Package required but not available: ‘rJava’

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

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
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: ‘rgl’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Alberto Krone-Martins <algol@sim.ul.pt>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alberto",
                    family = "Krone-Martins",
                    role = c("aut", "cre"),
                    email = "algol@sim.ul.pt")
as necessary.
Package required but not available: ‘RplotterPkg’

Packages suggested but not available for checking: 'knitr', '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?
Maintainer: ‘Bruno Melo <ctbrunomelo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Bruno", "M.", "S.", "S."),
                      family = "Melo",
                      role = "aut"),
               person(given = "Bruno",
                      family = "Melo",
                      role = "cre",
                      email = "ctbrunomelo@gmail.com"))
as necessary.
Package required but not available: ‘visNetwork’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) nc_open_CGLS.Rd:29-32: Lost braces
    29 | if(resolution == "300m"){
       |                         ^
checkRd: (-1) nc_open_CGLS.Rd:33-36: Lost braces
    33 | if(resolution == "1km"){
       |                        ^
Packages required but not available: '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?
Packages required but not available:
  'leaflet', 'oceanmap', 'dygraphs', 'htmlwidgets', 'plotly',
  'leaflet.extras2'

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Anne Philippe <anne.philippe@univ-nantes.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Anne",
                      family = "Philippe",
                      role = c("aut", "cre"),
                      email = "anne.philippe@univ-nantes.fr"),
               person(given = "Marie-Anne",
                      family = "Vibet",
                      role = "aut"))
as necessary.
Found the following files/directories:
  ‘data.csv’
Maintainer: ‘Hongen Zhang <hzhang.henry@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Hongen",
                    family = "Zhang",
                    role = c("aut", "cre"),
                    email = "hzhang.henry@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', '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(rcites)
  > library(tibble)
  > test_check("rcites")
  Error in `source_dir()`:
  ! Failed to evaluate './setup-rcites.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("rcites")
    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-rcites.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?
Package required but not available: ‘Hmisc’

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:
  '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?
Maintainer: ‘Sebastien Bihorel <sb.pmlab@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sebastien",
                    family = "Bihorel",
                    role = c("aut", "cre"),
                    email = "sb.pmlab@gmail.com")
as necessary.
Maintainer: ‘Wolfgang Konen <wolfgang.konen@fh-koeln.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Wolfgang",
                      family = "Konen",
                      role = c("aut", "cre"),
                      email = "wolfgang.konen@fh-koeln.de"),
               person(given = "Nikolaus",
                      family = "Hansen",
                      role = "aut",
                      email = "hansen.AT.lri.fr"))
as necessary.
Running examples in ‘rCMA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cmaCalcFitness
> ### Title: Calculate the fitness of a population.
> ### Aliases: cmaCalcFitness
> 
> ### ** Examples
> 
> cma <- cmaNew();
Error in loadNamespace(x) : there is no package called ‘rJava’
Calls: cmaNew ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘Hmisc’

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

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: ‘Rcmdr’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Aurora Torrente <etorrent@est-econ.uc3m.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Sara",
                      family = "Lopez-Pintado",
                      role = "aut",
                      email = "sl2929@columbia.edu"),
               person(given = "Aurora",
                      family = "Torrente.",
                      role = "aut",
                      email = "etorrent@est-econ.uc3m.es"),
               person(given = "Aurora",
                      family = "Torrente",
                      role = "cre",
                      email = "etorrent@est-econ.uc3m.es"))
as necessary.
Package required but not available: ‘Rcmdr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘David Leiva <dleivaur@ub.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Maribel",
                      family = "Pero",
                      role = "aut",
                      email = "mpero@ub.edu"),
               person(given = "David",
                      family = "Leiva",
                      role = c("aut", "cre"),
                      email = "dleivaur@ub.edu"),
               person(given = "Joan",
                      family = "Guardia",
                      role = "aut",
                      email = "jguardia@ub.edu"),
               person(given = "Antonio",
                      family = "Solanas",
                      role = "aut",
                      email = "antonio.solanas@ub.edu"))
as necessary.
Packages required but not available: 'Rcmdr', 'RcmdrMisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Daniel-Corneliu Leucuta <danny.ldc@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Daniel-Corneliu",
                    family = "Leucuta",
                    role = c("aut", "cre"),
                    email = "danny.ldc@gmail.com")
as necessary.
Packages required but not available: 'Rcmdr', 'epiR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Liviu Andronic <landronimirc@gmail.com>’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Yoshinobu Kanda <ycanda-tky@umin.ac.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yoshinobu",
                    family = "Kanda",
                    role = c("aut", "cre"),
                    email = "ycanda-tky@umin.ac.jp")
as necessary.
Package required but not available: ‘Rcmdr’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Francois Husson <francois.husson@institut-agro.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Francois",
                      family = "Husson",
                      role = c("aut", "cre"),
                      email = "francois.husson@institut-agro.fr"),
               person(given = "Julie",
                      family = "Josse",
                      role = "aut"),
               person(given = "Sebastien",
                      family = "Le",
                      role = "aut"))
as necessary.
Packages required but not available: 'FactoMineR', 'Rcmdr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Richard M. Heiberger <rmh@temple.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Richard", "M."),
                      family = "Heiberger",
                      role = c("aut", "cre"),
                      email = "rmh@temple.edu"),
               person(given = c("with", "contributions", "from", "Burt"),
                      family = "Holland",
                      role = "aut"))
as necessary.
Packages required but not available: 'HH', 'Rcmdr'

Package suggested but not available for checking: ‘rgl’

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

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: ‘A. C. Del Re <acdelre@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("A.", "C.", "Del"),
                    family = "Re",
                    role = c("aut", "cre"),
                    email = "acdelre@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: ‘Rcmdr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Andrew Heiss <andrew@andrewheiss.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Andrew",
                      family = "Heiss",
                      role = c("aut", "cre"),
                      email = "andrew@andrewheiss.com"),
               person(given = "Richard",
                      family = "Payne",
                      role = "aut"),
               person(given = "Christa",
                      family = "Schank",
                      role = "aut"),
               person(given = "Jessica",
                      family = "Reese",
                      role = "aut"))
as necessary.
Package required but not available: ‘Rcmdr’

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

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: 'orloca', 'orloca.es', 'Rcmdr'

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: ‘Achmad Fauzi Bagus F <fauzi.pandya@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Monalisa", "Sipahutar,Setia"),
                      family = "Pramana",
                      role = "aut",
                      email = "11.6790@stis.ac.id"),
               person(given = "Achmad",
                      family = "Fauzi",
                      role = c("aut", "cre"),
                      email = "fauzi.pandya@gmail.com"))
as necessary.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Arto Luoma <arto.luoma@wippies.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Arto",
                    family = "Luoma",
                    role = c("aut", "cre"),
                    email = "arto.luoma@wippies.com")
as necessary.
Packages required but not available: 'Rcmdr', 'demography', 'ftsa'

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Marcelo Goulart Correia <mgoulart.inc@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Marcelo", "Goulart"),
                    family = "Correia",
                    role = c("aut", "cre"),
                    email = "mgoulart.inc@gmail.com")
as necessary.
Package required but not available: ‘Rcmdr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Liviu Andronic <landronimirc@gmail.com>’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘John Fox <jfox@mcmaster.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "John",
                    family = "Fox",
                    role = c("aut", "cre"),
                    email = "jfox@mcmaster.ca")
as necessary.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘John Fox <jfox@mcmaster.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "John",
                    family = "Fox",
                    role = c("aut", "cre"),
                    email = "jfox@mcmaster.ca")
as necessary.
Package required but not available: ‘Rcmdr’

Package suggested but not available for checking: ‘rgl’

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

Package suggested but not available for checking: ‘RcmdrMisc’

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

Package suggested but not available for checking: ‘ROpenOffice’

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

Package suggested but not available for checking: ‘knitr’

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

Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
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.
Package required but not available: ‘Rcmdr’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) nonlinearAR1.sim.Rd:8: Lost braces; missing escapes or markup?
     8 | of the form z_n = g(z_{n-1}) + epsilon. A normal distribution is assumed for the innovations.
       |                       ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘modeest’

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

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: ‘qgraph’

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Erich Neuwirth <erich.neuwirth@univie.ac.at>’

The Description field contains
  Cynthia Brewer as described at http://colorbrewer2.org.
Please enclose URLs in angle brackets (<...>).
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rcrossref', 'rmarkdown'

VignetteBuilder package required 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:
  'cffr', 'devtools', 'rmarkdown', 'usethis'

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: ‘yaml’

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

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

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

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

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

VignetteBuilder package required 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', 'weights'

Package suggested but not available for checking: ‘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 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: ‘Joseph Wood <jwood000@gmail.com>’

Found the following (possibly) invalid URLs:
  URL: https://github.com/jwood000/RcppAlgos/issues/9#issue-467908452Issue%20#9
    From: NEWS.md
    Message: Invalid URL: '#' not allowed in fragment
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dirk",
                      family = "Eddelbuettel",
                      role = c("aut", "cre"),
                      email = "edd@debian.org"),
               person(given = "Romain",
                      family = "Francois",
                      role = "aut"),
               person(given = c("based", "on", "code", "written", "during"),
                      family = "2005",
                      role = "aut"),
               person(given = c("2006", "by", "Dominick"),
                      family = "Samperi",
                      role = "aut"))
as necessary.
Maintainer: ‘Dirk Eddelbuettel <edd@debian.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dirk",
                      family = "Eddelbuettel",
                      role = c("aut", "cre"),
                      email = "edd@debian.org"),
               person(given = "Romain",
                      family = "Francois",
                      role = "aut"),
               person(given = c("with", "contributions", "by", "David"),
                      family = "Reiss",
                      role = "aut"),
               person(given = c("and", "based", "on", "code", "written", "during"),
                      family = "2005",
                      role = "aut"),
               person(given = c("2006", "by", "Dominick"),
                      family = "Samperi",
                      role = "aut"))
as necessary.
Maintainer: ‘Zach DeBruine <zacharydebruine@gmail.com>’

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

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

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

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

VignetteBuilder package required for 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.
Specified C++11: support will be removed soon
Maintainer: ‘Dirk Eddelbuettel <edd@debian.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dirk",
                      family = "Eddelbuettel",
                      role = c("aut", "cre"),
                      email = "edd@debian.org"),
               person(given = "Romain",
                      family = "Francois",
                      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: ‘Shusei Eshima <shuseieshima@gmail.com>’

The Description field contains
  (2023) <arXiv:2305.19045>. Jagger uses patterns derived from
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
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’
Specified C++11: support will be removed soon
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Karl",
                    family = "Forner",
                    role = c("aut", "cre"),
                    email = "karl.forner@gmail.com")
as necessary.
Maintainer: ‘Kevin Ushey <kevinushey@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kevin",
                    family = "Ushey",
                    role = c("aut", "cre"),
                    email = "kevinushey@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:
    ‘print.rcpptimer.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jonathan Olmsted <jpolmsted@gmail.com>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘rtn.Rd’:
    http://dx.doi.org/10.1007/BF00143942
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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jamie Spaulding <jspaulding02@hamline.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jamie",
                      family = "Spaulding",
                      role = c("aut", "cre"),
                      email = "jspaulding02@hamline.edu"),
               person(given = "Keith",
                      family = "Morris",
                      role = "aut"))
as necessary.
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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for 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: person(given = "Johannes",
                    family = "Burkhardt",
                    role = c("aut", "cre"),
                    email = "johannes.burkhardt@gmail.com")
as necessary.
Maintainer: ‘J.S. Pierre <jean-sebastien.pierre@univ-rennes1.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jean-Sebastien",
                      family = "PIERRE",
                      role = c("aut", "cre")),
               person(given = "J.S.",
                      family = "Pierre",
                      role = "cre",
                      email = "jean-sebastien.pierre@univ-rennes1.fr"))
as necessary.
Package required but not available: ‘DT’

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

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

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/Rcssplot.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: ‘Colin Millar <colin.millar@ices.dk>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘rct3-package.Rd’:
    https://doi.org/10.1006/jmsc.1997.0222
  File ‘rct3.Rd’:
    https://doi.org/10.1006/jmsc.1997.0222
Maintainer: ‘Isidoro Garcia-Urquieta <isidoro.gu@gmail.com>’

The Description field contains
  <arXiv:1607.00698>.
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: ‘PSweight’

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: ‘Wojciech Rosa <w.rosa@pollub.pl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Wojciech",
                    family = "Rosa",
                    role = c("aut", "cre"),
                    email = "w.rosa@pollub.pl")
as necessary.
Package required but not available: ‘rJava’

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

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', 'roxygen2', 'rmarkdown', 'covr'

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

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

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.
Running ‘test-all.R’ [1s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("rdatacite")
  Loading required package: rdatacite
  Error in `source_dir()`:
  ! Failed to evaluate './helper-rdatacite.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("rdatacite")
    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-rdatacite.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
Packages required but not available: 'configr', 'usethis', 'yaml'

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’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("devtools")
  Error in library("devtools") : there is no package called 'devtools'
  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:
  'keyring', 'knitr', 'rmarkdown'

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

VignetteBuilder package required 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:
  'devtools', 'roxygen2', '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?
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: ‘Chi Seng Pun <cspun@ntu.edu.sg>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Chi", "Seng"),
                      family = "Pun",
                      role = c("aut", "cre"),
                      email = "cspun@ntu.edu.sg"),
               person(given = c("Matthew", "Zakharia"),
                      family = "Hadimaja",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'lintr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [3s/3s]
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?
Package required but not available: ‘redland’

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

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

VignetteBuilder package required for 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.

The Description field contains
  A client library for 'The Guardian' (https://www.guardian.com/) and
Please enclose URLs in angle brackets (<...>).

The BugReports field in DESCRIPTION has
  https://github.com/ironholds/rdian
which should likely be
  https://github.com/ironholds/rdian/issues
instead.
Maintainer: ‘Gennaro Tedesco: <gennarotedesco@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Gennaro",
                    family = "Tedesco",
                    role = c("aut", "cre"),
                    email = "gennarotedesco@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: ‘maotai’

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: ‘Christopher Bolen <cbolen1@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) farthest_point_sampling.Rd:28: Lost braces; missing escapes or markup?
    28 | space P = {p_1, ..., p_k}, such that each p_i is the farthest 
       |           ^
Maintainer: ‘Richard Reeve <richard.reeve@glasgow.ac.uk>’

The Description field contains
  <arXiv:1404.6520v3>.
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', 'rmarkdown'

VignetteBuilder package required 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’

Packages suggested but not available for checking: 'qpcR', 'knitr', 'kfigr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Christopher Strothmann <rdmpackage@gmail.com>’

The Description field contains
  presented in Strothmann et al. (2022) <arXiv:2201.03329> and Strothmann
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) computeCBMeasure.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:56: Lost braces in \itemize; meant \describe ?
Maintainer: ‘Christian Graul <christian.graul@gmail.com>’

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

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: ‘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
Package suggested but not available for checking: ‘quarto’

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Gaurav Sood <gsood07@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: ‘devtools’

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

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: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Hyungsuk Tak <hyungsuk.tak@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhirui",
                      family = "Hu",
                      role = "aut"),
               person(given = "Hyungsuk",
                      family = "Tak",
                      role = c("aut", "cre"),
                      email = "hyungsuk.tak@gmail.com"))
as necessary.

The Description field contains
  Also see Hu and Tak (2020) <arXiv:2005.08049>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Running ‘test-all.R’ [1s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("rdryad")
  Loading required package: rdryad
  Error in `source_dir()`:
  ! Failed to evaluate './helper-rdryad.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("rdryad")
    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-rdryad.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
Packages required but not available: 'Hmisc', 'ergm'

Package suggested but not available for checking: ‘sspse’

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:
    ‘helpers-process-tracing.R’ ‘process_tracing_estimator.Rd’
Maintainer: ‘Aaron J. Baraff <ajbaraff@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Aaron", "J."),
                    family = "Baraff",
                    role = c("aut", "cre"),
                    email = "ajbaraff@uw.edu")
as necessary.
Maintainer: ‘Hyungsuk Tak <hyungsuk.tak@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hyungsuk",
                      family = "Tak",
                      role = c("aut", "cre"),
                      email = "hyungsuk.tak@gmail.com"),
               person(given = "Kisung",
                      family = "You",
                      role = "aut"),
               person(given = c("Sujit", "K."),
                      family = "Ghosh",
                      role = "aut"),
               person(given = "Bingyue",
                      family = "Su",
                      role = "aut"))
as necessary.
Packages required but not available: 'knitr', 'rmarkdown'

Package suggested but not available for checking: ‘roxygen2’

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

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

VignetteBuilder package required for 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 Hoff <peter.hoff@duke.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chris",
                      family = "Suh",
                      role = "aut"),
               person(given = "Peter",
                      family = "Hoff",
                      role = c("aut", "cre"),
                      email = "peter.hoff@duke.edu"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

VignetteBuilder package required 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:
  'covr', 'lintr', 'shinytest2', 'spelling'

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

Package suggested but not available for checking: ‘dataui’

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

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

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:
  'shinytest2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # 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(reactRouter)
  > 
  > test_check("reactRouter")
  Error in `source_dir()`:
  ! Failed to evaluate './setup-shinytest2.R'.
  Caused by error in `loadNamespace()`:
  ! there is no package called 'shinytest2'
  Backtrace:
       ▆
    1. ├─testthat::test_check("reactRouter")
    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::loadNamespace(x) at ./setup-shinytest2.R:2:1
   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>`(`<S3: packageNotFoundError>`)
   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:
  'htmlwidgets', 'rmarkdown', 'knitr', '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?
Package required but not available: ‘polite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Subhadip Datta <subhadipdatta007@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Subhadip",
                    family = "Datta",
                    role = c("aut", "cre"),
                    email = "subhadipdatta007@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'DiagrammeR', '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: ‘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.
checkRd: (-1) reader-package.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:55: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Kasper Kristensen <kaskr@dtu.dk>’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Clemens Druee <druee@uni-trier.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Clemens",
                      family = "Druee",
                      role = c("aut", "cre"),
                      email = "druee@uni-trier.de"),
               person(given = "Universitaet",
                      family = "Trier",
                      role = "aut"))
as necessary.
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.
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?
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(readobj)
  > 
  > test_check("readobj")
  Failed with error:  'there is no package called 'rgl''
  Saving _problems/test-loadobj-61.R
  Failed with error:  'there is no package called 'rgl''
  Saving _problems/test-loadobj-74.R
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 11 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test-loadobj.R:30:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-loadobj.R:60:3'): can load more complex obj files ──────────────
  Error in `tinyobj2shapelist3d(rval)`: Please install.packages("rgl") to use this function!
  Backtrace:
      ▆
   1. ├─testthat::expect_is(...) at test-loadobj.R:60:3
   2. │ └─testthat::quasi_label(enquo(object), label)
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─readobj::read.obj(...)
   5.   └─readobj::tinyobj2shapelist3d(rval)
  ── Error ('test-loadobj.R:73:3'): can load obj files of rgl shapes written from nat ──
  Error in `tinyobj2shapelist3d(rval)`: Please install.packages("rgl") to use this function!
  Backtrace:
      ▆
   1. ├─testthat::expect_is(...) at test-loadobj.R:73:3
   2. │ └─testthat::quasi_label(enquo(object), label)
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─readobj::read.obj(...)
   5.   └─readobj::tinyobj2shapelist3d(rval)
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 11 ]
  Error:
  ! Test failures.
  Execution halted
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'covr', 'knitr', 'rmarkdown'

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mark",
                    family = "Ewing",
                    role = c("aut", "cre"),
                    email = "b.mark@ewingsonline.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?
checkRd: (-1) ReAD.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{pi}{An estimate of the stationary probabilities of four states {(0,0), (0,1), (1,0), (1,1)}.}
       |                                                                      ^
checkRd: (-1) em_hmm.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{pi}{An estimate of the stationary probabilities of four states {(0,0), (0,1), (1,0), (1,1)}.}
       |                                                                      ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

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

VignetteBuilder package required 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: ‘kableExtra’

Packages suggested but not available for checking:
  'devtools', 'Hmisc', 'knitr', 'rmarkdown', 'usethis', 'zen4R'

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', 'ropls'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ivan Fernandez-Val <ivanf@bu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Wesley",
                      family = "Graybill",
                      role = "aut"),
               person(given = "Mingli",
                      family = "Chen",
                      role = "aut"),
               person(given = "Victor",
                      family = "Chernozhukov",
                      role = "aut"),
               person(given = "Ivan",
                      family = "Fernandez-Val",
                      role = c("aut", "cre"),
                      email = "ivanf@bu.edu"),
               person(given = "Alfred",
                      family = "Galichon",
                      role = "aut"))
as necessary.
Maintainer: ‘Thomas Wieland <thomas.wieland.geo@googlemail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thomas",
                    family = "Wieland",
                    role = c("aut", "cre"),
                    email = "thomas.wieland.geo@googlemail.com")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) Automotive.Rd:29: Lost braces
    29 | Wikipedia (2018): \dQuote{Automobilindustrie --- Wikipedia{,} Die freie Enzyklopaedie}. \url{https://de.wikipedia.org/wiki/Automobilindustrie} (accessed October 14, 2018). Own postprocessing.
       |                                                           ^
checkRd: (-1) Automotive.Rd:33: Lost braces
    33 | Wikipedia (2018): \dQuote{Automobilindustrie --- Wikipedia{,} Die freie Enzyklopaedie}. \url{https://de.wikipedia.org/wiki/Automobilindustrie} (accessed October 14, 2018). 
       |                                                           ^
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/Bdecon.Rnw’
   ‘inst/doc/medde.Rnw’
   ‘inst/doc/rebayes.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:
  '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?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DateTime.Rd: ClassGroups
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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: ‘Louis Raimbault <Louis.Raimbault@icloud.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Louis",
                      family = "Raimbault",
                      role = c("aut", "cre"),
                      email = "louis.raimbault@icloud.com"),
               person(family = "A.Mokkadem",
                      role = "aut"),
               person(family = "M.Pelletier",
                      role = "aut"))
as necessary.

