necessary.
Maintainer: ‘Saip Ciss <saip.ciss@wanadoo.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Saip",
                    family = "Ciss",
                    role = c("aut", "cre"),
                    email = "saip.ciss@wanadoo.fr")
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: ‘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
Packages required but not available: 'NNS', '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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'rgl'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot3D
> ### Title: 3D plot using rgl
> ### Aliases: plot3D
> 
> ### ** Examples
> 
> pc <- rppca(pedLInv)
> plot3D(pc)
Error: Package "rgl" must be installed to use this function.
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Siddharth R <r.siddharthcse@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Aghila",
                      family = "G",
                      role = "aut"),
               person(given = "Siddharth",
                      family = "R",
                      role = c("aut", "cre"),
                      email = "r.siddharthcse@gmail.com"))
as necessary.
Maintainer: ‘Mihai Valcu <valcu@orn.mpg.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.
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?
Package required but not available: ‘spocc’

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: ‘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', '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?
Maintainer: ‘Jay Burns <jay.burns@sruc.ac.uk>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Vasyl Pihur <vpihur@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Vasyl",
                      family = "Pihur",
                      role = c("aut", "cre"),
                      email = "vpihur@gmail.com"),
               person(given = "Somnath",
                      family = "Datta",
                      role = "aut",
                      email = "somnath.datta@louisville.edu"),
               person(given = "Susmita",
                      family = "Datta",
                      role = "aut",
                      email = "susmita.datta@louisville.edu"))
as necessary.
Maintainer: ‘Quentin Grimonprez <quentingrim@yahoo.fr>’

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 required but not available: ‘rms’

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

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Zhaozhi Qian <qianzhaozhi@connect.hku.hk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Zhaozhi",
                    family = "Qian",
                    role = c("aut", "cre"),
                    email = "qianzhaozhi@connect.hku.hk")
as necessary.
Maintainer: ‘Frank Konietschke <frank.konietschke@charite.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Frank",
                      family = "Konietschke",
                      role = c("aut", "cre"),
                      email = "frank.konietschke@charite.de"),
               person(given = "Sarah",
                      family = "Friedrich",
                      role = "aut"),
               person(given = "Edgar",
                      family = "Brunner",
                      role = "aut"),
               person(given = "Markus",
                      family = "Pauly",
                      role = "aut"))
as necessary.
Running examples in ‘rankhazard-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rankhazard-package
> ### Title: Rank-hazard plots
> ### Aliases: rankhazard-package rankhazard
> ### Keywords: package hplot survival
> 
> ### ** Examples
> 
> library(survival)
> model <- coxph(Surv(time,status) ~ age + sex + ph.karno, data = cancer, x=TRUE)
> rankhazardplot(model, data=cancer)
Y-axis range:  0.608 1.49 
 
Relative hazards for each covarite: 
          Min. 1st Qu. Median 3rd Qu. Max.
age      0.743   0.917      1    1.08 1.27
sex      0.608   0.608      1    1.00 1.00
ph.karno 0.766   0.875      1    1.07 1.49
> library(rms)
Error in library(rms) : there is no package called ‘rms’
Execution halted
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?
checkRd: (-1) grottaBar.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:83: Lost braces in \itemize; meant \describe ?
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:
  '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: ‘Hsiuying Wang <wang@stat.nycu.edu.tw>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hsiuying",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "wang@stat.nycu.edu.tw"),
               person(given = "Yu-Chun",
                      family = "Lin",
                      role = "aut"),
               person(given = "Wan-Ting",
                      family = "Huang",
                      role = "aut"))
as necessary.
checkRd: (-1) rankL2R.Rd:18: Lost braces; missing escapes or markup?
    18 | where the vector dimension is 2^{response.number}.}
       |                                 ^
Package required but not available: ‘randomForestSRC’

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: ‘yaml’