The Description field contains
  Raimbault (2020) <arXiv:2011.14195>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

The BugReports field in DESCRIPTION has
  https://github.com/LouisRaimbault/RecAssoRules-R
which should likely be
  https://github.com/LouisRaimbault/RecAssoRules-R/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:
  'devtools', 'knitr', 'rgl', '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: ‘Mukul Chaware <mukul.chaware13@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mukul",
                    family = "Chaware",
                    role = c("aut", "cre"),
                    email = "mukul.chaware13@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?
Maintainer: ‘Leonardo Dapporto <leondap@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Leonardo",
                      family = "Dapporto",
                      role = c("aut", "cre"),
                      email = "leondap@gmail.com"),
               person(given = "Matteo",
                      family = "Ramazzotti",
                      role = "aut"),
               person(given = "Simone",
                      family = "Fattorini",
                      role = "aut"),
               person(given = "Roger",
                      family = "Vila",
                      role = "aut"),
               person(given = "Gerard",
                      family = "Talavera",
                      role = "aut"),
               person(given = c("Roger", "H.L."),
                      family = "Dennis",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tufte'

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

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

VignetteBuilder package required 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) recombinator.Rd:32-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) recombinator.Rd:35-38: Lost braces in \enumerate; meant \describe ?
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', '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: ‘Michael Hahsler <mhahsler@smu.edu>’

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Os",
                    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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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/BigData.rnw’
   ‘inst/doc/EVT.rnw’
   ‘inst/doc/Supervised.rnw’
   ‘inst/doc/WeightBased.rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Magdalena Chrapek <Magdalena.Chrapek@ujk.edu.pl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Magdalena",
                    family = "Chrapek",
                    role = c("aut", "cre"),
                    email = "magdalena.chrapek@ujk.edu.pl")
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?
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 = "David",
                      family = "Cortes",
                      role = "aut"),
               person(given = "Chih-Jen",
                      family = "Lin",
                      role = "aut"),
               person(given = "Yu-Chin",
                      family = "Juan",
                      role = "aut"),
               person(given = "Wei-Sheng",
                      family = "Chin",
                      role = "aut"),
               person(given = "Yong",
                      family = "Zhuang",
                      role = "aut"),
               person(given = "Bo-Wen",
                      family = "Yuan",
                      role = "aut"),
               person(given = "Meng-Yuan",
                      family = "Yang",
                      role = "aut"),
               person(given = c("other", "contributors.", "See", "file", "AUTHORS", "for"),
                      family = "details.",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) pseudo.geefit.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.geefit.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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', 'DT', 'colourpicker'

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

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

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

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

VignetteBuilder package required 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: ‘shelter’

Package suggested but not available for checking: ‘Hmisc’

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

Packages suggested but not available for checking:
  'Hmisc', 'knitr', 'rmarkdown', 'devtools', 'roxygen2', 'spelling',
  'rsconnect'

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check_queries
> ### Title: Check for Changes Between Two Query Reports
> ### Aliases: check_queries
> 
> ### ** Examples
> 
> # Minimal reproducible example
> old <- data.frame(
+   Identifier = c("100-1", "100-2", "200-1"),
+   Description = c("age check", "weight check", "lab miss"),
+   Query = c("is.na(age)", "is.na(weight)", "missing lab result"),
+   Code = c("100-1-1", "100-2-1", "200-1-1"),
+   stringsAsFactors = FALSE
+ )
> 
> new <- data.frame(
+   Identifier = c("100-1", "200-1", "300-1"),
+   Description = c("age check", "lab miss", "new query"),
+   Query = c("is.na(age)", "missing lab result (clarify)", "is.na(x)"),
+   stringsAsFactors = FALSE
+ )
> 
> res <- check_queries(old = old, new = new, report_title = "My Query Comparison")
Error in loadNamespace(x) : there is no package called ‘knitr’
Calls: check_queries ... 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: ‘keyring’

Packages suggested but not available for checking:
  'devtools', 'kableExtra', 'knitr', 'qwraps2', '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:
  'spelling', 'covr', 'kableExtra', 'knitr', 'rmarkdown', 'yaml'

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

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

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:
    ‘redSolve.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?
Maintainer: ‘Ivan Rivera <ivan.s.rivera@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ivan",
                    family = "Rivera",
                    role = c("aut", "cre"),
                    email = "ivan.s.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?
Maintainer: ‘Siddhartha Kundu <siddhartha_kundu@aiims.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Siddhartha",
                    family = "Kundu",
                    role = c("aut", "cre"),
                    email = "2021:ManuscriptUnderPreparation")
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: ‘Juan A. Ferrer-Bonsoms <jafhernandez@tecnun.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Juan", "A."),
                      family = "Ferrer-Bonsoms",
                      role = c("aut", "cre"),
                      email = "jafhernandez@tecnun.es"),
               person(given = "Laura",
                      family = "Jareno",
                      role = "aut"),
               person(given = "Angel",
                      family = "Rubio",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'BiocStyle', '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: '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?
Package required but not available: ‘roxygen2’

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:
  '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:
  'devtools', 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
File ‘rEDM/libs/rEDM.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Objects: ‘cppEDM/lib/libEDM.a’, ‘cppEDM/src/libEDM.a’

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

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

VignetteBuilder package required 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.
Maintainer: ‘Daniel Finnegan <dan.finnegan@gmail.com>’

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no 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'

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

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

VignetteBuilder package required for checking but 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 required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) make_refreshable.Rd:13: Lost braces
    13 | not that quotes need to be escaped (code{\"}).}
       |                                         ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

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

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

Package suggested but not available for checking: ‘registr’

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: 'kableExtra', 'Hmisc'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘William Belzak <wbelzak@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "William",
                    family = "Belzak",
                    role = c("aut", "cre"),
                    email = "wbelzak@gmail.com")
as necessary.
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?
Maintainer: ‘Daniel Crouch <djmcrouch@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Daniel", "J.M."),
                      family = "Crouch",
                      role = "aut"),
               person(given = c("Graham", "H.M.", "Goddard", "&", "Cathryn", "M."),
                      family = "Lewis",
                      role = "aut"),
               person(given = "Daniel",
                      family = "Crouch",
                      role = "cre",
                      email = "djmcrouch@gmail.com"))
as necessary.
Found the following files/directories:
  ‘EnvironmentalA.txt’ ‘EnvironmentalB.txt’ ‘Example.txt’
  ‘Example_Predictions.txt’ ‘Example_RRDist.txt’
  ‘Example_RRDistCol.TIF’ ‘Example_RRDistGrey.TIF’ ‘GeneticA.txt’
  ‘GeneticB.txt’ ‘Inds.txt’
Maintainer: ‘Billy Buchanan <Billy.Buchanan@fayette.kyschools.us>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Billy",
                    family = "Buchanan",
                    role = c("aut", "cre"),
                    email = "billy.buchanan@fayette.kyschools.us")
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 Antal <daniel.antal@ceemid.eu>’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) impute_down_nuts.Rd:21: Lost braces
    21 | NUTS typologies, defaults to code{"geo_var".}}
       |                                  ^
checkRd: (-1) validate_data_frame.Rd:19: Lost braces
    19 | NUTS typologies, defaults to code{"geo_var".}}
       |                                  ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘David Meyer <David.Meyer@R-project.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "David",
                    family = "Meyer",
                    role = c("aut", "cre"),
                    email = "david.meyer@r-project.org")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse', 'formattable', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(regmedint)
  > 
  > test_check("regmedint")
  Saving _problems/test-08_regmedint_class_user_methods-21.R
  [ FAIL 1 | WARN 0 | SKIP 18 | PASS 23 ]
  
  ══ Skipped tests (18) ══════════════════════════════════════════════════════════
  • {tidyverse} is not installed. (18): 'test-01_regmedint_class_ui.R:10:1',
    'test-03_fit_mreg.R:11:1', 'test-04_fit_yreg_linear.R:11:1',
    'test-04_fit_yreg_logistic.R:11:1', 'test-04_fit_yreg_loglinear.R:13:1',
    'test-04_fit_yreg_negbin.R:11:1', 'test-04_fit_yreg_poisson.R:11:1',
    'test-04_fit_yreg_survAFT_exp.R:11:1',
    'test-04_fit_yreg_survAFT_weibull.R:11:1', 'test-04_fit_yreg_survCox.R:11:1',
    'test-05_calc_myreg.R:11:1', 'test-06_calc_myreg_helpers_coef.R:11:1',
    'test-06_calc_myreg_helpers_vcov.R:11:1',
    'test-07_calc_myreg_mreg_linear_yreg_linear.R:11:1',
    'test-07_calc_myreg_mreg_linear_yreg_logistic.R:11:1',
    'test-07_calc_myreg_mreg_logistic_yreg_linear.R:11:1',
    'test-07_calc_myreg_mreg_logistic_yreg_logistic.R:11:1',
    'test-09_cross_check_with_sas_macro.R:10:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-08_regmedint_class_user_methods.R:16:5'): methods for regmedint ──
  Error in `mutate(., male = if_else(sex == "m", 1L, 0L), status = if_else(status == 0, 0L, 1L), bili_bin = if_else(bili > median(bili), 1L, 0L), alk_phos = alk.phos)`: could not find function "mutate"
  Backtrace:
      ▆
   1. └─pbc[complete.cases(pbc), ] %>% ... at test-08_regmedint_class_user_methods.R:16:5
  
  [ FAIL 1 | WARN 0 | SKIP 18 | PASS 23 ]
  Error:
  ! Test failures.
  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: ‘knitr’

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

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

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: ‘Alireza S. Mahani <alireza.s.mahani@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Alireza", "S."),
                      family = "Mahani",
                      role = c("aut", "cre"),
                      email = "alireza.s.mahani@gmail.com"),
               person(given = c("Mansour", "T.A."),
                      family = "Sharabiani",
                      role = "aut"))
as necessary.
checkRd: (-1) fbase1.binomial.Rd:32: Lost braces; missing escapes or markup?
    32 | In all base log-likelihood functions, we have dropped any additive terms that are independent of the distribution parameter, e.g. constant terms or those terms that are dependent on the response variable only. This is done for computational efficiency. Therefore, these functions cannot be used to obtain the absolute values of log-likelihood functions but only in the context of optimization and/or sampling. Users can write thin wrappers around these functions to add the constant terms to the function value. (Derivatives do not need correction. For binomial family, all factorial terms are ignored since they only depend on \code{n} and {y}.)
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
Packages required but not available:
  'DT', 'golem', 'loadeR', 'traineR', 'echarts4r'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Pawel Teisseyre <teisseyrep@ipipan.waw.pl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Pawel",
                      family = "Teisseyre",
                      role = c("aut", "cre"),
                      email = "teisseyrep@ipipan.waw.pl"),
               person(given = c("Robert", "A."),
                      family = "Klopotek",
                      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: ‘Yanming Di<diy@stat.oregonstate.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yanming",
                    family = "Di",
                    role = c("aut", "cre"),
                    email = "diy@stat.oregonstate.edu")
as necessary.
Packages required but not available: 'formattable', 'htmlwidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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  'knitr', 'rmarkdown', 'cdparcoord', 'keras'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Mathieu Gautier <mathieu.gautier@supagro.inra.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mathieu",
                      family = "Gautier",
                      role = c("aut", "cre"),
                      email = "mathieu.gautier@supagro.inra.fr"),
               person(given = "Alexander",
                      family = "Klassmann",
                      role = "aut"),
               person(given = "Renaud",
                      family = "Vitalis",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
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Cannot process vignettes
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  'bookdown', 'gap', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) plot.ehh.Rd:27: Lost braces
    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}} and \code{\link[graphics]{matplot}}). 
       |                                ^
checkRd: (-1) plot.ehhs.Rd:27: Lost braces
    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}}.
       |                                ^
File ‘rehh/libs/rehh.so’:
  Found non-API call to R: ‘SETLENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Calli Gross <calli@calligross.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Calli",
                    family = "Gross",
                    role = c("aut", "cre"),
                    email = "calli@calligross.de")
as necessary.
Maintainer: ‘Arnaud Buzzi <arnaud.buzzi@sia-partners.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Arnaud",
                    family = "Buzzi",
                    role = c("aut", "cre"),
                    email = "arnaud.buzzi@sia-partners.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
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Maintainer: ‘Fabien Laporte <fabien.laporte@inra.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Fabien",
                      family = "Laporte",
                      role = c("aut", "cre"),
                      email = "fabien.laporte@inra.fr"),
               person(given = "Tristan",
                      family = "Mary-Huard",
                      role = "aut"))
as necessary.
Package required but not available: ‘factoextra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Mark S. Handcock <handcock@stat.ucla.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Mark", "S."),
                    family = "Handcock",
                    role = c("aut", "cre"),
                    email = "handcock@stat.ucla.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
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Maintainer: ‘Miguel Rodríguez Asensio <miguel.rodriguezasensio@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Miguel", "Rodríguez"),
                    family = "Asensio",
                    role = c("aut", "cre"),
                    email = "miguel.rodriguezasensio@gmail.com")
as necessary.
Packages required but not available: 'xlsx', '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: ‘Werner A. Stahel <stahel@stat.math.ethz.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Werner", "A."),
                    family = "Stahel",
                    role = c("aut", "cre"),
                    email = "stahel@stat.math.ethz.ch")
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/relevance-descr.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Carter T. Butts <buttsc@uci.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Carter", "T."),
                    family = "Butts",
                    role = c("aut", "cre"),
                    email = "buttsc@uci.edu")
as necessary.
checkRd: (-1) rem.dyad.Rd:121: Lost braces; missing escapes or markup?
   121 | \item Single or multiple covariates, time varying: For \code{CovSnd}, \code{CovRec}, or \code{CovInt}, an \code{m} by \code{p} by {n} array whose respective dimensions index time (i.e., event number), covariate, and actor.  For \code{CovEvent}, a \code{m} by \code{p} by \code{n} by \code{n} array, whose dimensions are analogous to the previous case.
       |                                                                                                                                   ^
Maintainer: ‘Kenneth Tay <kjytay@stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Kenneth",
                      family = "Tay",
                      role = c("aut", "cre"),
                      email = "kjytay@stanford.edu"),
               person(given = "Robert",
                      family = "Tibshirani",
                      role = "aut"))
as necessary.

The Description field contains
  (2019) <arXiv:1912.01808> for details.
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
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Maintainer: ‘Alexander I. Jordan <alexander.jordan@h-its.org>’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Michael Hernandez <michael@hernandez.ai>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Michael",
                      family = "Hernandez",
                      role = c("aut", "cre"),
                      email = "micahel@hernandez.ai"),
               person(given = "Yuri",
                      family = "Balasanov",
                      role = "aut"))
as necessary.
Maintainer: ‘David Firth <d.firth@warwick.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("David", "Firth", "with", "contributions", "from", "Heather"),
                      family = "Turner",
                      role = "aut"),
               person(given = "John",
                      family = "Fox",
                      role = "aut"),
               person(given = "David",
                      family = "Firth",
                      role = "cre",
                      email = "d.firth@warwick.ac.uk"))
as necessary.
Running examples in ‘relliptical-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rtelliptical
> ### Title: Sampling Random Numbers from Truncated Multivariate Elliptical
> ###   Distributions
> ### Aliases: rtelliptical
> 
> ### ** Examples
> 
> library(ggplot2)
> library(ggExtra)
Error in library(ggExtra) : there is no package called ‘ggExtra’
Execution halted
Packages required but not available:
  'Familias', 'flextable', 'pedFamilias', 'pedtools'

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: ‘James M. Curran <j.curran@auckland.ac.nz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("James", "M."),
                    family = "Curran",
                    role = c("aut", "cre"),
                    email = "j.curran@auckland.ac.nz")
as necessary.
Package required but not available: ‘pammtools’

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

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

VignetteBuilder 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: ‘Gabor Csardi <csardi.gabor@gmail.com>’

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

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

VignetteBuilder 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: ‘Tony Wang <xwang@imedacs.com>’

The Description field contains
  <arXiv:2203.02771>. Methods for missing-not-at-random include
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
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  'knitr', 'rmarkdown', 'bookdown', 'spelling'

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Laurence Brandenberger <lbrandenberger@ethz.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Laurence",
                    family = "Brandenberger",
                    role = c("aut", "cre"),
                    email = "lbrandenberger@ethz.ch")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
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Package CITATION file contains call(s) to old-style citEntry().  Please
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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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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: ‘plotly’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Miguel F. Acevedo <acevedo@unt.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Miguel", "F."),
                    family = "Acevedo",
                    role = c("aut", "cre"),
                    email = "acevedo@unt.edu")
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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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: ‘Minji Lee <minjilee101@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Minji",
                      family = "Lee",
                      role = c("aut", "cre"),
                      email = "minjilee101@gmail.com"),
               person(given = "Zhihua",
                      family = "Su",
                      role = "aut"))
as necessary.
Maintainer: ‘Jordan Hayes <jhayes@ucr.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jordan",
                    family = "Hayes",
                    role = c("aut", "cre"),
                    email = "jhayes@ucr.edu")
as necessary.
Cannot process vignettes
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  'covr', 'devtools', 'knitr', 'pak', 'rmarkdown', 'yaml'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Juan Carlos Aledo <caledo@uma.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Juan", "Carlos"),
                    family = "Aledo",
                    role = c("aut", "cre"),
                    email = "caledo@uma.es")
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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Packages required but not available: 'config', 'rmarkdown', 'yaml'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Gourav Kumar Vani <kumaragri.vani1@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Gourav", "Kumar"),
                      family = "Vani",
                      role = c("aut", "cre"),
                      email = "kumaragri.vani1@gmail.com"),
               person(given = c("Dr.", "Vivek"),
                      family = "Badhe",
                      role = "aut",
                      email = "vivekbadhe.jbp@gmail.com"))
as necessary.
Packages required but not available: 'rgl', 'Seurat'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
No examples, no tests, no vignettes
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) twosidedPValuestobins.Rd:84: Lost braces; missing escapes or markup?
    84 | A matrix with \code{n.bins + 1} rows and {ncol(zmat)} columns, representing for each study the discretization chosed. Values are the between bin breaks. First and last values are the edges of the outmost bins.
       |                                          ^
checkRd: (-1) ztobins.Rd:90: Lost braces; missing escapes or markup?
    90 | A matrix with \code{n.bins + 1} rows and {ncol(zmat)} columns, representing for each study the discretization chosed. Values are the between bin breaks. First and last values are the edges of the outmost bins.
       |                                          ^
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?
Packages required but not available: 'dat', 'knitr'

Package suggested but not available for checking: ‘covr’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) method.A.Rd:200-205: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.A.Rd:206-211: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.A.Rd:231-236: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.A.Rd:237-242: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:201-206: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:207-212: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:232-237: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:238-243: Lost braces in \itemize; \value handles \item{}{} directly
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
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.
Packages suggested but not available for checking: 'knitr', 'roxygen2'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Dzmitry G Batrakou <d.batrakou@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Dzmitry", "G"),
                    family = "Batrakou",
                    role = c("aut", "cre"),
                    email = "d.batrakou@gmail.com")
as necessary.
Package required but not available: ‘colourpicker’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘David Hervas Marin <ddhervas@yahoo.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("David", "Hervas"),
                    family = "Marin",
                    role = c("aut", "cre"),
                    email = "ddhervas@yahoo.es")
as necessary.
Package required but not available: ‘flextable’

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

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Nick Parsons <nick.parsons@warwick.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Nick",
                    family = "Parsons",
                    role = c("aut", "cre"),
                    email = "nick.parsons@warwick.ac.uk")
as necessary.
Maintainer: ‘Francesco Napolitano <franapoli@gmail.com>’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) repo_build.Rd:44-47: Lost braces
    44 | ## chunk "item 1" {
       |                   ^
checkRd: (-1) repo_dependencies.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repo_dependencies.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repo_dependencies.Rd:51-53: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory 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', 'tufte', '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', 'survminer', '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', 'factoextra', 'clusterProfiler', 'enrichplot'

VignetteBuilder package required 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', 'knitr'

Package suggested but not available for checking: ‘covr’

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

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

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

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

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.
Maintainer: ‘Daniel Fischer <daniel.fischer@luke.fi>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Daniel",
                      family = "Fischer",
                      role = c("aut", "cre"),
                      email = "daniel.fischer@luke.fi"),
               person(given = "Alain",
                      family = "Berro",
                      role = "aut"),
               person(given = "Klaus",
                      family = "Nordhausen",
                      role = "aut"),
               person(given = "Anne",
                      family = "Ruiz-Gazen",
                      role = "aut"))
as necessary.
Package required but not available: ‘rJava’

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

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: 'knitr', 'rmarkdown'

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

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

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

Package suggested but not available for checking: ‘spelling’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate_impact.R’ ‘plot_repsd.R’ ‘repsd_pval.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’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yupeng He <yupeng.he.bioinfo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yupeng",
                    family = "He",
                    role = c("aut", "cre"),
                    email = "yupeng.he.bioinfo@gmail.com")
as necessary.
Running examples in ‘reqres-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Request
> ### Title: HTTP Request Handling
> ### Aliases: Request as.Request is.Request
> 
> ### ** Examples
> 
> fake_rook <- fiery::fake_request(
+   'http://example.com/test?id=34632&question=who+is+hadley',
+   content = 'This is an elaborate ruse',
+   headers = list(
+     Accept = 'application/json; text/*',
+     Content_Type = 'text/plain'
+   )
+ )
Error in loadNamespace(x) : there is no package called ‘fiery’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Maintainer: ‘Scott Chamberlain <myrmecocystus@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:
  'covr', 'pak', 'rmarkdown', 'knitr', 'roxygen2'

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:
    ‘Require2.R’ ‘helpers.R’ ‘pak.R’ ‘pkgDep3.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) NCBirths2004.Rd:16: Lost braces
    16 |     \item{\code{Smoker}}{Mother a smoker? code{No}, \code{Yes}}
       |                                               ^
Maintainer: ‘Tim Hesterberg <timhesterberg@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tim",
                    family = "Hesterberg",
                    role = c("aut", "cre"),
                    email = "timhesterberg@gmail.com")
as necessary.
checkRd: (-1) ExpandProbs.Rd:35: Lost braces; missing escapes or markup?
    35 |      {z_probs2 sqrt((n-1)/n) = t_probs,n-1}
       |      ^
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/resde-vignette.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', 'bookdown', 'knitr'

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

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘keras3’

Packages suggested but not available for checking:
  'covr', 'flextable', 'formattable', 'knitr', 'rmarkdown',
  'tensorflow', 'rticles', 'bookdown'

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Konstantin Hopf <konstantin.hopf@uni-bamberg.de>’

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', 'DT'

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

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: ‘Robin K. S. Hankin <hankin.robin@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) resistance.Rd:52: Lost braces
    52 |     \item B. Bollob\'{a}s, 1998.  \emph{Modern Graph Theory}.  Springer.
       |                      ^
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VignetteBuilder package required for checking but not installed: ‘knitr’
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DESCRIPTION file?
Maintainer: ‘Maeve Upton <uptonmaeve010@gmail.com>’

The Description field contains
  et al 2023) <arXiv:2301.09556>, spatio-temporal splines (Upton et al
  2023) <arXiv:2301.09556> and generalised additive models (Upton et al
  2023) <arXiv:2301.09556>.  This package facilitates data loading, model
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.
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DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yannick Marcon <yannick.marcon@obiba.org>’

The BugReports field in DESCRIPTION has
  https://github.com/obiba/resourcer
which should likely be
  https://github.com/obiba/resourcer/issues
instead.
Cannot process vignettes
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  'knitr', 'sparklyr', 'rmarkdown'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flag_resp
> ### Title: Flag respondents based on response quality indicators
> ### Aliases: flag_resp
> 
> ### ** Examples
> 
> res_dist_indicators <- resp_distributions(nep) # Create indicator data frame
> 
> flagged_respondents <- flag_resp(res_dist_indicators,
+                                  ii_mean > 3, # Flagging strategy 1
+                                  ii_sd < 2, # Flagging strategy 2
+                                  ii_mean > 3 & ii_sd > 2) # Flagging strategy 3
> flagged_respondents # A data frame with three columns, each corresponding to one flagging strategy
# A data frame: 1,222 × 4
      id `ii_mean > 3` `ii_sd < 2` `ii_mean > 3 & ii_sd > 2`
   <int> <lgl>         <lgl>       <lgl>                    
 1     1 TRUE          TRUE        FALSE                    
 2     2 TRUE          TRUE        FALSE                    
 3     3 FALSE         TRUE        FALSE                    
 4     4 TRUE          TRUE        FALSE                    
 5     5 TRUE          TRUE        FALSE                    
 6     6 NA            NA          NA                       
 7     7 TRUE          TRUE        FALSE                    
 8     8 TRUE          TRUE        FALSE                    
 9     9 TRUE          TRUE        FALSE                    
10    10 TRUE          TRUE        FALSE                    
# ℹ 1,212 more rows
> summary(flagged_respondents) # quickly compare flagging strategies

── Number of respondents flagged (Total N: 1222) 
            ii_mean > 3               ii_sd < 2 ii_mean > 3 & ii_sd > 2 
                    832                     934                       2 

── Agreement between flagging strategies 
Error in loadNamespace(x) : there is no package called ‘knitr’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ben Waxer <bwaxer@auriq.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ben",
                    family = "Waxer",
                    role = c("aut", "cre"),
                    email = "bwaxer@auriq.com")
as necessary.

The Description field contains
  http://www.auriq.com/documentation/source/install/index.html.
Please enclose URLs in angle brackets (<...>).
Cannot process vignettes
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  'knitr', 'rmarkdown', 'usethis'

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

Package suggested but not available for checking: ‘rsolr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Thomas P. Fuller <thomas.fuller@coherentlogic.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Thomas", "P."),
                    family = "Fuller",
                    role = c("aut", "cre"),
                    email = "thomas.fuller@coherentlogic.com")
as necessary.
Package required but not available: ‘rJava’

Packages suggested but not available for checking:
  'knitr', 'roxygen2', '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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VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Dmitry Selivanov <selivanov.dmitriy@gmail.com>’

Found the following (possibly) invalid URLs:
  URL: https://app.gitter.im/#/room/#RestRserve_community:gitter.im
    From: README.md
    Message: Invalid URL: '#' not allowed in fragment
Cannot process vignettes
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  'lintr', 'knitr', 'rmarkdown'

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

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

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:
    ‘as_result.Rd’ ‘bind.R’ ‘bind.Rd’ ‘result.R’ ‘result.Rd’
Package required but not available: ‘rmarkdown’

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

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: ‘Miron B. Kursa <M.Kursa@icm.edu.pl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Miron", "B."),
                    family = "Kursa",
                    role = c("aut", "cre"),
                    email = "m.kursa@icm.edu.pl")
as necessary.
Cannot process vignettes
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  'pak', 'knitr', 'rmarkdown'

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

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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: ‘rgl’

Package suggested but not available for checking: ‘spelling’

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

VignetteBuilder 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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Cannot process vignettes
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  'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) harmonize_values.Rd:44: Lost braces; missing escapes or markup?
    44 | \item{perl}{Use perl-like regex? Defaults to {FALSE}.}
       |                                              ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘DT’

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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: ‘Michael C Koohafkan <michael.koohafkan@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Michael", "C"),
                    family = "Koohafkan",
                    role = c("aut", "cre"),
                    email = "michael.koohafkan@gmail.com")
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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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: ‘Julien Boelaert <jubo.stats@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Julien",
                    family = "Boelaert",
                    role = c("aut", "cre"),
                    email = "jubo.stats@gmail.com")
as necessary.
checkRd: (-1) cpUpper.Rd:39: Lost braces
    39 | \code{"fastfloyd"}{ (default) uses an iterative variant of the Floyd-Warshall algorithm, in which the check of consistency of the current observation with a given cluster is done in a single step of the Floyd-Warshall algorithm. Much faster than \code{"floyd"}.}
       |                   ^
checkRd: (-1) cpUpper.Rd:41: Lost braces
    41 | \code{"floyd"}{ uses the algorithm described in Crawford and Pendakur (2013): at each step the complete Floyd-Warshall algorithm is run to check whether each cluster can accomodate the current observation.}
       |               ^
Package required but not available: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
Package required but not available: ‘boot.pval’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BSgenome', 'BSgenome.Hsapiens.UCSC.hg38'

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

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Packages required but not available: 'config', 'DT', 'golem', 'redcapAPI'

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  'gt', 'knitr', 'rmarkdown', 'spelling', 'usethis'

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

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Packages required but not available:
  'bookdown', 'knitr', 'papaja', 'rmarkdown', 'worcs'

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Packages required but not available: 'knitr', 'usethis'

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

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Package required but not available: ‘plotly’

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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.
'::' or ':::' import not declared from: ‘Matrix’
'library' or 'require' call not declared from: ‘Matrix’
Cannot process vignettes
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  'covr', 'Hmisc', 'knitr', 'rmarkdown', 'roxygen2'

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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  'devtools', 'knitr', 'lintr', '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: ‘Pablo Barbera <pbarbera@usc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Pablo",
                      family = "Barbera",
                      role = c("aut", "cre"),
                      email = "pbarbera@usc.edu"),
               person(given = "Michael",
                      family = "Piccirilli",
                      role = "aut",
                      email = "mrp2181@columbia.edu"),
               person(given = "Andrew",
                      family = "Geisler",
                      role = "aut"),
               person(given = "Wouter",
                      family = "van Atteveldt",
                      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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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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Cannot process vignettes
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  'knitr', 'rmarkdown', 'leaflet', 'leaflet.extras', 'tidyverse', '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
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Maintainer: ‘Ankur Chakravarthy <ankur.chakravarthy.10@ucl.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ankur",
                      family = "Chakravarthy",
                      role = c("aut", "cre"),
                      email = "ankur.chakravarthy.10@ucl.ac.uk"),
               person(family = "PhD",
                      role = "aut"))
as necessary.
Maintainer: ‘Shangzhi Hong <shangzhi-hong@hotmail.com>’

The Description field contains
  <arXiv:2004.14823>.
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
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Maintainer: ‘Miron Bartosz Kursa <M.Kursa@icm.edu.pl>’

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’

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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:
    ‘common_names.R’ ‘distribution.R’ ‘fb_tbl.R’
Maintainer: ‘Karthik Ram <karthik.ram@gmail.com>’

The Description field contains
  of the 'rOpenSci' suite (http://ropensci.org).
Please enclose URLs in angle brackets (<...>).
Problems with news in ‘NEWS.md’:
No news entries found.
Maintainer: ‘John Kloke <johndkloke@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "John",
                      family = "Kloke",
                      role = c("aut", "cre"),
                      email = "johndkloke@gmail.com"),
               person(given = "Joseph",
                      family = "McKean",
                      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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Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
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: ‘Dimitri Justeau-Allaire <dimitri.justeau@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Dimitri",
                      family = "Justeau-Allaire",
                      role = c("aut", "cre"),
                      email = "dimitri.justeau@gmail.com"),
               person(given = "Grégoire",
                      family = "Blanchard",
                      role = "aut"),
               person(given = "Thomas",
                      family = "Ibanez",
                      role = "aut"),
               person(given = "Xavier",
                      family = "Lorca",
                      role = "aut"),
               person(given = "Ghislain",
                      family = "Vieilledent",
                      role = "aut"),
               person(given = "Philippe",
                      family = "Birnbaum",
                      role = "aut"))
as necessary.
Package required but not available: ‘rJava’

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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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  'covr', 'DT', 'kableExtra', 'knitr', 'plotly', 'rmarkdown',
  'rmdformats'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Dirk Eddelbuettel <edd@debian.org>’

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Please add one, modifying
  Authors@R: person(given = "Dirk",
                    family = "Eddelbuettel",
                    role = c("aut", "cre"),
                    email = "edd@debian.org")
as necessary.
'library' or 'require' calls not declared from:
  ‘rpanel’ ‘tkrplot’
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: ‘usethis’

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

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

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

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Packages required but not available: 'plotly', 'ftsa'

Package suggested but not available for checking: ‘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.
Perhaps the ‘VignetteBuilder’ information is missing from the
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Maintainer: ‘Markus Loecher <Markus.Loecher@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Markus",
                    family = "Loecher",
                    role = c("aut", "cre"),
                    email = "Markus.Loecher@gmail.com")
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?
Running ‘test-all.R’ [2s/2s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("rgbif")
  Loading required package: rgbif
  Error in `source_dir()`:
  ! Failed to evaluate './helper-rgbif.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("rgbif")
    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-rgbif.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: ‘Joseph Kelly <josephkelly@post.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Joseph",
                      family = "Kelly",
                      role = c("aut", "cre"),
                      email = "josephkelly@post.harvard.edu"),
               person(given = "Hyungsuk",
                      family = "Tak",
                      role = "aut"),
               person(given = "Carl",
                      family = "Morris",
                      role = "aut"))
as necessary.
Cannot process vignettes
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  'devtools', 'FactoMineR', '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
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Maintainer: ‘Cristian Quiroz-Moreno <cristianquirozd1997@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
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  '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?
Problems with news in ‘NEWS.md’:
No news entries found.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'googleCloudStorageR',
  'leaflet.extras2', 'spelling'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘John Ruscio <ruscio@tcnj.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "John",
                    family = "Ruscio",
                    role = c("aut", "cre"),
                    email = "ruscio@tcnj.edu")
as necessary.
checkRd: (-1) GenDataPopulation.Rd:21: Lost braces
    21 | {data}{Population of data}
       |       ^
checkRd: (-1) GenDataSample.Rd:23: Lost braces
    23 | {data}{Sample of data}
       |       ^
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'mapview'

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

VignetteBuilder package required for 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.
Malformed Description field: should contain one or more complete sentences.
Maintainer: ‘Alberto Almuiña <albertogonzalezalmuinha@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alberto",
                    family = "Almuiña",
                    role = c("aut", "cre"),
                    email = "albertogonzalezalmuinha@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: ‘Lorenzo Rimella <lorenzo.rimella@hotmail.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Lorenzo",
                    family = "Rimella",
                    role = c("aut", "cre"),
                    email = "lorenzo.rimella@hotmail.it")
as necessary.
Maintainer: ‘Aymeric Stamm <aymeric.stamm@math.cnrs.fr>’

The Description field contains
  Miolane et al. (2020) <arXiv:2004.04667>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘connection.R’ ‘level-set.R’ ‘lie-group.R’ ‘manifold.R’ ‘open-set.R’
    ‘spd-matrices.R’ ‘utils.R’
checkRd: (-1) RiemannianMetric.Rd:450-453: Lost braces
   450 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
checkRd: (-1) RiemannianMetric.Rd:484-487: Lost braces
   484 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
checkRd: (-1) RiemannianMetric.Rd:588-591: Lost braces
   588 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
Maintainer: ‘Jose Miguel Cotes Torres <jmcotes@unal.edu.co>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Jose", "Miguel", "Cotes", "Torres.", "Universidad", "Nacional", "de", "Colombia", "-", "Sede"),
                      family = "Medellin",
                      role = "aut"),
               person(given = c("Jose", "Miguel", "Cotes"),
                      family = "Torres",
                      role = "cre",
                      email = "jmcotes@unal.edu.co"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Author field differs from that derived from Authors@R
  Author:    ‘George Vega Yon [aut, cre] (<https://orcid.org/0000-0002-3171-0844>), Jorge Fábrega Lacoa [ctb], Joshua Kunst [ctb], Raphaël Velt [cph] (gexf-js library), Gephi Consortium [cph] (GEXF language), Cornelius Fritz [rev] (JOSS reviewer), Jonathan Cardoso Silva [rev] (JOSS reviewer)’
  Authors@R: ‘George Vega Yon [aut, cre] (ORCID: <https://orcid.org/0000-0002-3171-0844>), Jorge Fábrega Lacoa [ctb], Joshua Kunst [ctb], Raphaël Velt [cph] (gexf-js library), Gephi Consortium [cph] (GEXF language), Cornelius Fritz [rev] (what: JOSS reviewer), Jonathan Cardoso Silva [rev] (what: JOSS reviewer)’
Package has ‘vignettes’ subdirectory 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', 'rmarkdown', 'knitr', 'rtracklayer'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) Ghana_2021_school_attendance.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Ghana_2021_school_attendance_geometry.Rd:75: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("María", "José"),
                      family = "Haro-Delicado",
                      role = "aut"),
               person(given = "Virgilio",
                      family = "Gómez-Rubio",
                      role = c("aut", "cre"),
                      email = "virgilio.gomez@uclm.es"),
               person(given = "Francisco",
                      family = "Parreńo-Torres",
                      role = "aut"))
as necessary.
Package required but not available: ‘rgl’

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

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: ‘rgl’

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

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: ‘Danail Obreschkow <danail.obreschkow@gmail.com>’

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

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

Packages suggested but not available for checking:
  'rmarkdown', 'alphashape3d', 'downlit', 'pkgdown', 'manipulateWidget'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Francisco Richter <richtf@usi.ch>’

The Description field contains
  Environments." <arXiv:2304.01956>.
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: '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: ‘rlist’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jalpa Joshi Dave <jalpa@tatvic.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Jalpa", "Joshi"),
                    family = "Dave",
                    role = c("aut", "cre"),
                    email = "jalpa@tatvic.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: ‘Marcin Szymanski <ms32035@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Marcin",
                    family = "Szymanski",
                    role = c("aut", "cre"),
                    email = "ms32035@gmail.com")
as necessary.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
Author field differs from that derived from Authors@R
  Author:    ‘Michal Bojanowski [aut, cre] (<https://orcid.org/0000-0001-7503-852X>, Kozminski University), David Schoch [aut] (<https://orcid.org/0000-0003-2952-4812>)’
  Authors@R: ‘Michal Bojanowski [aut, cre] (ORCID: <https://orcid.org/0000-0001-7503-852X>, affil: Kozminski University), David Schoch [aut] (ORCID: <https://orcid.org/0000-0003-2952-4812>)’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
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: 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from 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) code_sawtooth_design.Rd:53: Lost braces
    53 | /url{http://www.sawtoothsoftware.com/help/lighthouse-studio/manual/index.html?hid_web_cbc_exporting.html}
       |     ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Thomas P. Fuller <thomas.fuller@coherentlogic.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Thomas", "P."),
                    family = "Fuller",
                    role = c("aut", "cre"),
                    email = "thomas.fuller@coherentlogic.com")
as necessary.
Package required but not available: ‘rJava’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Yichuan Bai <ycbai@iastate.edu>’

The Description field contains
  <arXiv:2307.12325>.
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', '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: ‘Adam Mantz <amantz@slac.stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Adam",
                    family = "Mantz",
                    role = c("aut", "cre"),
                    email = "amantz@slac.stanford.edu")
as necessary.
Packages required but not available: 'RJDBC', 'rJava'

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.
Maintainer: ‘Feng Chen <feng.chen@unsw.edu.au>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Gerry Tonkin-Hill <g.tonkinhill@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', 'ggtree'

VignetteBuilder package required 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:
  'box.linters', 'config', 'lintr', 'yaml'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Victhor Sartório <victhor@dme.ufrj.br>’

The Description field contains
  See Neal (2017) <arXiv:1701.02434> for further details on Hamiltonian
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Rezgar Arabzadeh <rezgararabzadeh@ut.ac.ir>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Rezgar", "Arabzadeh;", "Shahab"),
                      family = "Araghinejad",
                      role = "aut"),
               person(given = "Rezgar",
                      family = "Arabzadeh",
                      role = "cre",
                      email = "rezgararabzadeh@ut.ac.ir"))
as necessary.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Shonosuke Sugasawa <shonosuke622@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Shonosuke",
                    family = "Sugasawa",
                    role = c("aut", "cre"),
                    email = "shonosuke622@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Christophe Dutang <christophe.dutang@ensimag.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Christophe",
                      family = "Dutang",
                      role = c("aut", "cre"),
                      email = "christophe.dutang@ensimag.fr"),
               person(given = "Julie",
                      family = "Barthes",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Found the following files/directories:
  ‘mydata.rda’ ‘thedata.rda’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) GenerateClusterData.Rd:34: Lost braces; missing escapes or markup?
    34 | origin, v_1, -v_1, v_2, -v_2, v_3, -v_3,..., v_{(numberOfClusters-1)/2},
       |                                                ^
checkRd: (-1) GenerateClusterData.Rd:35: Lost braces; missing escapes or markup?
    35 | -v_{(numberOfClusters-1)/2} (if \code{numberOfClusters} is odd)
       |    ^
checkRd: (-1) GenerateClusterData.Rd:36: Lost braces; missing escapes or markup?
    36 | origin, v_1, -v_1, v_2, -v_2, v_3, -v_3,..., v_{(numberOfClusters-1)/2}
       |                                                ^
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:21-22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:23-24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:25-26: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:27-28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:29-30: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:31-32: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:33-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:35-36: Lost braces
    35 |    \item{pam_cluster_64_7_5715},{N=64, seven clusters with 5715 vectors per
       |                                 ^
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:37-38: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:39-40: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:21-22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:23-24: Lost braces in \enumerate; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ei-ji Nakama <nakama@ki.rim.or.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Junji",
                      family = "NAKANO",
                      role = "aut",
                      email = "nakanoj@ism.ac.jp"),
               person(given = "Ei-ji",
                      family = "Nakama",
                      role = c("aut", "cre"),
                      email = "nakama@ki.rim.or.jp"))
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?
Package required but not available: ‘lomb’

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: ‘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.
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?
Package required but not available: ‘ecmwfr’

Packages suggested but not available for checking:
  'roxygen2', '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: 'pedtools', 'kinship2'

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xiang",
                      family = "LI",
                      role = c("aut", "cre"),
                      email = "ynaulx@gmail.com"),
               person(given = "Linna",
                      family = "MA",
                      role = "aut"))
as necessary.
Maintainer: ‘Xiang LI <ynaulx@gmail.com>’

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

VignetteBuilder package required 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', 'SuperLearner'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'mimic.demo', 'eicu.demo', 'knitr', 'rmarkdown', 'rticles',
  '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: ‘Steffen Moritz <steffen.moritz10@gmail.com>’

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:
  'covr', 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'leaflet', 'kableExtra', '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: ‘Xinyuan Fan <fxy22@mails.tsinghua.edu.cn>’

The Description field contains
  and Wu (2024) <arXiv:2403.00600>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Packages required but not available: 'Rdimtools', 'T4cluster', 'maotai'

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) iex.chart.Rd:23: Lost braces; missing escapes or markup?
    23 | r takes only of of the values accepted IN API request. {"5y", "2y", "1y", "ytd", "6m", "3m", "1m", "1d"}
       |                                                        ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Kean Ming Tan <ktan@umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Kean", "Ming"),
                    family = "Tan",
                    role = c("aut", "cre"),
                    email = "ktan@umn.edu")
as necessary.