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: person(given = "Dirk",
                    family = "Eddelbuettel",
                    role = c("aut", "cre"),
                    email = "edd@debian.org")
as necessary.
Maintainer: ‘Markus Loecher <markus.loecher@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Markus",
                      family = "Loecher",
                      role = c("aut", "cre"),
                      email = "markus.loecher@gmail.com"),
               person(given = "Madhav",
                      family = "Kumar",
                      role = "aut",
                      email = "madhavkumar2005@gmail.com"))
as necessary.
Packages required but not available: 'rJava', 'openNLPdata', 'slowraker'

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?
Package required but not available: ‘rlist’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) user_log_dir.Rd:48: Lost braces
    48 | \\env{$XDG_CACHE_HOME} if defined
       |      ^
Package required but not available: ‘yaml’

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.
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?
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?
Packages required but not available: 'rms', 'Hmisc'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'keyring', 'knitr', 'rmarkdown', 'roxygen2',
  '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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Luis Cayuela <luis.cayuela@urjc.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Luis",
                      family = "Cayuela",
                      role = c("aut", "cre"),
                      email = "luis.cayuela@urjc.es"),
               person(given = c("Nicholas", "J."),
                      family = "Gotelli",
                      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: ‘Boris Leroy <leroy.boris@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Boris",
                    family = "Leroy",
                    role = c("aut", "cre"),
                    email = "leroy.boris@gmail.com")
as necessary.
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 = "Jiali",
                      family = "Mei",
                      role = "aut"),
               person(given = c("authors", "of", "the", "ARPACK", "library.", "See", "file", "AUTHORS", "for"),
                      family = "details.",
                      role = "aut"))
as necessary.
Maintainer: ‘Johann Gaebler <me@jgaeb.com>’

The Description field contains
  Disparate Impact" Jung et al. (2024) <arXiv:1809.05651>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘pins’

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: 'devtools', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ye Tian <ye.t@columbia.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ye",
                      family = "Tian",
                      role = c("aut", "cre"),
                      email = "ye.t@columbia.edu"),
               person(given = "Yang",
                      family = "Feng",
                      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?
Package required but not available: ‘DT’

Package suggested but not available for checking: ‘covr’

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

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', 'bcmaps'

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:
    ‘findblocks_bc.Rd’ ‘getdata_bc.Rd’ ‘listdata_bc.Rd’ ‘opendata_bc.Rd’
    ‘utils.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: ‘Joshua O'Brien <joshmobrien@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Joshua",
                    family = "O'Brien",
                    role = c("aut", "cre"),
                    email = "joshmobrien@gmail.com")
as necessary.
Maintainer: ‘Martin Seilmayer <m.seilmayer@hzdr.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Martin",
                    family = "Seilmayer",
                    role = c("aut", "cre"),
                    email = "m.seilmayer@hzdr.de")
as necessary.
Maintainer: ‘Paul Murrell <paul@stat.auckland.ac.nz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Paul",
                    family = "Murrell",
                    role = c("aut", "cre"),
                    email = "paul@stat.auckland.ac.nz")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'leaflet', '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', '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’
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: ‘Michael Fay <mfay@niaid.nih.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Michael",
                    family = "Fay",
                    role = c("aut", "cre"),
                    email = "mfay@niaid.nih.gov")
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?
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/RDperm.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?
Maintainer: ‘Alicja Wolny-Dominiak <alicja.wolny-dominiak@ue.katowice.pl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Waldemar", "W."),
                      family = "Koczkodaj",
                      role = "aut"),
               person(given = "Feng",
                      family = "Li",
                      role = "aut"),
               person(given = "Alicja",
                      family = "Wolny-Dominiak",
                      role = c("aut", "cre"),
                      email = "alicja.wolny-dominiak@ue.katowice.pl"))
as necessary.
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/RationalExp.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Yixuan Qiu <yixuan.qiu@cos.name>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yixuan",
                    family = "Qiu",
                    role = c("aut", "cre"),
                    email = "yixuan.qiu@cos.name")
as necessary.
Maintainer: ‘Solveig Pospiech <s.pospiech@gmx.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Solveig",
                      family = "Pospiech",
                      role = c("aut", "cre"),
                      email = "s.pospiech@gmx.de"),
               person(given = "Wiebke",
                      family = "Fahlbusch",
                      role = "ctb"))
as necessary.
Package required but not available: ‘rlist’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Graham Williams <Graham.Williams@togaware.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.
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
Maintainer: ‘Ozvan Bocher <bocherozvan@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ozvan",
                      family = "Bocher",
                      role = c("aut", "cre"),
                      email = "bocherozvan@gmail.com"),
               person(given = "Hervé",
                      family = "Perdry",
                      role = "aut"))
as necessary.
Package required but not available: ‘bedr’