The Description field contains
  Journal of the Royal Statistical Society: Series B. <arXiv:1604.08697>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Pavel V. Moskalev <moskalefff@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Pavel", "V."),
                      family = "Moskalev",
                      role = c("aut", "cre"),
                      email = "moskalefff@gmail.com"),
               person(given = c("Alexey", "G."),
                      family = "Bukhovets",
                      role = "aut"),
               person(given = c("Tatyana", "Ya."),
                      family = "Biruchinskay",
                      role = "aut"))
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:
  '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', '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: ‘Joel Carlson <jnkcarlson@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Joel",
                    family = "Carlson",
                    role = c("aut", "cre"),
                    email = "jnkcarlson@gmail.com")
as necessary.
Maintainer: ‘John Ruscio <ruscio@tcnj.edu>’

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

VignetteBuilder package required 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 ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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.
Cannot process vignettes
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  'knitr', 'rmarkdown', 'yaml'

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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:
    ‘population_utils.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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  'covr', 'knitr', 'rmarkdown'

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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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  'kableExtra', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
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  'devtools', 'htmlwidgets', 'kableExtra', 'knitr', 'roxygen2', 'DT'

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

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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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  'knitr', 'rmarkdown', 'tidyverse', 'printr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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  'kableExtra', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
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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: ‘Daniel P. Palomar <daniel.p.palomar@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.

The Description field contains
  parity portfolios. <arXiv:1311.4057>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
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checkRd: (-1) riskParityPortfolio.Rd:163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:168: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:169: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:170: Lost braces in \itemize; meant \describe ?
Maintainer: ‘David Ardia <david.ardia.ch@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’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Maintainer: ‘Saralees Nadarajah <mbbsssn2@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 = "mbbsssn2@manchester.ac.uk"),
               person(given = "Stephen",
                      family = "Chan",
                      role = "aut"))
as necessary.
Package required but not available: ‘rms’

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  'pec', 'randomForestSRC', 'SuperLearner'

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Cannot process vignettes
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Maintainer: ‘Paramita Saha-Chaudhuri <paramita.sahachaudhuri.work@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Patrick", "J."),
                      family = "Heagerty",
                      role = "aut",
                      email = "heagerty@u.washington.edu"),
               person(given = c("packaging", "by", "Paramita"),
                      family = "Saha-Chaudhuri",
                      role = "aut",
                      email = "paramita.sahachaudhuri.work@gmail.com"),
               person(given = "Paramita",
                      family = "Saha-Chaudhuri",
                      role = "cre",
                      email = "paramita.sahachaudhuri.work@gmail.com"))
as necessary.
Cannot process vignettes
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Running ‘test-all.R’ [1s/2s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("ritis")
  Loading required package: ritis
  
  Attaching package: 'ritis'
  
  The following object is masked from 'package:stats':
  
      terms
  
  Error in `source_dir()`:
  ! Failed to evaluate './helper-ritis.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("ritis")
    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-ritis.R:4:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─cli::cli_abort(...)
   18.     └─rlang::abort(...)
  Execution halted
Maintainer: ‘Gregory Pasternack <gpast@ucdavis.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gregory",
                      family = "Pasternack",
                      role = c("aut", "cre"),
                      email = "gpast@ucdavis.edu"),
               person(given = "Rafaeli",
                      family = "Arroyo",
                      role = "aut",
                      email = "rtoarroyo@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:
    ‘plotdensity.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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DESCRIPTION file?
Maintainer: ‘Peter Reichert <peter.reichert@emeriti.eawag.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Peter",
                    family = "Reichert",
                    role = c("aut", "cre"),
                    email = "peter.reichert@emeriti.eawag.ch")
as necessary.
Maintainer: ‘Aleksander Mendyk <mfmendyk@cyf-kr.edu.pl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Aleksander",
                      family = "Mendyk",
                      role = c("aut", "cre"),
                      email = "mfmendyk@cyf-kr.edu.pl"),
               person(given = c("with", "contributions", "from", "Sebastian"),
                      family = "Polak.",
                      role = "aut",
                      email = "mfpolak@@cyf-kr.edu.pl"))
as necessary.
checkRd: (-1) RivivcA.Rd:7: Lost braces
     7 | This is the major function to be called where numerical convolution ad/or deconvolution might be used for a linear in vitro in vivo correlation level A. It performes either numerical convolution via /code{NumConv()} or deconvolution via /code{NumDeconv()} and correlates their results with the known.data object via linear regression \code{lm()}. If you just want raw results of convolution/deconvolution then call explicitely \code{\link{NumConv}} or \code{link{NumDeconv}}
       |                                                                                                                                                                                                             ^
checkRd: (-1) RivivcA.Rd:7: Lost braces
     7 | This is the major function to be called where numerical convolution ad/or deconvolution might be used for a linear in vitro in vivo correlation level A. It performes either numerical convolution via /code{NumConv()} or deconvolution via /code{NumDeconv()} and correlates their results with the known.data object via linear regression \code{lm()}. If you just want raw results of convolution/deconvolution then call explicitely \code{\link{NumConv}} or \code{link{NumDeconv}}
       |                                                                                                                                                                                                                                                   ^
Package required but not available: ‘OCNet’

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  'knitr', 'rmarkdown', 'bookdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Gabriela Cohen-Freue <gcohen@stat.ubc.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gabriela",
                      family = "Cohen-Freue",
                      role = c("aut", "cre"),
                      email = "gcohen@stat.ubc.ca"),
               person(given = "Davor",
                      family = "Cubranic",
                      role = "aut"),
               person(given = c("with", "contributions", "from", "B."),
                      family = "Kaufmann",
                      role = "aut"),
               person(given = "R.H.",
                      family = "Zamar",
                      role = "aut"))
as necessary.
Packages required but not available: 'devtools', 'rlist', 'RSelenium'

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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: ‘Michael C Koohafkan <michael.koohafkan@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
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Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Cannot process vignettes
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  'knitr', 'rmarkdown', 'usethis', 'visNetwork'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Jeroen Ooms <jeroen@berkeley.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jeroen",
                      family = "Ooms",
                      role = c("aut", "cre"),
                      email = "jeroen@berkeley.edu"),
               person(given = "Forbes",
                      family = "Lindesay",
                      role = "aut"))
as necessary.
Cannot process vignettes
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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: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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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.

Package installs .java files.
Package has FOSS license, installs .class/.jar but has no 'java' directory.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rJava.Rcheck/00install.out’ for details.
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.
Package required but not available: ‘rJava’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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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’
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
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  'BiocStyle', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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DESCRIPTION file?
Maintainer: ‘Carlos Prieto <cprietos@usal.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Carlos",
                      family = "Prieto",
                      role = c("aut", "cre"),
                      email = "cprietos@usal.es"),
               person(given = "David",
                      family = "Barrios",
                      role = "aut",
                      email = "metal@usal.es"))
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: ‘Aaron Schumacher <ajschumacher@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Aaron",
                      family = "Schumacher",
                      role = c("aut", "cre"),
                      email = "ajschumacher@gmail.com"),
               person(given = "Håkon",
                      family = "Malmedal",
                      role = "aut"),
               person(given = "Måns",
                      family = "Magnusson",
                      role = "aut"))
as necessary.
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Package required but not available: ‘JuliaCall’

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Cannot process vignettes
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Shruti Gupta <shrutigupta34@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Shruti",
                      family = "Gupta",
                      role = c("aut", "cre"),
                      email = "shrutigupta34@gmail.com"),
               person(given = "Coda",
                      family = "Hale"),
               person(given = "Yammer",
                      family = "Inc.",
                      role = c("ctb", "cph")))
as necessary.
Package required but not available: ‘rJava’

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

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

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manual.
Package required but not available: ‘rJava’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Mutua Kilai <kilaimutua@gmail.com>’

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  Authors@R: person(given = "Mutua",
                    family = "Kilai",
                    role = c("aut", "cre"),
                    email = "kilaimutua@gmail.com")
as necessary.
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Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Maintainer: ‘Titus K Rotich <rktitus@uoeld.ac.ke>’

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Please add one, modifying
  Authors@R: person(given = c("Titus", "K"),
                    family = "Rotich",
                    role = c("aut", "cre"),
                    email = "rktitus@uoeld.ac.ke")
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:
    ‘higher_order_metadata.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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Packages required but not available: 'highcharter', 'keyring', 'PTXQC'

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  'htmlwidgets', 'rmarkdown', 'kableExtra', 'knitr', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Aldo Marchetto <aldo.marchetto@cnr.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Aldo",
                    family = "Marchetto",
                    role = c("aut", "cre"),
                    email = "aldo.marchetto@cnr.it")
as necessary.
Maintainer: ‘Md Ashad Alam <malam@tulane.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Md", "Ashad"),
                    family = "Alam",
                    role = c("aut", "cre"),
                    email = "malam@tulane.edu")
as necessary.
Maintainer: ‘Dennis Boos <boos@ncsu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Dennis", "D."),
                      family = "Boos",
                      role = "aut"),
               person(given = "Douglas",
                      family = "Nychka",
                      role = "aut"),
               person(given = "Dennis",
                      family = "Boos",
                      role = "cre",
                      email = "boos@ncsu.edu"))
as necessary.
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
Maintainer: ‘Luke Winslow <lawinslow@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Luke",
                      family = "Winslow",
                      role = c("aut", "cre"),
                      email = "lawinslow@gmail.com"),
               person(given = "Jordan",
                      family = "Read",
                      role = "aut"),
               person(given = "Richard",
                      family = "Woolway",
                      role = "aut"),
               person(given = "Jennifer",
                      family = "Brentrup",
                      role = "aut"),
               person(given = "Taylor",
                      family = "Leach",
                      role = "aut"),
               person(given = "Jake",
                      family = "Zwart",
                      role = "aut"),
               person(given = "Sam",
                      family = "Albers",
                      role = "aut"),
               person(given = "Doug",
                      family = "Collinge",
                      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: 'knitr', 'rmarkdown'

VignetteBuilder package required 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 ‘rlang/libs/rlang.so’:
  Found non-API calls to R: ‘ENCLOS’, ‘OBJECT’, ‘PRENV’, ‘PRVALUE’,
    ‘R_PromiseExpr’, ‘Rf_allocSExp’, ‘Rf_findVarInFrame3’, ‘SETLENGTH’,
    ‘SET_BODY’, ‘SET_CLOENV’, ‘SET_ENCLOS’, ‘SET_FORMALS’,
    ‘SET_GROWABLE_BIT’, ‘SET_OBJECT’, ‘SET_TRUELENGTH’, ‘SET_TYPEOF’,
    ‘XTRUELENGTH’
These entry points may be removed soon:
‘SET_ENCLOS’, ‘ENCLOS’, ‘OBJECT’, ‘SET_TYPEOF’, ‘SET_FORMALS’, ‘SET_BODY’, ‘SET_CLOENV’, ‘XTRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
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: ‘Patricia Conde-Clemente <patricia.condeclemente@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Patricia",
                      family = "Conde-Clemente",
                      role = c("aut", "cre"),
                      email = "patricia.condeclemente@gmail.com"),
               person(given = c("Jose", "M."),
                      family = "Alonso",
                      role = "aut"),
               person(given = "Gracian",
                      family = "Trivino",
                      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: ‘Wei-Min Wang <wmwang@gmail.com>’

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

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

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

VignetteBuilder 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: ‘Dmitry Otryakhin <d.otryakhin.acad@protonmail.ch>’

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

The Description field contains
  Otryakhin and Podolskij (2018) <arXiv:1802.06373>, and also different
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: ‘Jouni Helske <jouni.helske@iki.fi>’

Found the following (possibly) invalid file URI:
  URI: https//cranlogs.r-pkg.org:443/badges/Rlibeemd
    From: README.md
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.
Package required but not available: ‘leidenAlg’

Packages suggested but not available for checking:
  'EnhancedVolcano', 'gprofiler2', 'knitr', 'plotly', 'rmarkdown',
  'Seurat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Michael Piccirilli <michael.r.piccirilli@gmail.com>’

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

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
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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.
Package required but not available: ‘yaml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘You-Gan Wang <you-gan.wang@qut.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "You-Gan",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "you-gan.wang@qut.edu.au"),
               person(given = "Benoit",
                      family = "Liquet",
                      role = "aut"),
               person(given = "Aurelien",
                      family = "Callens",
                      role = "aut"),
               person(given = "Na",
                      family = "Wang.",
                      role = "aut"))
as necessary.
Maintainer: ‘Yusuf Bilgic <bilgic@geneseo.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yusuf",
                      family = "Bilgic",
                      role = c("aut", "cre"),
                      email = "bilgic@geneseo.edu"),
               person(given = "Herb",
                      family = "Susmann",
                      role = "aut"),
               person(given = "Joseph",
                      family = "McKean",
                      role = "aut"))
as necessary.
Maintainer: ‘Yingsong Hu <yingsonghu@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yingsong",
                      family = "Hu",
                      role = c("aut", "cre"),
                      email = "yingsonghu@hotmail.com"),
               person(given = "Wayne",
                      family = "Murray",
                      role = "aut"),
               person(given = "Yin",
                      family = "Shan",
                      role = "aut"),
               person(family = "Australia.",
                      role = "aut"))
as necessary.
Maintainer: ‘Sunny Kumar <sunny.nitie14@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sunny",
                    family = "Kumar",
                    role = c("aut", "cre"),
                    email = "sunny.nitie14@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
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Maintainer: ‘Tong He <hetong007@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Tong",
                      family = "He",
                      role = c("aut", "cre"),
                      email = "hetong007@gmail.com"),
               person(given = "Oliver",
                      family = "Keyes",
                      role = "ctb"))
as necessary.

The Description field contains
  in Chinese (http://www.ltp-cloud.com/).
Please enclose URLs in angle brackets (<...>).
Packages required but not available:
  'rhandsontable', 'leaflet', 'DT', '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.
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DESCRIPTION file?
Maintainer: ‘Carlos Trucios <ctrucios@gmail.com>’

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

VignetteBuilder 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: 'rmarkdown', 'visNetwork', 'knitr'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/rmake-intro.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'

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

Packages suggested but not available for checking:
  'dygraphs', 'rsconnect', 'downlit', 'cleanrmd'

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) setOption.Matlab.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setOption.Matlab.Rd:40-41: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘matlib’

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: 'rJava', 'yaml'

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

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Marshall",
                    family = "Brown",
                    role = c("aut", "cre"),
                    email = "mdbrown@fredhutch.org")
as necessary.
Packages required but not available: 'rmarkdown', 'knitr'

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: ‘rmarkdown’

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

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

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

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Mark Peterson <mark.phillip.peterson@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mark",
                    family = "Peterson",
                    role = c("aut", "cre"),
                    email = "mark.phillip.peterson@gmail.com")
as necessary.
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', 'rmarkdown', 'knitr', 'gt', 'tidycmprsk'

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:
    ‘model-table.R’
Running ‘testthat.R’ [10s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rmdl)
  Loading required package: vctrs
  Loading required package: tibble
  
  Attaching package: 'tibble'
  
  The following object is masked from 'package:vctrs':
  
      data_frame
  
  
  Attaching package: 'rmdl'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > 
  > test_check("rmdl")
  Interaction term `green` was applied to exposure term `witch`
  Interaction term `green` was applied to exposure term `witch`
  Interaction term `west` was applied to exposure term `witch`
  Using `fundamental` decomposition pattern: 
  - Mediation term: NA
  - Stratifying term: NA
  Using `fundamental` decomposition pattern: 
  - Mediation term: NA
  - Stratifying term: NA
  Interaction term `green` was applied to exposure term `witch`
  Saving _problems/test-terms-213.R
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 204 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • Skipping (1): 'test-formulas.R:57:2'
  • empty test (3): 'test-interaction.R:41:1', 'test-model-table.R:272:1',
    'test-patterns.R:36:1'
  • {tidycmprsk} is not installed (1): 'test-models.R:82:2'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-terms.R:213:2'): interaction terms are appropriately made ──────
  Error in `expect(length(t), 5)`: `ok` must be `TRUE` or `FALSE`, not the number 5.
  Backtrace:
      ▆
   1. └─testthat::expect(ok = length(t)) at test-terms.R:213:9
   2.   └─testthat:::check_bool(ok)
   3.     └─testthat:::stop_input_type(...)
   4.       └─rlang::abort(message, ..., call = call, arg = arg)
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 204 ]
  Error:
  ! Test failures.
  Execution halted
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: ‘knitr’

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  'roxygen2', 'rmarkdown', 'pkgdown', 'covr', 'spelling', 'DT'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Johan Larsson <johanlarsson@outlook.com>’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Johann R. Kleinbub <johann.kleinbub@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Johann", "R."),
                      family = "Kleinbub",
                      role = c("aut", "cre"),
                      email = "johann.kleinbub@gmail.com"),
               person(given = "Fabian",
                      family = "Ramseyer",
                      role = "aut"))
as necessary.
Maintainer: ‘Junhewk Kim <junhewk.kim@gmail.com>’

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thomas",
                    family = "Lumley",
                    role = c("aut", "cre"),
                    email = "t.lumley@auckland.ac.nz")
as necessary.
Maintainer: ‘Henrik Bengtsson <henrikb@braju.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Lukasz Smaga <ls@amu.edu.pl>’

The Description field contains
  <arXiv:2306.03883>). These procedures enable us to verify the overall
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘plotly’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: support will be removed soon
Maintainer: ‘Ryan M. Hope <rmh3093@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Ryan", "M."),
                    family = "Hope",
                    role = c("aut", "cre"),
                    email = "rmh3093@gmail.com")
as necessary.
Running examples in ‘Rmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: group.CI
> ### Title: Group Confidence Interval
> ### Aliases: group.CI
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> require(latticeExtra)
Loading required package: latticeExtra
> with(group.CI(weight~feed,chickwts),
+  segplot(feed~weight.lower+weight.upper,center=weight.mean)
+ )
> 
> require(Hmisc)
Loading required package: Hmisc
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Hmisc’
> with(group.CI(Temp~Month,airquality),
+  xYplot(Cbind(Temp.mean,Temp.lower,Temp.upper)~numericScale(Month),type="b",ylim=c(60,90))
+ )
Error in xYplot(Cbind(Temp.mean, Temp.lower, Temp.upper) ~ numericScale(Month),  : 
  could not find function "xYplot"
Calls: with -> with.default -> eval -> eval
Execution halted
File ‘Rmixmod/libs/Rmixmod.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘mixmod.a’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages required but not available: 'RMixtCompUtilities', '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.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Robert M. Kirkpatrick <rkirkpatrick2@vcu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Robert", "M."),
                    family = "Kirkpatrick",
                    role = c("aut", "cre"),
                    email = "rkirkpatrick2@vcu.edu")
as necessary.
Maintainer: ‘Herdiantri Sufriyana <herdi@nycu.edu.tw>’

The Description field contains
  <https://htmlpreview.github.io/?https://github.com/herdiantrisufriyana/rmlnomogram/blob/master/doc/ml_nomogram_exemplar.html>.
Please enclose URLs in angle brackets (<...>).
Cannot process vignettes
Packages suggested but not available for checking: 'tidyverse', '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: ‘Jan Wijffels <jwijffels@bnosac.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("See", "file"),
                      family = "AUTHORS",
                      role = "aut"),
               person(given = "Jan",
                      family = "Wijffels",
                      role = "cre",
                      email = "jwijffels@bnosac.be"))
as necessary.
Package required but not available: ‘rJava’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jan Wijffels <jwijffels@bnosac.be>’

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: 'RMOAjars', 'rJava'

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

VignetteBuilder package required 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: 'fabR', 'madshapR'

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’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘decrypt.Rd’ ‘encrypt.Rd’ ‘encrypt_raw.Rd’
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', 'rgl', 'ecr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Henrik A. Friberg <haf@mosek.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "MOSEK",
                      family = "ApS",
                      role = "aut"),
               person(given = c("Henrik", "A."),
                      family = "Friberg",
                      role = "cre",
                      email = "haf@mosek.com"))
as necessary.
Found the following calls to attach():
File ‘Rmosek/R/builder.R’:
  attach(builderenv, pos, name, warn.conflicts)
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?
Maintainer: ‘Priyam Das <pdas@ncsu.edu>’

The Description field contains
  Described in the paper : Das (2016) <arXiv:1604.08616> .
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Packages required but not available: 'rms', 'Hmisc', 'knitr'

Package suggested but not available for checking: ‘cmdstanr’

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

VignetteBuilder package required 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', 'devtools', 'flextable', 'Hmisc'

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', 'htmlTable', 'knitr'

Packages suggested but not available for checking:
  'plotly', 'rmsb', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Kentaro Ueno <ueno_kentaro@kuhp.kyoto-u.ac.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kentaro",
                    family = "Ueno",
                    role = c("aut", "cre"),
                    email = "ueno_kentaro@kuhp.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?
Maintainer: ‘Uwe Menzel <uwemenzel@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Uwe",
                    family = "Menzel",
                    role = c("aut", "cre"),
                    email = "uwemenzel@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’
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?
Maintainer: ‘Lu Mao <lmao@biostat.wisc.edu>’

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Iain", "M."),
                      family = "Johnstone",
                      role = "aut"),
               person(given = "Zongming",
                      family = "Ma",
                      role = "aut"),
               person(given = c("Patrick", "O."),
                      family = "Perry",
                      role = "aut"),
               person(given = "Morteza",
                      family = "Shahram",
                      role = "aut"),
               person(given = "Evan",
                      family = "Biederstedt",
                      role = c("aut", "cre"),
                      email = "evan.biederstedt@gmail.com"))
as necessary.