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: 'ieegio', 'ravepipeline', 'threeBrain'

Package suggested but not available for checking: ‘plotly’

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

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.
Packages required but not available: 'knitr', 'targets', 'yaml'

Packages suggested but not available for checking:
  'ieegio', 'rmarkdown', 'shidashi', 'threeBrain', 'visNetwork',
  'distill'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Davide Massidda <davide.massidda@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Giulio",
                      family = "Vidotto",
                      role = "aut",
                      email = "giulio.vidotto@unipd.it"),
               person(given = "Stefano",
                      family = "Noventa",
                      role = "aut",
                      email = "stefano.noventa@uni-tuebingen.de"),
               person(given = "Davide",
                      family = "Massidda",
                      role = c("aut", "cre"),
                      email = "davide.massidda@gmail.com"),
               person(given = "Marco",
                      family = "Vicentini",
                      role = "aut",
                      email = "marco.vicentini@gmail.com"))
as necessary.
Packages required but not available:
  'config', 'golem', 'kableExtra', 'plotly', '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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

Package suggested but not available for checking: ‘lidR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Amanda Rehbein <amanda.rehbein@usp.br>’

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', 'covr', '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?
Maintainer: ‘Wilson Freitas <wilson.freitas@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Wilson",
                    family = "Freitas",
                    role = c("aut", "cre"),
                    email = "wilson.freitas@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: ‘Diego Gallardo <dgallardo@ubiobio.cl>’

The Description field contains
  Gallardo and Saulo <arXiv:2110.04428> The package also provides tools
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Failed with error:  ‘unused argument (quitely = TRUE)’

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
checkRd: (-1) beast.Rd:13: height/width attributes should be in pixels
checkRd: (-1) minesweeper.Rd:9: height/width attributes should be in pixels
checkRd: (-1) tetris.Rd:9: height/width attributes should be in pixels
File ‘Rbeast/libs/Rbeast.so’:
  Found non-API call to R: ‘OBJECT’
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.
Author field differs from that derived from Authors@R
  Author:    ‘Wacek Kusnierczyk <waku@idi.ntnu.no>’
  Authors@R: ‘Wacek Kusnierczyk [aut, cre], Dirk Eddelbuettel [ctb], Berend Hasselman [ctb]’
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', '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', 'rmarkdown', 'gam'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', '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', 'lintr', '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:
  '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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Jialun Zhang <reatank@foxmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jialun",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "reatank@foxmail.com"),
               person(given = "Zhilan",
                      family = "Fan",
                      role = "aut"),
               person(given = "Hang",
                      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’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘dygraphs’

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: ‘Abdelmoneim Amer Desouki <desouki@hhu.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Abdelmoneim", "Amer"),
                    family = "Desouki",
                    role = c("aut", "cre"),
                    email = "desouki@hhu.de")
as necessary.

The Description field contains
  Desouki, M. Roeder, A. Ngonga (2019) <arXiv:1903.10326>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Marco Scutari <scutari@bnlearn.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jean-Baptiste",
                      family = "Denis",
                      role = c("aut", "cre")),
               person(given = "Marco",
                      family = "Scutari",
                      role = c("ctb", "cre"),
                      email = "scutari@bnlearn.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: ‘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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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 J. Keele <luke.keele@gmail.com>’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Bahadir Yuzbasi <b.yzb@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Bahadir",
                      family = "Yuzbasi",
                      role = c("aut", "cre"),
                      email = "b.yzb@hotmail.com"),
               person(given = "Mohammad",
                      family = "Arashi",
                      role = "aut"),
               person(given = "Fikri",
                      family = "Akdeniz",
                      role = "aut"))
as necessary.

The Description field contains
  Yuzbasi et al. (2019) <arXiv:1910.03660>. Special cases of this
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Found the following significant warnings:
  Main_functions.cpp:40:54: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = unsigned int; T1 = arma::mtOp<unsigned int, arma::mtOp<unsigned int, arma::Col<unsigned int>, arma::op_rel_eq>, arma::op_find_simple>; out_eT = unsigned int; typename arma::arma_not_cx<in_eT>::result = unsigned int]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rbridge.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-15 (Debian 15.2.0-9) 15.2.0’
Specified C++11: support will be removed soon
Maintainer: ‘Serguei Rouzinov <rouzinovs@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Serguei",
                      family = "Rouzinov",
                      role = c("aut", "cre"),
                      email = "rouzinovs@gmail.com"),
               person(given = "André",
                      family = "Berchtold",
                      role = "aut"))
as necessary.
Maintainer: ‘Xiang Zhou <xiang_zhou@fas.harvard.edu>’

The BugReports field in DESCRIPTION has
  https://github.com/xiangzhou09/rbw
which should likely be
  https://github.com/xiangzhou09/rbw/issues
instead.
Package required but not available: ‘lidR’

Package suggested but not available for checking: ‘EBImage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 = "Baoluo",
                      family = "Sun",
                      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.

The Description field contains
  Sun and Tan (2020) <arXiv:2009.09286>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
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.
Maintainer: ‘Amir Goldberg <amirgo@stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Amir",
                      family = "Goldberg",
                      role = c("aut", "cre"),
                      email = "amirgo@stanford.edu"),
               person(given = c("Sarah", "K."),
                      family = "Stein",
                      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: ‘Qiao Liu <liuqiao@stanford.edu>’

The Description field contains
  methods is given in Liu (2022) <arXiv:2212.05925>.
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: '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: ‘Herdiantri Sufriyana <herdi@tmu.edu.tw>’

The Description field contains
  <https://htmlpreview.github.io/?https://github.com/herdiantrisufriyana/rcausim/blob/master/doc/causal_simulation_exemplar.html>.
Please enclose URLs in angle brackets (<...>).
Cannot process vignettes
Packages suggested but not available for checking:
  'kableExtra', '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: ‘Samuel D. Pimentel <spi@berkeley.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Samuel", "D."),
                    family = "Pimentel",
                    role = c("aut", "cre"),
                    email = "spi@berkeley.edu")
as necessary.
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: ‘Samuel D. Pimentel <spi@berkeley.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Samuel", "D."),
                    family = "Pimentel",
                    role = c("aut", "cre"),
                    email = "spi@berkeley.edu")
as necessary.
Packages required but not available: 'redcapAPI', 'yaml', 'keyring'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Dr. Fayed Alshammri <fayed333@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Fayed",
                      family = "Alshammri",
                      role = "aut"),
               person(given = c("Dr.", "Fayed"),
                      family = "Alshammri",
                      role = "cre",
                      email = "fayed333@hotmail.com"))
as necessary.
Maintainer: ‘Jean Morrison <jeanm@uchicago.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jean",
                    family = "Morrison",
                    role = c("aut", "cre"),
                    email = "jeanm@uchicago.edu")
as necessary.

The Description field contains
  <arXiv:1702.06986>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Found the following files/directories:
  ‘temp.RData’
Maintainer: ‘Charles J. Geyer <geyer@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 = "geyer@umn.edu"),
               person(given = c("Glen", "D."),
                      family = "Meeden",
                      role = "aut",
                      email = "gmeeden@umn.edu"),
               person(given = c("incorporates", "code", "from", "cddlib", "written", "by", "Komei"),
                      family = "Fukuda",
                      role = "aut",
                      email = "fukuda@ifor.math.ethz.ch",
                      comment = c(ROR = "ver 0.94f")))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', '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?