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

The BugReports field in DESCRIPTION has
  https://github.com/evanbiederstedt/RMTstat
which should likely be
  https://github.com/evanbiederstedt/RMTstat/issues
instead.
Maintainer: ‘Chenyu Ren <chenyu.ren@connect.polyu.hk>’

The Description field contains
  Ting Li, Zhongyuan Lyu, Chenyu Ren, Dong Xia (2023) <arXiv:2302.04437>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Sara Viviani <sara.viviani@yahoo.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Carlo",
                      family = "Cafiero",
                      role = "aut"),
               person(given = "Sara",
                      family = "Viviani",
                      role = c("aut", "cre"),
                      email = "sara.viviani@yahoo.it"),
               person(given = "Mark",
                      family = "Nord",
                      role = "aut"))
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘RM.weights-package.Rd’:
    \keyword{ Conditional maximum likelihood, Rasch mo [TRUNCATED]
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’
checkRd: (-1) myTarGetClientList.Rd:33: Lost braces
    33 | {MyTarget API Documenation}{https://target.my.com/doc/api/detailed/#resource_agency_clients}
       |                            ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mixtools', '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?
Packages required but not available: 'AnnotationHub', 'ensembldb'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'recount3'

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', 'rnaturalearthhires', 'tmap'

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) rncl.Rd:53-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:59-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:65-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:73-78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:80-84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:86-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:92-93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:98-99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:101-102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:107-110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:112-115: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:117-119: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:121-124: Lost braces in \itemize; \value handles \item{}{} directly
Maintainer: ‘Kam Hamidieh <khamidieh@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kam",
                    family = "Hamidieh",
                    role = c("aut", "cre"),
                    email = "khamidieh@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: ‘Yasuhiro Sato <sato.yasuhiro.36c@kyoto-u.jp>’

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: ‘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.
checkRd: (-1) NlistServersInCategory.Rd:11: 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?
Maintainer: ‘Jan C. Thiele <rnetlogo@gmx.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Jan", "C."),
                    family = "Thiele",
                    role = c("aut", "cre"),
                    email = "rnetlogo@gmx.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.
Package required but not available: ‘rJava’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Kasper Welbers <kasperwelbers@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Kasper", "Welbers", "&", "Wouter"),
                      family = "van Atteveldt",
                      role = "aut"),
               person(given = "Kasper",
                      family = "Welbers",
                      role = "cre",
                      email = "kasperwelbers@gmail.com"))
as necessary.
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.
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'rdflib', 'knitr', 'rfigshare', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) nexml_get.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:35: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Ruizhe Chen <rchen18@uic.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hesen",
                      family = "Li",
                      role = "aut"),
               person(given = "Ruizhe",
                      family = "Chen",
                      role = c("aut", "cre"),
                      email = "rchen18@uic.edu"),
               person(given = "Hai",
                      family = "Nguyen",
                      role = "aut"),
               person(given = "Yu-Che",
                      family = "Chung",
                      role = "aut"),
               person(given = "Ran",
                      family = "Gao",
                      role = "aut"),
               person(given = "Hakan",
                      family = "Demirtas",
                      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: ‘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.
Packages required but not available: 'heatmaply', 'knitr'

Package suggested but not available for checking: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘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:
  '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 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/rnnmf.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Bastiaan Quast <bquast@gmail.com>’

The Description field contains
  <arXiv:1412.3555>) and vanilla RNN.
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:
  'covr', 'knitr', 'rmarkdown', 'vcr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # 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(rnpn)
  > 
  > test_check("rnpn")
  Error in `source_dir()`:
  ! Failed to evaluate './helper-rnpn.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("rnpn")
    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-rnpn.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:
  'DT', 'dygraphs', 'knitr', 'leaflet', 'rmarkdown', 'spelling'

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jongbin",
                    family = "Jung",
                    role = c("aut", "cre"),
                    email = "me@jongbin.com")
as necessary.

The Description field contains
  implemented in Jung et al. (2017) <arXiv:1702.04690> based on Rosenbaum
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
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:
  'roxygen2', 'knitr', 'covr', 'rmarkdown', 'lintr'

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

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:
    ‘projectRoads.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Aymeric Stamm <aymeric.stamm@math.cnrs.fr>’

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

The Description field contains
  package. See Aleman-Gomez et al. (2021) <arXiv:2103.08874> for details
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘plotly’

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

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jeff",
                      family = "Gentry",
                      role = "aut",
                      email = "geoffjentry@gmail.com"),
               person(given = c("Duncan", "Temple"),
                      family = "Lang",
                      role = "aut",
                      email = "duncan@r-project.org"),
               person(given = "Pablo",
                      family = "Barbera",
                      role = "cre",
                      email = "pablo.barbera@nyu.edu"))
as necessary.
Package required but not available: ‘pammtools’

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 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/imputation.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Paul Smirnov <s.paul@mail.ru>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Paul",
                    family = "Smirnov",
                    role = c("aut", "cre"),
                    email = "s.paul@mail.ru")
as necessary.
Packages required but not available: 'fda.usc', 'goffda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Carlos Trucios <ctrucios@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Carlos",
                    family = "Trucios",
                    role = c("aut", "cre"),
                    email = "ctrucios@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: 'tidyverse', 'SuperLearner', 'AIPW'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Joseph Blubaugh <jestonblu@gmail.com>’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘networkD3’

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: 'leaflet', 'mapedit'

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: ‘Daniel Grose <dan.grose@lancaster.ac.uk>’

The Description field contains
  (2014) <arXiv:1204.3358> and Agamennoni et al. (2018)
  of Ruckdeschel et al. (2014) <arXiv:1204.3358>, as well as the
  <arXiv:2007.03238>.
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?
Packages required but not available: 'DT', 'flextable'

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/robmed-intro.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Wennan Chang <wnchang@iu.edu>’

The Description field contains
  <arXiv:2005.11599>.
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', 'usethis', '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', 'devtools', 'vcr', 'knitr', 'covr', 'rmarkdown',
  'DiagrammeR', 'mapview'

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(robotoolbox)
  > 
  > test_check("robotoolbox")
  Error in `source_dir()`:
  ! Failed to evaluate './setup-robotoolbox.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("robotoolbox")
    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-robotoolbox.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', '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: ‘Aditya Mishra <amishra@flatironinstitute.org>’

The Description field contains
  <arXiv:1909.04990>.
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: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jakob Raymaekers <j.raymaekers@maastrichtuniversity.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jakob",
                    family = "Raymaekers",
                    role = c("aut", "cre"),
                    email = "j.raymaekers@maastrichtuniversity.nl")
as necessary.

The Description field contains
  F. (2022) <arXiv:2202.08060>.  All algorithms run in quasilinear time.
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'
Package has ‘vignettes’ subdirectory but apparently 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?
checkRd: (-1) predict.robu.Rd:36-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.robu.Rd:43-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.robu.Rd:50-55: Lost braces in \itemize; meant \describe ?
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: ‘A. Randriamiharisoa <exelami@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alfio",
                      family = "Marazzi",
                      role = "aut",
                      email = "Alfio.Marazzi@unisante.ch"),
               person(given = "Jean-Luc",
                      family = "Muralti",
                      role = "aut"),
               person(given = "A.",
                      family = "Randriamiharisoa",
                      role = "cre",
                      email = "exelami@gmail.com"))
as necessary.
Maintainer: ‘Ray Bai <raybaistat@gmail.com>’

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

The Description field contains
  (2020) <arXiv:2005.02930> for correcting and quantifying publication
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Erlis Ruli <erlisr@yahoo.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.

The Description field contains
  by Ruli et al. (2017) <arXiv:1706.01752>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Charles Bouveyron <charles.bouveyron@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Charles", "Bouveyron", "&", "Stephane"),
                      family = "Girard",
                      role = "aut"),
               person(given = "Charles",
                      family = "Bouveyron",
                      role = "cre",
                      email = "charles.bouveyron@gmail.com"))
as necessary.
Maintainer: ‘Chuan Hong <hong.chuan.hannah@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chuan",
                      family = "Hong",
                      role = c("aut", "cre"),
                      email = "hong.chuan.hannah@gmail.com"),
               person(given = "Yong",
                      family = "Chen",
                      role = "aut"),
               person(given = "Yang",
                      family = "Ning",
                      role = "aut"),
               person(given = "Hao",
                      family = "Wu",
                      role = "aut"))
as necessary.
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/robustfa-knitr.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Zijian Guo <zijguo@stat.rutgers.edu>’

The Description field contains
  variables via TSHT('Guo et al.' (2016) <arXiv:1603.05224>) and
  SearchingSampling('Guo' (2021) <arXiv:2104.06911>), which are effective
  <arXiv:1609.06713>).
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Santiago I. Hurtado <santih@carina.fcaglp.unlp.edu.ar>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Santiago", "I."),
                    family = "Hurtado",
                    role = c("aut", "cre"),
                    email = "santih@carina.fcaglp.unlp.edu.ar")
as necessary.
Note: skipping ‘simulationStudies.Rnw’ due to unavailable dependencies:
  'lemon'
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently 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?
Maintainer: ‘Youyi Fong <youyifong@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Youyi",
                    family = "Fong",
                    role = c("aut", "cre"),
                    email = "youyifong@gmail.com")
as necessary.
Maintainer: ‘Maria del Carmen Calatrava Moreno <mc.calatrava.moreno@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Maria", "del", "Carmen", "Calatrava"),
                      family = "Moreno",
                      role = c("aut", "cre"),
                      email = "mc.calatrava.moreno@gmail.com"),
               person(given = "Thomas",
                      family = "Auzinger",
                      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: ‘Ian M. Johnson <ijca2013@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Ian", "M."),
                    family = "Johnson",
                    role = c("aut", "cre"),
                    email = "ijca2013@gmail.com")
as necessary.
Maintainer: ‘Claudio Agostinelli <claudio.agostinelli@unitn.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Claudio",
                      family = "Agostinelli",
                      role = c("aut", "cre"),
                      email = "claudio.agostinelli@unitn.it"),
               person(given = c("Victor", "J."),
                      family = "Yohai",
                      role = "aut",
                      email = "victoryohai@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: ‘Luke McGuinness <luke.mcguinness@bristol.ac.uk>’

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

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

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

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: ‘formattable’

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: ‘Martin Lauss <martin.lauss@med.lu.se>’

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ben",
                    family = "Sherwood",
                    role = c("aut", "cre"),
                    email = "ben.sherwood@ku.edu")
as necessary.
Problems with news in ‘NEWS.md’:
No news entries found.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) descriptiveTable.Rd:18: Lost braces
    18 | other object type that does not fail in code{model.frame(object)}.}
       |                                             ^
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 R. Webber <jwebber@geo.umass.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Jeffrey", "R."),
                    family = "Webber",
                    role = c("aut", "cre"),
                    email = "jwebber@geo.umass.edu")
as necessary.
Packages required but not available: 'rgl', 'EBImage'

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

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

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

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

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

VignetteBuilder package required 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: ‘roxygen2’

Package suggested but not available for checking: ‘covr’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘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 ‘rocNIT.Rd’:
    \keyword{Non-inferiority test, receiver operating  [TRUNCATED]
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/rococo.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Felix G.M. Ernst <felix.gm.ernst@outlook.com>’

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’
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
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.
Package required but not available: ‘plotly’

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently 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: ‘Fabio Centofanti <fabio.centofanti@unina.it>’

The Description field contains
  described in Centofanti et al. (2021) <arXiv:2112.10643>.  It allows
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘fda.usc’

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', '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: ‘Benjamin Schwendinger <benjaminschwe@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Benjamin",
                    family = "Schwendinger",
                    role = c("aut", "cre"),
                    email = "benjaminschwe@gmail.com")
as necessary.
checkRd: (-1) ROI_plugin_build_equality_constraints.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_equality_constraints.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:29: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_solve.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available: 'smarter', 'MiRKAT'

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: 'when', 'xlsx'

Packages suggested but not available for checking:
  'DiagrammeR', 'knitr', 'pivottabler', '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', '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: ‘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.
Package required but not available: ‘tosca’

Package suggested but not available for checking: ‘covr’

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

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: ‘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.
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:
  'rmarkdown', 'knitr', 'DiagrammeR'

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: ‘Pingping Qu <quping14@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Pingping",
                      family = "Qu",
                      role = c("aut", "cre"),
                      email = "quping14@gmail.com"),
               person(given = "John",
                      family = "Crowley",
                      role = "aut"))
as necessary.
Maintainer: ‘Alberto Almuiña <albertogonzalezalmuinha@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alberto",
                    family = "Almuiña",
                    role = c("aut", "cre"),
                    email = "albertogonzalezalmuinha@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', '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: ‘Evan Biederstedt <evan.biederstedt@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jeffrey",
                      family = "Horner",
                      role = "aut"),
               person(given = "Evan",
                      family = "Biederstedt",
                      role = c("aut", "cre"),
                      email = "evan.biederstedt@gmail.com"))
as necessary.
Maintainer: ‘Yoann Robin <yoann.robin.k@gmail.com>’

The Description field contains
  generator, see Mezzadri, F. (2007) <arXiv:math-ph/0609050>.
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:
  '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: ‘Bob Rudis <bob@rud.is>’

Found the following (possibly) invalid file URI:
  URI: CODE_OF_CONDUCT.md
    From: README.md
Problems with news in ‘NEWS.md’:
No news entries found.
Maintainer: ‘Ruokun Huang <hruokun.2008@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ruokun",
                    family = "Huang",
                    role = c("aut", "cre"),
                    email = "hruokun.2008@gmail.com")
as necessary.
Maintainer: ‘Thomas P. Fuller <thomas.fuller@coherentlogic.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Thomas", "P."),
                    family = "Fuller",
                    role = c("aut", "cre"),
                    email = "thomas.fuller@coherentlogic.com")
as necessary.
Maintainer: ‘Mukul Chaware <mukul.chaware13@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mukul",
                    family = "Chaware",
                    role = c("aut", "cre"),
                    email = "mukul.chaware13@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc'

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

VignetteBuilder package required 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.
Running ‘test-all.R’ [1s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("rorcid")
  Loading required package: rorcid
  Error in `source_dir()`:
  ! Failed to evaluate './helper-rorcid.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("rorcid")
    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-rorcid.R:11:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─cli::cli_abort(...)
   18.     └─rlang::abort(...)
  Execution halted
Author field differs from that derived from Authors@R
  Author:    ‘Max Czapanskiy [aut, cre] (0000-0002-6302-905X), Shirel Kahane-Rapport [aut] (<https://orcid.org/0000-0002-5208-1100>), Jeremy Goldbogen [aut] (<https://orcid.org/0000-0002-4170-7294>)’
  Authors@R: ‘Max Czapanskiy [aut, cre] (ORCID-ID: 0000-0002-6302-905X), Shirel Kahane-Rapport [aut] (ORCID: <https://orcid.org/0000-0002-5208-1100>), Jeremy Goldbogen [aut] (ORCID: <https://orcid.org/0000-0002-4170-7294>)’
Maintainer: ‘Martin Wiegand <Martin.Wiegand@mrc-bsu.cam.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Martin",
                    family = "Wiegand",
                    role = c("aut", "cre"),
                    email = "martin.wiegand@mrc-bsu.cam.ac.uk")
as necessary.

The Description field contains
  Wiegand and Nadarajah (2019) <arXiv:1903.09556>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Nicola Lunardon <nicola.lunardon@unimib.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Nicola",
                      family = "Lunardon",
                      role = c("aut", "cre"),
                      email = "nicola.lunardon@unimib.it"),
               person(given = "Giovanna",
                      family = "Menardi",
                      role = "aut"),
               person(given = "Nicola",
                      family = "Torelli",
                      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: ‘keras’

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’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rosetteApi)
  > 
  > test_check("rosetteApi")
  Saving _problems/test_api-8.R
  Saving _problems/test_api-19.R
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 13 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_api.R:3:3'): httr::GET function mocks correctly ────────────────
  <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_api.R:3:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  ── Error ('test_api.R:14:3'): httr::POST functions mock correctly ──────────────
  <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_api.R:14:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 13 ]
  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?
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                ^
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                       ^
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                                  ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Michel",
                      family = "Ballings",
                      role = c("aut", "cre"),
                      email = "michel.ballings@gmail.com"),
               person(given = "Dirk",
                      family = "Van den Poel",
                      role = "aut"))
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/rotations-intro.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: ‘htmlwidgets’

Package suggested but not available for checking: ‘pagedown’

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

Package suggested but not available for checking: ‘pagedown’

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Marie Delacre <marie.delacre@ulb.ac.be>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘Intention.Rd’:
    \keyword{Reminder,}
Running examples in ‘routr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RouteStack
> ### Title: Combine multiple routes for sequential routing
> ### Aliases: RouteStack
> 
> ### ** Examples
> 
> # Create a new stack
> routes <- RouteStack$new()
> 
> # Populate it wih routes
> first <- Route$new()
> first$add_handler('all', '*', function(request, response, keys, ...) {
+   message('This will always get called first')
+   TRUE
+ })
> second <- Route$new()
> second$add_handler('get', '/demo/', function(request, response, keys, ...) {
+   message('This will get called next if the request asks for /demo/')
+   TRUE
+ })
> routes$add_route(first, 'first')
> routes$add_route(second, 'second')
> 
> # Send a request through
> rook <- fiery::fake_request('http://example.com/demo/', method = 'get')
Error in loadNamespace(x) : there is no package called ‘fiery’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘roxygen2’

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.
Package required but not available: ‘knitr’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘roxygen2’

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘roxygen2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘roxygen2’

Package suggested but not available for checking: ‘pkgdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘roxygen2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘roxygen2’

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

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: ‘Adam Spannbauer <spannbaueradam@gmail.com>’

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

Package suggested but not available for checking: ‘covr’

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 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: ‘rmarkdown’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  '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?
Maintainer: ‘Adrian Bowman <adrian.bowman@glasgow.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(family = "Bowman",
                      role = "aut"),
               person(family = "Bowman",
                      role = "aut"),
               person(family = "Gibson",
                      role = "aut"),
               person(family = "Crawford",
                      role = "aut"),
               person(given = "Adrian",
                      family = "Bowman",
                      role = "cre",
                      email = "adrian.bowman@glasgow.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.
checkRd: (-1) Clyde.Rd:8: Lost braces
     8 | These data record the water quality, in terms of dissolved oxygen (\code{DO}) on a percentage scale, at a number of sampling stations (\code{Station}) on the River Clyde.  The date (\code{Day}, \\code{Month}, \code{Year}) is also available, along with the day of the year (\code{Doy} between 1 and 365) and an identified (\code{id}) of the survey on which each measurement was made.
       |                                                                                                                                                                                                         ^
checkRd: (-1) rp.pos.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:31-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:43: Lost braces in \itemize; meant \describe ?
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:
  'rmarkdown', 'devtools', 'knitr', 'usethis'

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: ‘Stephan Dlugosz <stephan.dlugosz@googlemail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Stephan",
                    family = "Dlugosz",
                    role = c("aut", "cre"),
                    email = "stephan.dlugosz@googlemail.com")
as necessary.
Maintainer: ‘Giuliano Galimberti <giuliano.galimberti@unibo.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Giuliano",
                      family = "Galimberti",
                      role = c("aut", "cre"),
                      email = "giuliano.galimberti@unibo.it"),
               person(given = "Gabriele",
                      family = "Soffritti",
                      role = "aut"),
               person(given = c("Matteo", "Di"),
                      family = "Maso",
                      role = "aut"))
as necessary.

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Manuel David Peris Diaz <madape@alumni.uv.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Manuel", "David", "Peris"),
                      family = "Diaz",
                      role = c("aut", "cre"),
                      email = "madape@alumni.uv.es"),
               person(given = c("Maria", "Isabel", "Alcoriza"),
                      family = "Balaguer",
                      role = "aut"))
as necessary.
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 = "Shengyu",
                      family = "Zhang",
                      role = "aut",
                      email = "syzhang@uw.edu"),
               person(given = "Douglas",
                      family = "Martin",
                      role = "aut",
                      email = "doug@amath.washington.edu"))
as necessary.
Maintainer: ‘Timothy I. Cannings <timothy.cannings@ed.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Timothy", "I."),
                      family = "Cannings",
                      role = c("aut", "cre"),
                      email = "timothy.cannings@ed.ac.uk"),
               person(given = c("Richard", "J."),
                      family = "Samworth",
                      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: 'roxygen2', 'knitr'

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

Package suggested but not available for checking: ‘spelling’

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Colin FAY <contact@colinfay.me>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Colin",
                    family = "FAY",
                    role = c("aut", "cre"),
                    email = "contact@colinfay.me")
as necessary.
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:
  '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: 'tidyverse', '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: ‘gt’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Peter Filzmoser <peter.filzmoser@tuwien.ac.at>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Peter",
                      family = "Filzmoser",
                      role = c("aut", "cre"),
                      email = "peter.filzmoser@tuwien.ac.at"),
               person(given = "Sukru",
                      family = "Acitas",
                      role = "aut"),
               person(given = "Birdal",
                      family = "Senoglu",
                      role = "aut"),
               person(given = "Maximilian",
                      family = "Plattner",
                      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: ‘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("Devin", "C."),
                      family = "Koestler",
                      role = "aut"),
               person(family = "Ph.D.",
                      role = "aut"))
as necessary.
checkRd: (-1) plotImage.blcTree.Rd:17: Lost braces
    17 |   \item{method}{Method to determine width of columns that represent classes: \dQuote{weight} (subject weight in class) or dQuote{binary} (depth in tree).}
       |                                                                                                                                 ^
checkRd: (-1) plotImage.glcTree.Rd:16: Lost braces
    16 |   \item{method}{Method to determine width of columns that represent classes: \dQuote{weight} (subject weight in class) or dQuote{binary} (depth in tree).}
       |                                                                                                                                 ^
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: ‘Sascha Herrmann <sascha.herrmann.consulting@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sascha",
                    family = "Herrmann",
                    role = c("aut", "cre"),
                    email = "sascha.herrmann.consulting@gmail.com")
as necessary.
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’
checkRd: (-1) get.poetry.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{output}{Can be any or a combination of the input terms {'author', 'title', 'lines', 'linecount'}. If NULL, all
       |                                                              ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rgl’

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

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

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

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.
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: ‘Pierre Lafaye de Micheaux <lafaye@unsw.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Pierre", "Lafaye"),
                      family = "de Micheaux",
                      role = c("aut", "cre"),
                      email = "lafaye@unsw.edu.au"),
               person(given = "Benoit",
                      family = "Liquet",
                      role = "aut"),
               person(given = "Jeremie",
                      family = "Riou",
                      role = "aut"))
as necessary.
Maintainer: ‘Torsten Schoeps <torsten.schoeps@bioinf.med.uni-goettingen.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Heiko", "Mannsperger", "with", "contributions", "of", "Stephan"),
                      family = "Gade",
                      role = "aut"),
               person(given = "Torsten",
                      family = "Schoeps",
                      role = "cre",
                      email = "torsten.schoeps@bioinf.med.uni-goettingen.de"))
as necessary.
Packages required but not available: 'gam', 'Hmisc'

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

VignetteBuilder 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: ‘Tomas Boril <borilt@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: ‘dygraphs’

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', 'rms', '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: ‘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.
Packages required but not available: 'mixtools', 'oeli'

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: ‘John Ruscio <ruscio@tcnj.edu>’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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: ‘Miguel Conde <miguelco2000@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Miguel",
                    family = "Conde",
                    role = c("aut", "cre"),
                    email = "miguelco2000@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’
checkRd: (-1) check_node.Rd:11: Lost braces
    11 | \item{x}{\\code{list}, the node to check}
       |                ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently 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: ‘Thomas J. Leeper <thosjleeper@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: ‘rmarkdown’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Chanseok Park <statpnu@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?
Packages required but not available: 'tidyverse', 'Hmisc', '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', '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: ‘rcdk’

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:
  'yaml', 'rmarkdown', 'knitr', 'keyring', 'kableExtra'

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', 'yaml'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) ex.Rd:20: Lost braces
    20 | Execute a ops-dag using `code{wrap()}` data as values.
       |                              ^
checkRd: (-1) sql_node.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{expand_braces}{logical if TRUE use {col} notation to ensure {col} is a column name.}
       |                                          ^
checkRd: (-1) sql_node.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{expand_braces}{logical if TRUE use {col} notation to ensure {col} is a column name.}
       |                                                                   ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) R2_lik.Rd:37: Lost braces; missing escapes or markup?
    37 | \code{R2_lik()} is also computed for LMMs and GLMMs in the {MuMIn} package.
       |                                                            ^
checkRd: (-1) R2_pred.Rd:32: Lost braces; missing escapes or markup?
    32 | Note that the version of \code{binaryPGLMM()} in the package ape is replaced by a version contained within {rr2} that outputs all of the required information for the calculation of R2_resid.
       |                                                                                                            ^
checkRd: (-1) R2_resid.Rd:69: Lost braces; missing escapes or markup?
    69 | Note that the version of \code{binaryPGLMM()} in the package ape is replaced by a version contained within {rr2} that outputs all of the required information for the calculation of \code{R2_resid()}
       |                                                                                                            ^
Maintainer: ‘Wei Jiang <wjiangaa@connect.ust.hk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Wei",
                      family = "Jiang",
                      role = c("aut", "cre"),
                      email = "wjiangaa@connect.ust.hk"),
               person(given = "Jing-Hao",
                      family = "Xue",
                      role = "aut"),
               person(given = "Weichuan",
                      family = "Yu",
                      role = "aut"))
as necessary.
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
Maintainer: ‘Yi He <yi.he@stats.oxon.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yi",
                      family = "He",
                      role = c("aut", "cre"),
                      email = "yi.he@stats.oxon.org"),
               person(given = "Yuelin",
                      family = "Zhao",
                      role = "aut"))
as necessary.
Package required but not available: ‘warbleR’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jeffrey Endelman <endelman@wisc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jeffrey",
                    family = "Endelman",
                    role = c("aut", "cre"),
                    email = "endelman@wisc.edu")
as necessary.
Maintainer: ‘Brad Cable <brad@bcable.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Brad",
                    family = "Cable",
                    role = c("aut", "cre"),
                    email = "brad@bcable.net")
as necessary.
Maintainer: ‘Ludovik Çoba <Ludovik.Coba@inf.unibz.it>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘rrecsys.Rd’:
    http://dx.doi.org/10.1109/MC.2009.263
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:
  'spelling', 'vcr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘spelling.R’ [0s/0s]
  Running ‘test-all.R’ [1s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("rredlist")
  Loading required package: rredlist
  Error in `source_dir()`:
  ! Failed to evaluate './helper-rredlist.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("rredlist")
    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-rredlist.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?
Maintainer: ‘Michael Treadwell <michael.treadwell@interworks.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Michael",
                    family = "Treadwell",
                    role = c("aut", "cre"),
                    email = "michael.treadwell@interworks.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) lateformeeting.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:13: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) regrad.Rd:46: Lost braces; missing escapes or markup?
    46 |  \item \code{x-axis} {1st column: The names of the different institutions}
       |                      ^
checkRd: (-1) regrad.Rd:47: Lost braces; missing escapes or markup?
    47 |  \item \code{y-axis} {2nd column: The value to show completeness}
       |                      ^
Packages required but not available: 'xlsx', 'rJava'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Bowen Wang <bowenwang7@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Bowen",
                    family = "Wang",
                    role = c("aut", "cre"),
                    email = "bowenwang7@gmail.com")
as necessary.
Maintainer: ‘Houtao Deng <softwaredeng@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: ‘ecospat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Panos Toulis <panos.toulis@chicagobooth.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Panos",
                    family = "Toulis",
                    role = c("aut", "cre"),
                    email = "panos.toulis@chicagobooth.edu")
as necessary.
checkRd: (-1) rrinf_clust.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{clustering}{A \code{List} that specifies a clustering of datapoint indexes {1, ..., n}. See \link{example_clustering} for details.}
       |                                                                                  ^
checkRd: (-1) rrtest_clust.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{clustering}{A \code{List} that specifies a clustering of datapoint indexes {1, ..., n}.
       |                                                                                  ^
Maintainer: ‘Matthias Greiner <matthias.greiner@bfr.bund.de>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘rriskDistributions-package.Rd’:
    \concept{
      Beta, Normal, Lognormal, Cauhy, Chi-Quad [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?
Packages required but not available: 'Morpho', 'rgl'

Packages suggested but not available for checking:
  'ddpcr', '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:
    ‘sort_tips.Rd’ ‘sort_tips.r’ ‘tips.r’ ‘validate_rankedPhylo.r’
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?
Specified C++11: support will be removed soon
checkRd: (-1) mrrr.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:69-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:71-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:74: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking:
  'rlist', 'ddpcr', 'geomorph', 'rmarkdown', 'knitr', 'kableExtra',
  'rgl', 'Morpho', 'evolqg'

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

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

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

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

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

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

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

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

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: ‘Beatriz Cobo Rodríguez <beacr@ugr.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Beatriz", "Cobo"),
                      family = "Rodríguez",
                      role = c("aut", "cre"),
                      email = "beacr@ugr.es"),
               person(given = c("María", "del", "Mar", "Rueda"),
                      family = "García",
                      role = "aut"),
               person(given = c("Antonio", "Arcos"),
                      family = "Cebrián",
                      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: ‘Prabhanjan Tattar <prabhanjannt@gmail.com>’

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

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘CART_Dummy.Rd’:
    \keyword{CART, partitions}
  File ‘CT.Rd’:
    \keyword{smoothing, hanning}
  File ‘GC.Rd’:
    \keyword{Logistic Regression, Credit data}
  File ‘octane.Rd’:
    \keyword{Histogram, Stem-and-leaf plots}
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', '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:
  '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?
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: ‘Paulo Prado <prado@ib.usp.br>’

The Description field contains
  Resampling Stats (http://www.resample.com) is an add-in for running
Please enclose URLs in angle brackets (<...>).
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: 'leafem', 'leaflet', 'tmap', 'calendR'

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tobias Verbeke <tobias.verbeke@openanalytics.eu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tobias",
                    family = "Verbeke",
                    role = c("aut", "cre"),
                    email = "tobias.verbeke@openanalytics.eu")
as necessary.
Maintainer: ‘Xiuquan (Xander) Wang <xiuquan.wang@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xiuquan",
                      family = "Wang",
                      role = "aut",
                      comment = "Xander"),
               person(given = "Xiuquan",
                      family = "Wang",
                      role = "cre",
                      email = "xiuquan.wang@gmail.com",
                      comment = "Xander"))
as necessary.
checkRd: (-1) rSCA.modeling.Rd:61: Lost braces; missing escapes or markup?
    61 |                 a predefined string to specify how the information of leaf nodes will be stored in the map file. A full list of options for mapvalue is: {mean, max, min, median, interval, radius, variation, random}. Default value is "mean". Use "interval" to get an interval bounded by the minimum and maximum values, (i.e., [min, max]). The option of "radius" will output the mean and the radius [i.e., (max - min) / 2] at the same time. Use "variation" to output the mean and the standard deviation. The option of "random" will output the information as an interval like the "interval" option, but it will use a random value within the interval as the predicted value.
       |                                                                                                                                                          ^
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: '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 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: ‘Sai Chimata <schimata@yotabitesllc.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sai",
                    family = "Chimata",
                    role = c("aut", "cre"),
                    email = "schimata@yotabitesllc.com")
as necessary.
Package required but not available: ‘rsconnect’

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', 'quarto', 'rmarkdown'

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'FactoMineR', '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: ‘Mudassir Shabbir <mudassir.shabbir@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mudassir",
                      family = "Shabbir",
                      role = c("aut", "cre"),
                      email = "mudassir.shabbir@gmail.com"),
               person(given = "Nabil",
                      family = "Mustafa",
                      role = "aut"),
               person(given = "Saurabh",
                      family = "Ray",
                      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: ‘EL KHMISSI Mohamed <mohamed.el-khmissi01@etu.umontpellier.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("EL", "KHMISSI"),
                    family = "Mohamed",
                    role = c("aut", "cre"),
                    email = "mohamed.el-khmissi01@etu.umontpellier.fr")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', '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', 'fdm2id'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optimal_alpha_boot
> ### Title: The optimal alpha for rSDR via bootstrap resampling
> ### Aliases: optimal_alpha_boot
> 
> ### ** Examples
> 
> library(ManifoldOptim)
Loading required package: Rcpp
> library(rSDR)
> library(future)
> library(future.apply)
> utils::data("ionosphere", package = "fdm2id")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘fdm2id’
Calls: <Anonymous> -> find.package
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Mitra Ebrahimpoor<mitra.ebrahimpoor@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mitra",
                    family = "Ebrahimpoor",
                    role = c("aut", "cre"),
                    email = "mitra.ebrahimpoor@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: ‘ggExtra’

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Zhiyong Zhang <zhiyongzhang@nd.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ke-Hai",
                      family = "Yuan",
                      role = "aut"),
               person(given = "Zhiyong",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "zhiyongzhang@nd.edu"))
as necessary.
Maintainer: ‘Subhasree Bose <subhasree10.7@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Subhasree", "Bose", "with", "contributons", "from", "Saptarsi"),
                      family = "Goswami.",
                      role = "aut",
                      email = "subhasree10.7@gmail.com"),
               person(given = "Subhasree",
                      family = "Bose",
                      role = "cre",
                      email = "subhasree10.7@gmail.com"))
as necessary.
Package required but not available: ‘openNLP’

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: ‘Youhua Chen <haydi@126.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Youhua", "Chen,Tsung-Jen"),
                      family = "Shen",
                      role = "aut"),
               person(given = "Youhua",
                      family = "Chen",
                      role = "cre",
                      email = "haydi@126.com"))
as necessary.
Maintainer: ‘Simon Urbanek <Simon.Urbanek@r-project.org>’

Package has FOSS license, installs .class/.jar but has no 'java' directory.

The BugReports field in DESCRIPTION has
  https://github.com/s-u/Rserve
which should likely be
  https://github.com/s-u/Rserve/issues
instead.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘BODY’, ‘FORMALS’, ‘R_Consolefile’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘SET_OBJECT’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’
These entry points may be removed soon:
‘BODY’, ‘FORMALS’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Maintainer: ‘Martin Zaefferer <martin.zaefferer@gmx.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Wolfgang",
                      family = "Konen",
                      role = "aut",
                      email = "wolfgang.konen@fh-koeln.de"),
               person(given = "Martin",
                      family = "Zaefferer",
                      role = c("aut", "cre"),
                      email = "martin.zaefferer@gmx.de"),
               person(given = c("Patrick", "Koch;", "Bug"),
                      family = "hunting",
                      role = "aut"),
               person(given = c("testing", "by", "Ayodele"),
                      family = "Fasika",
                      role = "aut"),
               person(given = "Ashwin",
                      family = "Kumar",
                      role = "aut"),
               person(given = "Prawyn",
                      family = "Jebakumar",
                      role = "aut"))
as necessary.
Packages required but not available:
  'bookdown', 'knitr', 'usethis', 'yaml', 'ymlthis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Brad Cable <brad@bcable.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Brad",
                    family = "Cable",
                    role = c("aut", "cre"),
                    email = "brad@bcable.net")
as necessary.
Maintainer: ‘Jonathan Dench <jdenc017@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jonathan",
                    family = "Dench",
                    role = c("aut", "cre"),
                    email = "jdenc017@gmail.com")
as necessary.
Package required but not available: ‘flextable’

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', 'devtools', '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: '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:
    ‘calculate_indices.Rd’ ‘get_stac_data.R’ ‘get_stac_data.Rd’
    ‘landsat_mask_function.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Yumi Kondo <y.kondo@stat.ubc.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yumi",
                    family = "Kondo",
                    role = c("aut", "cre"),
                    email = "y.kondo@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: ‘Johannes Burkhardt <johannes.burkhardt@gmail.com>’

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

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

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

VignetteBuilder package required for 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 F. Petrowski <pfpetrowski@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Paul", "F."),
                    family = "Petrowski",
                    role = c("aut", "cre"),
                    email = "pfpetrowski@gmail.com")
as necessary.
'library' or 'require' call not declared from: ‘plot3D’
Package required but not available: ‘BayesianTools’

Packages suggested but not available for checking:
  'covr', '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: ‘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 = "Gabe",
                      family = "Becker",
                      role = "aut"),
               person(given = "Jan",
                      family = "Vogel",
                      role = "aut"))
as necessary.
Package required but not available: ‘restfulr’

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.Rnw’
(Is a VignetteBuilder field missing?)

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:
  'quarto', 'knitr', 'rmarkdown', 'spelling', 'usethis'

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: ‘Mark van der Loo <mark.vanderloo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mark",
                    family = "van der Loo",
                    role = c("aut", "cre"),
                    email = "mark.vanderloo@gmail.com")
as necessary.
Package required but not available: ‘validate’

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.
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', 'INLA'

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Theodore",
                    family = "Lytras",
                    role = c("aut", "cre"),
                    email = "thlytras@gmail.com")
as necessary.
Maintainer: ‘Tiago Mendes Dantas <t.mendesdantas@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Tiago", "Mendes"),
                    family = "Dantas",
                    role = c("aut", "cre"),
                    email = "t.mendesdantas@gmail.com")
as necessary.
Maintainer: ‘Melina Vidoni <melinavidoni@santafe-conicet.gov.ar>’

Found the following (possibly) invalid file URIs:
  URI: reference/get_shortest_path.html
    From: inst/doc/igraph.html
  URI: reference/index.html
    From: inst/doc/rsppfp.html
  URI: reference/direct_graph.html
    From: inst/doc/rsppfp.html
  URI: reference/parse_vpath.html
    From: inst/doc/rsppfp.html
  URI: articles/benchmark.html
    From: README.md
  URI: articles/references.html
    From: README.md

Found the following URLs which should use \doi (with the DOI name only):
  File ‘modify_graph_hsu.Rd’:
    https://doi.org/10.1007/978-3-642-03095-6_60
  File ‘modify_graph_vd.Rd’:
    https://doi.org/10.1016/j.ejor.2004.01.032
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Subhasree Bose <subhasree10.7@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Subhasree",
                    family = "Bose",
                    role = c("aut", "cre"),
                    email = "subhasree10.7@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'lintr', '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?
Maintainer: ‘Busra Sevinc <busra.sevincc@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Busra",
                      family = "Sevinc",
                      role = c("aut", "cre"),
                      email = "busra.sevincc@gmail.com"),
               person(given = "Bekir",
                      family = "Cetintav",
                      role = "aut"),
               person(given = "Melek",
                      family = "Esemen",
                      role = "aut"),
               person(given = "Selma",
                      family = "Gurler",
                      role = "aut"))
as necessary.
Maintainer: ‘Rezgar Arabzadeh <rezgararabzadeh@ut.ac.ir>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rezgar",
                      family = "Arabzadeh",
                      role = c("aut", "cre"),
                      email = "rezgararabzadeh@ut.ac.ir"),
               person(given = "Parisa",
                      family = "Aberi",
                      role = "aut"),
               person(given = "Kaveh",
                      family = "Panaghi",
                      role = "aut"),
               person(given = "Shahab",
                      family = "Araghinejad",
                      role = "aut"),
               person(given = "Majid",
                      family = "Montaseri",
                      role = "aut"))
as necessary.
Maintainer: ‘Shawn T. O'Neil <shawn.oneil@cgrb.oregonstate.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Shawn", "T."),
                    family = "O'Neil",
                    role = c("aut", "cre"),
                    email = "shawn.oneil@cgrb.oregonstate.edu")
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.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘geom-funs.R’
Package required but not available: ‘shinystan’

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.
Package required but not available: ‘mixtools’

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:
  'shinystan', '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:
  'usethis', 'knitr', 'roxygen2', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [6s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rstantools)
  This is rstantools version 2.5.0
  > 
  > foo <- function(x) {"test function"}
  > 
  > if (identical(Sys.getenv("TRAVIS"), "true")) {
  +   test_check("rstantools", filter = "methods")
  + } else {
  +   test_check("rstantools")
  + }
  Saving _problems/test-rstan_config-43.R
  Saving _problems/test-rstan_create_package-66.R
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 42 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-rstan_config.R:40:1'): (code run outside of `test_that()`) ─────
  Error: Please install package 'usethis' to use function 'rstan_create_package'.
  Backtrace:
      ▆
   1. └─rstantools::rstan_create_package(...) at test-rstan_config.R:40:1
  ── Error ('test-rstan_create_package.R:63:5'): (code run outside of `test_that()`) ──
  Error: Please install package 'usethis' to use function 'rstan_create_package'.
  Backtrace:
      ▆
   1. └─rstantools::rstan_create_package(...) at test-rstan_create_package.R:63:5
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 42 ]
  Error:
  ! Test failures.
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Xuehui YANG <jianghang@bagualu.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Xuehui",
                    family = "YANG",
                    role = c("aut", "cre"),
                    email = "jianghang@bagualu.net")
as necessary.
Maintainer: ‘Peter Hoff <peter.hoff@duke.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Peter",
                      family = "Hoff",
                      role = c("aut", "cre"),
                      email = "peter.hoff@duke.edu"),
               person(given = "Alexander",
                      family = "Franks",
                      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 required but not available: ‘googleway’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Josef Leydold <josef.leydold@wu.ac.at>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Josef",
                    family = "Leydold",
                    role = c("aut", "cre"),
                    email = "josef.leydold@wu.ac.at")
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?
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Rsubbotools)
  > test_check("Rsubbotools")
  Error in `source_dir()`:
  ! Failed to evaluate './helper_functions.R'.
  Caused by error in `library()`:
  ! there is no package called 'usethis'
  Backtrace:
       ▆
    1. ├─testthat::test_check("Rsubbotools")
    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(usethis) at ./helper_functions.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
Maintainer: ‘Martin Atzmueller <martin@atzmueller.net>’

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

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: ‘Layla Parast <parast@austin.utexas.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Layla",
                    family = "Parast",
                    role = c("aut", "cre"),
                    email = "parast@austin.utexas.edu")
as necessary.
Maintainer: ‘Rohan Sadler <rohan.sadler@ausvet.com.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Evan",
                      family = "Sergeant",
                      role = "aut"),
               person(given = "Rohan",
                      family = "Sadler",
                      role = "cre",
                      email = "rohan.sadler@ausvet.com.au"))
as necessary.
Package required but not available: ‘epiR’

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:
    ‘lp.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?
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/1s]
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?
Maintainer: ‘Kasper Welbers <kasperwelbers@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Kasper",
                      family = "Welbers",
                      role = c("aut", "cre"),
                      email = "kasperwelbers@gmail.com"),
               person(given = "Wouter",
                      family = "van Atteveldt",
                      role = "aut"))
as necessary.
Package required but not available: ‘keyring’

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: ‘Johan Jordaan <djjordaan@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Johan",
                    family = "Jordaan",
                    role = c("aut", "cre"),
                    email = "djjordaan@gmail.com")
as necessary.
Maintainer: ‘Haydar Demirhan <haydar.demirhan@rmit.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Haydar",
                    family = "Demirhan",
                    role = c("aut", "cre"),
                    email = "haydar.demirhan@rmit.edu.au")
as necessary.
Package required but not available: ‘flextable’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Miron B. Kursa <M.Kursa@icm.edu.pl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Miron", "B."),
                    family = "Kursa",
                    role = c("aut", "cre"),
                    email = "m.kursa@icm.edu.pl")
as necessary.
Maintainer: ‘David Zarruk Valencia <davidzarruk@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("David", "Zarruk", "Valencia", "&", "Rodrigo", "Azuero"),
                      family = "Melo",
                      role = "aut"),
               person(given = c("David", "Zarruk"),
                      family = "Valencia",
                      role = "cre",
                      email = "davidzarruk@gmail.com"))
as necessary.
Maintainer: ‘John Ruscio <ruscio@tcnj.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "John",
                      family = "Ruscio",
                      role = c("aut", "cre"),
                      email = "ruscio@tcnj.edu"),
               person(given = "Shirley",
                      family = "Wang",
                      role = "aut",
                      email = "shirleywang@g.harvard.edu"))
as necessary.
Maintainer: ‘Mateu Menendez-Serra <mateu.menendez@ceab.csic.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mateu",
                      family = "Menendez-Serra",
                      role = c("aut", "cre"),
                      email = "mateu.menendez@ceab.csic.es"),
               person(given = c("Vicente", "J."),
                      family = "Ontiveros",
                      role = "aut"),
               person(given = c("Emilio", "O."),
                      family = "Casamayor",
                      role = "aut"),
               person(given = "David",
                      family = "Alonso",
                      role = "aut"))
as necessary.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘RTCC.Rd’:
    https://doi.org/10.1038/s41396-019-0454-4
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’
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                              ^
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                                    ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mockery)
  > library(RTD)
  > 
  > test_check("RTD")
  Saving _problems/test-td-24.R
  Saving _problems/test-td-45.R
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-td.R:12:3'): td_upload works with mock ─────────────────────────
  <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-td.R:12:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  ── Error ('test-td.R:32:3'): td_upload works with mock when the table already exists ──
  <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-td.R:32:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  Error:
  ! Test failures.
  Execution halted
Maintainer: ‘Claas-Thido Pfaff <claas-thido.pfaff@idiv-biodiversity.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Claas-Thido",
                    family = "Pfaff",
                    role = c("aut", "cre"),
                    email = "claas-thido.pfaff@idiv-biodiversity.de")
as necessary.
Packages required but not available: 'FactoMineR', 'explor'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jake Anderson <ajakef@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jake",
                    family = "Anderson",
                    role = c("aut", "cre"),
                    email = "ajakef@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: ‘Loren Collingwood <loren.collingwood@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Timothy", "P."),
                      family = "Jurka",
                      role = "aut"),
               person(given = "Loren",
                      family = "Collingwood",
                      role = c("aut", "cre"),
                      email = "loren.collingwood@gmail.com"),
               person(given = c("Amber", "E."),
                      family = "Boydstun",
                      role = "aut"),
               person(given = "Emiliano",
                      family = "Grossman",
                      role = "aut"),
               person(given = "Wouter",
                      family = "van Atteveldt",
                      role = "aut"))
as necessary.
Maintainer: ‘Lingxiao Li <lilingxiao@mail.sdu.edu.cn>’

The Description field contains
  discussed in Barigozzi et al. (2022) <arXiv:2206.09800>, and Barigozzi
  et al. (2023) <arXiv:2303.18163>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
Package required but not available: ‘knitr’

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

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

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?
Packages required but not available:
  'rmarkdown', 'bookdown', 'htmlwidgets', 'knitr'

Package suggested but not available for checking: ‘leaflet’

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: ‘Tomas Okal <tomas.okal@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tomas",
                    family = "Okal",
                    role = c("aut", "cre"),
                    email = "tomas.okal@gmail.com")
as necessary.
Maintainer: ‘Paul Saary <rtk@paulsaary.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Paul",
                      family = "Saary",
                      role = c("aut", "cre"),
                      email = "rtk@paulsaary.de"),
               person(given = "Falk",
                      family = "Hildebrand",
                      role = "aut"))
as necessary.
Specified C++11: support will be removed soon
Packages required but not available: 'knitr', 'gt', 'bookdown'

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

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

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:
    ‘str_rtl.Rd’
Packages required but not available: 'lidR', 'keras', 'rgl', 'tensorflow'

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

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

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', '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:
  > # 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(rtoot)
  > 
  > test_check("rtoot")
  Error in `source_dir()`:
  ! Failed to evaluate './setup-rtoot.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("rtoot")
    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-rtoot.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', 'tidyverse'

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

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

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’
checkRd: (-1) rt_GET.Rd:13: Lost braces
    13 | code{\link[httr]{GET}} (\code{TRUE}) or not (\code{FALSE})}
       |     ^
checkRd: (-1) rt_POST.Rd:13: Lost braces
    13 | code{\link[httr]{POST}} (\code{TRUE}) or not (\code{FALSE})}
       |     ^
Package has ‘vignettes’ subdirectory 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: ‘Avi Blinder <aviblinder@gmail.com>’

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘Houjie Wang <wanghoujie6688@gmail.com>’

The Description field contains
  Wang, H. & Yoshida, R. (2020) <arXiv:2003.00677>. Details about
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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

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

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

The Description field contains
  (https://github.com/tercen/TSON).
Please enclose URLs in angle brackets (<...>).
Maintainer: ‘Babak Naimi <naimi.b@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Babak",
                    family = "Naimi",
                    role = c("aut", "cre"),
                    email = "naimi.b@gmail.com")
as necessary.
checkRd: (-1) rts.Rd:32: Lost braces
    32 | If a name of a raster time series file is provided for the \code{x} argument, it acts the same as code{\link[rts]{read.rts}}.
       |                                                                                                       ^
Maintainer: ‘Chanseok Park <statpnu@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.

The Description field contains
  Park and Wang (2018)<arXiv:1807.02215>. This work was partially
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:
  'spelling', 'knitr', 'rmarkdown', 'vcr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
No news entries found.
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(testthat)
  > library(RTTWebClient)
  > test_check("RTTWebClient")
  Error in `source_dir()`:
  ! Failed to evaluate './setup-RTTWebClient.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("RTTWebClient")
    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]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(...)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at ./setup-RTTWebClient.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<S3: packageNotFoundError>`)
   17.   └─cli::cli_abort(...)
   18.     └─rlang::abort(...)
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(Rtumblr)
  > 
  > test_check("Rtumblr")
  Error in `source_dir()`:
  ! Failed to evaluate './setup-Rtumblr.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("Rtumblr")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", 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-Rtumblr.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 required but not available: ‘rgl’

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

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: ‘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?
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:
  'DT', 'flextable', 'formods', 'onbrand', 'plotly', 'rhandsontable',
  'yaml'

Packages suggested but not available for checking:
  'babelmixr2', 'knitr', 'nlmixr2lib', 'nlmixr2', 'rmarkdown',
  'shinybusy', 'ubiquity'

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:
  'bookdown', 'gtsummary', 'quarto', 'rmarkdown', 'roxygen2', 'table1',
  'tidyverse', 'usethis'

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', 'covr', '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?
Maintainer: ‘Bryan Jenks <bryanjenks@protonmail.com>’

The BugReports field in DESCRIPTION has
  https://github.com/tallguyjenks/runes
which should likely be
  https://github.com/tallguyjenks/runes/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.
Cannot process vignettes
Packages suggested but not available for checking:
  'modeest', 'knitr', 'spelling'

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mauricio",
                    family = "Santelices",
                    role = c("aut", "cre"),
                    email = "m.santelicesa@gmail.com")
as necessary.
Maintainer: ‘Johann Gagnon-Bartsch <johanngb@umich.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Johann",
                    family = "Gagnon-Bartsch",
                    role = c("aut", "cre"),
                    email = "johanngb@umich.edu")
as necessary.
checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^
Package required but not available: ‘FactoMineR’

Package suggested but not available for checking: ‘mixOmics’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Valpha.Rd:15: Lost braces; missing escapes or markup?
    15 |   \item{V}{a numeric vector with (i,j) entry: V[i,j] = P(theta_{i} >= theta[alpha_{j}]|data) }
       |                                                                ^
checkRd: (-1) Valpha.Rd:15: Lost braces; missing escapes or markup?
    15 |   \item{V}{a numeric vector with (i,j) entry: V[i,j] = P(theta_{i} >= theta[alpha_{j}]|data) }
       |                                                                                   ^
Maintainer: ‘Etor Arza <etorarza@gmail.com>’

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

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

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("rvertnet")
  > 
  > test_check("rvertnet")
  Error in `source_dir()`:
  ! Failed to evaluate './helper-rvertnet.R'.
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("rvertnet")
    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-rvertnet.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:
  '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: ‘Wei Guo <wei.guo3@nih.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Wei",
                    family = "Guo",
                    role = c("aut", "cre"),
                    email = "wei.guo3@nih.gov")
as necessary.
Maintainer: ‘Charles Determan Jr <cdetermanjr@gmail.com>’

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

Found the following (possibly) invalid file URI:
  URI: CRAN.R-project.org
    From: README.md
Maintainer: ‘Alun Thomas <Alun.Thomas@utah.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alun",
                    family = "Thomas",
                    role = c("aut", "cre"),
                    email = "alun.thomas@utah.edu")
as necessary.
Package required but not available: ‘rJava’

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?
No examples, no tests, no vignettes
Maintainer: ‘Alexey Seleznev <selesnow@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alexey",
                    family = "Seleznev",
                    role = c("aut", "cre"),
                    email = "selesnow@gmail.com")
as necessary.
Maintainer: ‘Parker Holzer <parker.holzer@yale.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Parker",
                    family = "Holzer",
                    role = c("aut", "cre"),
                    email = "parker.holzer@yale.edu")
as necessary.

The Description field contains
  <arXiv:2005.14083>, which is a particular application of the radial
  al. (2020) <arXiv:2005.14083> when publishing results that use this
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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Navarro Fabien <fnavarro@math.cnrs.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "F.",
                      family = "Navarro",
                      role = "aut"),
               person(given = "C.",
                      family = "Chesneau",
                      role = "aut"),
               person(given = "Navarro",
                      family = "Fabien",
                      role = "cre",
                      email = "fnavarro@math.cnrs.fr"))
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) HardThresh.Rd:15: Lost braces; missing escapes or markup?
    15 | \code{x} filtered result (y 1_{|y|>t}).
       |                               ^
checkRd: (-1) SoftThresh.Rd:15: Lost braces; missing escapes or markup?
    15 | \code{x} filtered result (y 1_{|y|>t}).
       |                               ^
Package has ‘vignettes’ subdirectory 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', '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: ‘rJava’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Mafalda Sá Ferreira <msm.ferreira@campus.fct.unl.pt>’

The Description field contains
  <arXiv:2112.07508v3> and Oliveira et al. (2021) <arXiv:2102.05373v2>.
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', 'covr', 'spelling', 'rmarkdown'

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Brad",
                    family = "Cable",
                    role = c("aut", "cre"),
                    email = "brad@bcable.net")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', '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: ‘marked’

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Andy South <southandy@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Andy",
                    family = "South",
                    role = c("aut", "cre"),
                    email = "southandy@gmail.com")
as necessary.
Malformed Title field: should not end in a period.
Package required but not available: ‘networkD3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Eric Hare <eric@omnianalytics.io>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alex",
                      family = "Shum",
                      role = "aut",
                      email = "alex@ALShum.com"),
               person(given = "Eric",
                      family = "Hare",
                      role = "cre",
                      email = "eric@omnianalytics.io"))
as necessary.
Packages required but not available: 'rJava', 'rcdk'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Running examples in ‘rxode2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: .rxDocTable
> ### Title: Print out a table in the documentation
> ### Aliases: .rxDocTable
> ### Keywords: internal
> 
> ### ** Examples
> 
> .rxDocTable(rxReservedKeywords)
Error: package "knitr" needed for this function to work
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:
  'devtools', 'exams', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Found the following significant warnings:
  yacas/include/yacas/utf8/checked.h:268:34: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  yacas/include/yacas/utf8/unchecked.h:179:40: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Ryacas0.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-15 (Debian 15.2.0-9) 15.2.0’
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:
  'devtools', 'exams', 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Mukul Chaware <mukul.chaware13@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mukul",
                    family = "Chaware",
                    role = c("aut", "cre"),
                    email = "mukul.chaware13@gmail.com")
as necessary.

The Description field contains
  'Yandex Translate' (https://translate.yandex.com/) is a statistical
  https://tech.yandex.com/translate/doc/dg/concepts/About-docpage/ .
Please enclose URLs in angle brackets (<...>).
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for 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 August <tomaug@ceh.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tom",
                    family = "August",
                    role = c("aut", "cre"),
                    email = "tomaug@ceh.ac.uk")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', '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: 'factoextra', 'FactoMineR'

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.
Maintainer: ‘Joris Bierkens <j.bierkens@vu.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Joris",
                    family = "Bierkens",
                    role = c("aut", "cre"),
                    email = "j.bierkens@vu.nl")
as necessary.

The Description field contains
  <arXiv:1607.03188> applied and Bouncy Particle Sampler
  <arXiv:1510.02451> for a Gaussian target and Student distribution.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) ZigZagLogistic.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                   ^
checkRd: (-1) ZigZagLogistic.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                                 ^
checkRd: (-1) ZigZagLogistic.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{dataY}{Vector of length n containing {0, 1}-valued observations of the dependent variable y.}
       |                                            ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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) ciReg.Rd:10: Lost braces
    10 | \item{fit}{an object of class{lm}, i.e. the output from \code{\link{lm}}.}
       |                              ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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:
    ‘s3_check_for_file.R’ ‘s3_file_size.R’ ‘s3_get.Rd’ ‘s3_get_files.R’
    ‘s3_parse_uri.R’
Package required but not available: ‘sparklyr’

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’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘fit_density_ratio.R’ ‘fit_plug_and_play.R’
Package has ‘vignettes’ subdirectory 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: ‘Zhongyang Zhang <zhongyang.zhang@mssm.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhongyang",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "zhongyang.zhang@mssm.edu"),
               person(given = "Ke",
                      family = "Hao",
                      role = "aut"),
               person(given = c("Nancy", "R."),
                      family = "Zhang",
                      role = "ctb"))
as necessary.
Maintainer: ‘Jakub Nowosad <nowosad.jakub@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'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', '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: ‘Zhong Guan <zguan@iusb.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Zhong",
                    family = "Guan",
                    role = c("aut", "cre"),
                    email = "zguan@iusb.edu")
as necessary.
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: 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?
Maintainer: ‘Rampal S. Etienne <r.s.etienne@rug.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Rampal", "S.", "Etienne", "&", "Bart"),
                      family = "Haegeman",
                      role = "aut"),
               person(given = c("Rampal", "S."),
                      family = "Etienne",
                      role = "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’
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/sadists.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'config', 'DT', 'golem', 'htmlwidgets', 'leaflet', 'SUMMER',
  'surveyPrev', 'bookdown', 'leaflegend', 'leafsync', 'plotly'

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Sheerin Dahwan Aziz <sheerindahwan@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Azka",
                      family = "Ubaidillah",
                      role = "aut"),
               person(given = c("Sheerin", "Dahwan"),
                      family = "Aziz",
                      role = c("aut", "cre"),
                      email = "sheerindahwan@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: ‘Rizki Ananda Fauziah <rizkiananda133@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Rizki", "Ananda"),
                      family = "Fauziah",
                      role = c("aut", "cre"),
                      email = "rizkiananda133@gmail.com"),
               person(given = c("Ika", "Yuni"),
                      family = "Wulansari",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Velia Tri Marliana <221810642@stis.ac.id>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Velia", "Tri"),
                      family = "Marliana",
                      role = c("aut", "cre"),
                      email = "221810642@stis.ac.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’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Rizqina Rahmati <221810583@stis.ac.id>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rizqina",
                      family = "Rahmati",
                      role = c("aut", "cre"),
                      email = "221810583@stis.ac.id"),
               person(given = "Azka",
                      family = "Ubaidillah",
                      role = "aut"))
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: ‘Wicak Surya Hasani <221710052@stis.ac.id>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Wicak", "Surya"),
                      family = "Hasani",
                      role = c("aut", "cre"),
                      email = "221710052@stis.ac.id"),
               person(given = "Azka",
                      family = "Ubaidillah",
                      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?
Package required but not available: ‘FSelector’

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

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: ‘Yolanda Marhuenda <y.marhuenda@umh.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Isabel",
                      family = "Molina",
                      role = "aut"),
               person(given = "Yolanda",
                      family = "Marhuenda",
                      role = c("aut", "cre"),
                      email = "y.marhuenda@umh.es"))
as necessary.
Maintainer: ‘Sebastian Warnholz <wahani@gmail.com>’

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

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

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

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

VignetteBuilder package required 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: ‘emdi’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Asun Lubiano <lubiano@uniovi.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Wolfgang",
                      family = "Trutschnig",
                      role = "aut",
                      email = "wolfgang@trutschnig.net"),
               person(given = "Asun",
                      family = "Lubiano",
                      role = c("aut", "cre"),
                      email = "lubiano@uniovi.es"))
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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘Alexander Ly <a.ly@jasp-stats.org>’

The Description field contains
  (2019) "Safe Testing" <arXiv:1906.07801>, for details on safe logrank
  Horizon" <arXiv:2011.06931v3> and Turner, Ly and Grunwald (2021) "Safe
  beyond" <arXiv:2106.02693> for details on safe contingency table tests.
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?
Packages required but not available:
  'DT', 'htmlwidgets', 'plotly', 'Tendril'

Packages suggested but not available for checking:
  'shinytest', 'safetyGraphics', 'yaml'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'datamods', 'htmlwidgets', 'safetyCharts', 'sortable', 'yaml'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'shinytest', 'usethis', 'listviewer',
  'shinybusy'

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: 'formattable', 'knitr'

Package suggested but not available for checking: ‘vote’

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

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: ‘Santos J. González-Rojí <santosjose.gonzalez@ehu.eus>’

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 ‘Dragonera.Rd’:
    https://doi.org/10.1016/j.apenergy.2017.09.030
  File ‘EstacaDeBares.Rd’:
    https://doi.org/10.1016/j.oceaneng.2015.05.038
    https://doi.org/10.1109/JOE.2016.2529400
  File ‘SailoR-package.Rd’:
    https://doi.org/10.5194/gmd-13-3221-2020
  File ‘WRF.Rd’:
    https://doi.org/10.1002/2017JD027511
    https://doi.org/10.1007/s00382-019-04673-9
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:
    ‘class-2-differential.r’ ‘dual-apply.r’ ‘dual-math.r’
    ‘dual-summary.r’ ‘dual-test-near-equality.r’ ‘dual.r’ ‘dualFun1.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rlist’

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: ‘Yuwen Gu <yuwen.gu@uconn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yuwen",
                      family = "Gu",
                      role = c("aut", "cre"),
                      email = "yuwen.gu@uconn.edu"),
               person(given = "Hui",
                      family = "Zou",
                      role = "aut",
                      email = "zouxx019@umn.edu"))
as necessary.
Package required but not available: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Scott Vander Wiel <scottv@lanl.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hannah",
                      family = "Director",
                      role = "aut"),
               person(given = c("Scott", "Vander"),
                      family = "Wiel",
                      role = c("aut", "cre"),
                      email = "scottv@lanl.gov"),
               person(given = "James",
                      family = "Gattiker",
                      role = "aut"))
as necessary.
Maintainer: ‘Alexander Rix <alexrix@umich.edu>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘approxdist.Rd’:
    https://doi.org/10.1101/2019.12.26.19015859
  File ‘nonlogistic.Rd’:
    https://doi.org/10.1101/2019.12.26.19015859
  File ‘obsloglik.Rd’:
    https://doi.org/10.1101/2019.12.26.19015859
  File ‘obsloglikEM.Rd’:
    https://doi.org/10.1101/2019.12.26.19015859
  File ‘sensitivity.Rd’:
    https://doi.org/10.1101/2019.12.26.19015859
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Norbert Krautenbacher <norbert.krautenbacher@tum.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Norbert",
                      family = "Krautenbacher",
                      role = c("aut", "cre"),
                      email = "norbert.krautenbacher@tum.de"),
               person(given = "Kevin",
                      family = "Strauss",
                      role = "aut"),
               person(given = "Maximilian",
                      family = "Mandl",
                      role = "aut"),
               person(given = "Christiane",
                      family = "Fuchs",
                      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 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: ‘Michael Baldassaro <mbaldassaro@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Michael",
                    family = "Baldassaro",
                    role = c("aut", "cre"),
                    email = "mbaldassaro@gmail.com")
as necessary.
Maintainer: ‘Arne Henningsen <arne.henningsen@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) binaryChoice.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:111: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:113: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:114: Lost braces in \itemize; \value handles \item{}{} directly
Running ‘Mroz87SelectionTest.R’ [3s/3s]
  Comparing ‘Mroz87SelectionTest.Rout’ to ‘Mroz87SelectionTest.Rout.save’ ... OK
  Running ‘binarySelectionOutcome.R’ [7s/8s]
  Comparing ‘binarySelectionOutcome.Rout’ to ‘binarySelectionOutcome.Rout.save’ ... OK
  Running ‘fail.R’ [2s/2s]
  Comparing ‘fail.Rout’ to ‘fail.Rout.save’ ... OK
  Running ‘heckitIvTest.R’ [2s/2s]
  Comparing ‘heckitIvTest.Rout’ to ‘heckitIvTest.Rout.save’ ... OK
  Running ‘intervalTest.R’ [9s/10s]
  Comparing ‘intervalTest.Rout’ to ‘intervalTest.Rout.save’ ... OK
  Running ‘invMillsRatioTest.R’ [10s/11s]
  Comparing ‘invMillsRatioTest.Rout’ to ‘invMillsRatioTest.Rout.save’ ...30a31,37
> 
> Attaching package: 'VGAM'
> 
> The following object is masked from 'package:sampleSelection':
> 
>     probit
> 
75a83,84
> 
> No Hauck-Donner effect found in any of the estimates
  Running ‘probit.R’ [3s/3s]
  Comparing ‘probit.Rout’ to ‘probit.Rout.save’ ... OK
  Running ‘selection.R’ [11s/12s]
  Comparing ‘selection.Rout’ to ‘selection.Rout.save’ ... OK
Maintainer: ‘Hongchao Qi <hcqi1992@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hongchao",
                      family = "Qi",
                      role = c("aut", "cre"),
                      email = "hcqi1992@gmail.com"),
               person(given = "Fang",
                      family = "Zhu",
                      role = "aut"))
as necessary.
Maintainer: ‘Hugo Andres Gutierrez Rojas <hagutierrezro@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Hugo", "Andres", "Gutierrez"),
                    family = "Rojas",
                    role = c("aut", "cre"),
                    email = "hagutierrezro@gmail.com")
as necessary.
Cannot process vignettes
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: ‘DT’

Packages suggested but not available for checking:
  'roxygen2', '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:
  '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: ‘William Wheeler <WheelerB@imsweb.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Mitchell", "H."),
                      family = "Gail",
                      role = "aut"),
               person(given = "William",
                      family = "Wheeler",
                      role = "cre",
                      email = "WheelerB@imsweb.com"))
as necessary.
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.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jonathan",
                      family = "Lisic",
                      role = c("aut", "cre"),
                      email = "jlisic@gmail.com"),
               person(given = "Anton",
                      family = "Grafström",
                      role = "aut"))
as necessary.
Maintainer: ‘Juliane Manitz <r@manitz.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Juliane",
                      family = "Manitz",
                      role = c("aut", "cre"),
                      email = "r@manitz.org"),
               person(given = "Mark",
                      family = "Hempelmann",
                      role = "ctb"),
               person(given = "Goeran",
                      family = "Kauermann",
                      role = "ctb"),
               person(given = "Helmut",
                      family = "Kuechenhoff",
                      role = "aut"),
               person(given = "Shuai",
                      family = "Shao",
                      role = "ctb"),
               person(given = "Cornelia",
                      family = "Oberhauser",
                      role = "ctb"),
               person(given = "Nina",
                      family = "Westerheide",
                      role = "ctb"),
               person(given = "Manuel",
                      family = "Wiesenfarth",
                      role = "ctb"))
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: ‘Diana Trutschel <Diana.Trutschel@dzne.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Diana",
                      family = "Trutschel",
                      role = c("aut", "cre"),
                      email = "diana.trutschel@dzne.de"),
               person(given = "Hendrik",
                      family = "Treutler",
                      role = "aut"))
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/my-vignette.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?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'formattable'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Emilio Lopez Escobar <emilio@quantos.mx>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Emilio", "Lopez"),
                      family = "Escobar",
                      role = c("aut", "cre", "cph"),
                      email = "emilio@quantos.mx"),
               person(given = c("Ernesto", "Barrios"),
                      family = "Zamudio",
                      role = "ctb",
                      email = "ebarrios@itam.mx"),
               person(given = c("Juan", "Francisco", "Munoz"),
                      family = "Rosas",
                      role = "ctb",
                      email = "jfmunoz@go.ugr.es"))
as necessary.

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', '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?
Maintainer: ‘Haoming Jiang <jianghm.ustc@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Haoming",
                      family = "Jiang",
                      role = c("aut", "cre"),
                      email = "jianghm.ustc@gmail.com"),
               person(given = "Yukun",
                      family = "Ma",
                      role = "aut"),
               person(given = "Han",
                      family = "Liu",
                      role = "aut"),
               person(given = "Kathryn",
                      family = "Roeder",
                      role = "aut"),
               person(given = "Xingguo",
                      family = "Li",
                      role = "aut"),
               person(given = "Tuo",
                      family = "Zhao",
                      role = "aut"))
as necessary.
Specified C++11: support will be removed soon
Maintainer: ‘Rob Tibshirani <tibs@stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "R.",
                      family = "Tibshirani",
                      role = "aut"),
               person(given = c("Michael", "J."),
                      family = "Seo",
                      role = "aut"),
               person(given = "G.",
                      family = "Chu",
                      role = "aut"),
               person(given = "Balasubramanian",
                      family = "Narasimhan",
                      role = "aut"),
               person(given = "Jun",
                      family = "Li",
                      role = "aut"),
               person(given = "Rob",
                      family = "Tibshirani",
                      role = "cre",
                      email = "tibs@stanford.edu"))
as necessary.
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
Package required but not available: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jiayi Ji <Jiayi.Ji@mountsinai.org>’

The Description field contains
  cancer data <arXiv:2012.06093>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Florian Lecocq <florian.lecocq@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.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘samurais-package.Rd’:
    https://doi.org/10.1002/widm.1298
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
checkRd: (-1) ModelHMMR-class.Rd:37: Lost braces; missing escapes or markup?
    37 |         class {StatHMMR}).
       |               ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Alireza S. Mahani <alireza.s.mahani@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Mansour", "T.A."),
                      family = "Sharabiani",
                      role = "aut"),
               person(given = c("Alireza", "S."),
                      family = "Mahani",
                      role = c("aut", "cre"),
                      email = "alireza.s.mahani@gmail.com"))
as necessary.
Maintainer: ‘Robert Myles McDonnell <robertmylesmcdonnell@gmail.com>’

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

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

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

VignetteBuilder package required for 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: c(person(given = "Gábor",
                      family = "Csárdi",
                      role = c("aut", "cre"),
                      email = "csardi.gabor@gmail.com"),
               person(given = "January",
                      family = "Weiner",
                      role = "aut"))
as necessary.
Package required but not available: ‘htmlwidgets’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Maintainer: ‘Murtaza Nasir <mail@murtaza.cc>’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [65s/72s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(santoku)
  > 
  > test_check("santoku")
  Saving _problems/test-breaks-190.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 10591 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-breaks.R:190:3'): brk_quantiles ────────────────────────────────
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `brk_quantiles(1:3/4, weights = 1:10)(x, FALSE, TRUE, FALSE)`: The package "Hmisc" is required to use `weights` in brk_quantiles()
  Backtrace:
      ▆
   1. └─brk_quantiles(1:3/4, weights = 1:10)(x, FALSE, TRUE, FALSE) at test-breaks.R:190:3
   2.   └─rlang::check_installed("Hmisc", reason = "to use `weights` in brk_quantiles()")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 10591 ]
  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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from 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:
    ‘cmc_psat.Rd’ ‘h-fun.R’ ‘mc-test.R’ ‘tshift.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Masami Saga <msaga@mtb.biglobe.ne.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("The", "Institute", "of", "Statistical"),
                      family = "Mathematics",
                      role = "aut"),
               person(given = "Masami",
                      family = "Saga",
                      role = "cre",
                      email = "msaga@mtb.biglobe.ne.jp"))
as necessary.
Maintainer: ‘Stuart K. Grange <stuart.grange@york.ac.uk>’

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?
Error(s) in re-building vignettes:
  ...
--- re-building ‘garch_tests_example.Rnw’ using Sweave
Loading required package: stats4

Attaching package: ‘sarima’

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

    spectrum


Error: processing vignette 'garch_tests_example.Rnw' failed with diagnostics:
 chunk 2 (label = setup) 
Error in library("fGarch") : there is no package called ‘fGarch’

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

--- re-building ‘white_noise_tests.Rnw’ using Sweave
Loading required package: stats4

Attaching package: ‘sarima’

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

    spectrum

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

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

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

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

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: ‘ggiraph’

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dtwSP
> ### Title: Calculate DTW alignment of two snow profiles
> ### Aliases: dtwSP
> 
> ### ** Examples
> 
> 
> ## Align a modeled and a manual snow profile, primarily based on default settings:
> dtwAlignment <- dtwSP(SPpairs$A_modeled, SPpairs$A_manual, open.end = FALSE)
Error in r[i1] - r[if (lag < (len <- length(r))) -len:-(len - lag + 1L) else i0] : 
  non-numeric argument to binary operator
Calls: dtwSP ... format_snowprofileLayers -> snowprofileLayers -> diff -> diff.default
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Steven Walker <steve.walker@utoronto.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Original", "by"),
                      family = "Littell",
                      role = "aut"),
               person(family = "Milliken",
                      role = "aut"),
               person(family = "Stroup",
                      role = "aut"),
               person(family = "Wolfinger",
                      role = "aut"),
               person(given = c("modifications", "by", "Douglas"),
                      family = "Bates",
                      role = "aut",
                      email = "bates@stat.wisc.edu"),
               person(given = "Martin",
                      family = "Maechler",
                      role = "aut"),
               person(given = "Ben",
                      family = "Bolker",
                      role = "aut"),
               person(given = "Steven",
                      family = "Walker",
                      role = c("aut", "cre"),
                      email = "steve.walker@utoronto.ca"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently 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’
checkRd: (-1) gen.ds.Rd:43-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gen.ds.Rd:50-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gen.ds.Rd:64-65: Lost braces
    64 |    \item{the dependence parameter \code{dep} or the vector of dependence parameters \code{dep}. When missing, these coefficients are obtained from independent standard uniform sampling.
       |         ^
checkRd: (-1) gen.ds.Rd:66: Lost braces
    66 |    \item{the list \code{asy} of asymmetric weights \eqn{\beta_{i,b}} for \eqn{b \in B}  and \eqn{i \in b}. When missing, these coefficients are obtained from independent standard uniform sampling followed by renormalization in order to satisfy the sum-to-one constraints.}
       |         ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: '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:
    ‘as_SpatRaster.Rd’ ‘clip_bands.Rd’ ‘get_band_names.Rd’
    ‘get_spatial_resolution.Rd’ ‘get_spectral_band_names.Rd’
    ‘merge_tiles.Rd’ ‘save_by_resolution.Rd’ ‘select_bands.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'BSgenome.Hsapiens.UCSC.hg19', 'BSgenome.Hsapiens.UCSC.hg38'

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

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: ‘Mo Huang <mohuangx@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.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘SAVER-package.Rd’:
    https://doi.org/10.1038/s41592-018-0033-z
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Michael P. Fay <mfay@niaid.nih.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Michael", "P."),
                    family = "Fay",
                    role = c("aut", "cre"),
                    email = "mfay@niaid.nih.gov")
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: ‘Tiago Santos <teixeiradossantos@tugraz.at>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Layla Parast <parast@austin.utexas.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Layla",
                    family = "Parast",
                    role = c("aut", "cre"),
                    email = "parast@austin.utexas.edu")
as necessary.
Maintainer: ‘Viktoriya Krakovna <vkrakovna@gmail.com>’

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

The Description field contains
  (2015), <arXiv:1506.02371>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
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
Package suggested but not available for checking: ‘knitr’

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) setData.ReducedRankRegressions.Rd:14-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setData.ReducedRankRegressions.Rd:17-18: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory 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: ‘Meiyue Wang <mwang024@ucr.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Meiyue",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "mwang024@ucr.edu"),
               person(given = "Shizhong",
                      family = "Xu",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown', '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: ‘Arash A. Amini <amini.aa@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Arash", "A."),
                    family = "Amini",
                    role = c("aut", "cre"),
                    email = "amini.aa@gmail.com")
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘sbmSDP-package.Rd’:
    \keyword{ 
      community detection
      stochastic block mo [TRUNCATED]
Maintainer: ‘Matthew Ludkin <m.ludkin1@lancaster.ac.uk>’

The Description field contains
  <doi:10.1080/10618600.2000.10474879>; Ludkin (2019) <arXiv:1909.09421>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘drawblock.dp.Rd’:
    http://doi.org/10.17635/lancaster/thesis/296
  File ‘sampler.dp.Rd’:
    http://doi.org/10.17635/lancaster/thesis/296
  File ‘sampler.rj.Rd’:
    http://doi.org/10.17635/lancaster/thesis/296
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Frank D. Mann <frankdmann@gmail.com>’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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: ‘Simon Urbanek <simon.urbanek@r-project.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Lee",
                      family = "Wilkinson",
                      role = "aut",
                      email = "leland.wilkinson@gmail.com"),
               person(given = "Anushka",
                      family = "Anand",
                      role = "aut"),
               person(given = "Simon",
                      family = "Urbanek",
                      role = "cre",
                      email = "simon.urbanek@r-project.org"))
as necessary.
Package required but not available: ‘rJava’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: support will be removed soon
Maintainer: ‘Niloy Biswas <niloy_biswas@g.harvard.edu>’

The Description field contains
  <arXiv:2204.01668>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Author field differs from that derived from Authors@R
  Author:    ‘Hadley Wickham [aut], Thomas Lin Pedersen [cre, aut] (<https://orcid.org/0000-0002-5147-4711>), Dana Seidel [aut], Posit Software, PBC [cph, fnd] (03wc8by49)’
  Authors@R: ‘Hadley Wickham [aut], Thomas Lin Pedersen [cre, aut] (ORCID: <https://orcid.org/0000-0002-5147-4711>), Dana Seidel [aut], Posit Software, PBC [cph, fnd] (ROR: <https://ror.org/03wc8by49>)’
Maintainer: ‘Tingni Sun <tingni@wharton.upenn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tingni",
                    family = "Sun",
                    role = c("aut", "cre"),
                    email = "tingni@wharton.upenn.edu")
as necessary.
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.
Packages required but not available: 'gt', 'knitr', 'kableExtra'

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

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’

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', 'usethis'

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Xudong Han <hanxd1217@163.com>’

The Description field contains
  Thomas N. Kipf (2017) <arXiv:1609.02907v4>) to construct the gene-cell
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Packages required but not available: 'AdaptGauss', 'mixtools'

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’
checkRd: (-1) get.events.Rd:51: Lost braces
    51 |   code{\link[deSolve]{events}}
       |       ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Martin Maechler <maechler@stat.math.ethz.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Valentin",
                      family = "Rousson",
                      role = "aut",
                      email = "rousson@ifspm.unizh.ch"),
               person(given = "Martin",
                      family = "Maechler",
                      role = c("aut", "cre"),
                      email = "maechler@stat.math.ethz.ch"))
as necessary.
Maintainer: ‘Yining Chen <y.chen101@lse.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yining",
                      family = "Chen",
                      role = c("aut", "cre"),
                      email = "y.chen101@lse.ac.uk"),
               person(given = "Richard",
                      family = "Samworth",
                      role = "aut"))
as necessary.
Maintainer: ‘Ravi Selker <selker.ravi@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ravi",
                    family = "Selker",
                    role = c("aut", "cre"),
                    email = "selker.ravi@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:
  '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?
Maintainer: ‘Uwe Ligges <ligges@statistik.tu-dortmund.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Uwe",
                      family = "Ligges",
                      role = c("aut", "cre"),
                      email = "ligges@statistik.tu-dortmund.de"),
               person(given = "Martin",
                      family = "Maechler",
                      role = "aut"),
               person(given = "Sarah",
                      family = "Schnackenberg",
                      role = "aut"))
as necessary.
Package required but not available: ‘htmlwidgets’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Amit Frishberg <amfrishberg@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Amit",
                      family = "Frishberg",
                      role = c("aut", "cre"),
                      email = "amfrishberg@gmail.com"),
               person(given = "Naama",
                      family = "Peshes-Yaloz",
                      role = "aut"),
               person(given = "Irit",
                      family = "Gat-Viks",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Blair Drummond <blair.robert.drummond@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Blair",
                      family = "Drummomd",
                      role = "aut"),
               person(given = "Mathieu",
                      family = "Dextraze",
                      role = "ctb"),
               person(given = "Blair",
                      family = "Drummond",
                      role = "cre",
                      email = "blair.robert.drummond@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: ‘Xin Shao<xin_shao@zju.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Xin",
                    family = "Shao",
                    role = c("aut", "cre"),
                    email = "xin_shao@zju.edu.cn")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', '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: ‘Seurat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Alexander Marx <amarx@mpi-inf.mpg.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alexander",
                    family = "Marx",
                    role = c("aut", "cre"),
                    email = "amarx@mpi-inf.mpg.de")
as necessary.
Package required but not available: ‘Seurat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Alicja Wolny-Dominiak<woali@ue.katowice.pl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Peter",
                      family = "Adamic",
                      role = "aut"),
               person(given = "Alicja",
                      family = "Wolny-Dominiak",
                      role = c("aut", "cre"),
                      email = "woali@ue.katowice.pl"))
as necessary.
Maintainer: ‘"Yonas Ghebremichael Weldeselassie" <yonas.weldeselassie@open.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Yonas", "Ghebremichael"),
                      family = "Weldeselassie",
                      role = "aut"),
               person(given = "Heather",
                      family = "Whitaker",
                      role = "aut"),
               person(given = "Paddy",
                      family = "Farrington",
                      role = "aut"),
               person(given = c("\"Yonas", "Ghebremichael"),
                      family = "Weldeselassie\"",
                      role = "cre",
                      email = "yonas.weldeselassie@open.ac.uk"))
as necessary.
Package required but not available: ‘Seurat’

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

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

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

Packages suggested but not available for checking:
  'plotly', '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
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', 'shinytest'

VignetteBuilder package required for checking but not installed: ‘knitr’
'library' or 'require' calls not declared from:
  ‘doSNOW’ ‘foreach’ ‘iterators’ ‘reshape’ ‘rlecuyer’ ‘snow’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘Seurat’

Packages suggested but not available for checking:
  'covr', 'DT', 'kableExtra', 'knitr', 'ontoProc', 'pkgdown', 'plotly',
  'rmarkdown', 'spelling', '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?
Packages required but not available: 'DT', 'mmints'

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:
  '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?
Cannot process vignettes
Packages suggested but not available for checking:
  'kableExtra', '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: ‘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.
Packages required but not available: 'Seurat', 'networkD3'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Daisuke Murakami <dmuraka@ism.ac.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Daisuke",
                      family = "Murakami",
                      role = c("cre", "aut"),
                      email = "dmuraka@ism.ac.jp"),
               person(given = "Narumasa",
                      family = "Tsutsumida",
                      role = "ctb"),
               person(given = "Takahiro",
                      family = "Yoshida",
                      role = "ctb"),
               person(given = "Tomoki",
                      family = "Nakaya",
                      role = "ctb"),
               person(given = "Lu",
                      family = "Binbin",
                      role = "ctb"))
as necessary.

The Description field contains
  <arXiv:1905.00266>.
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:
  'roxygen2', 'knitr', 'rmarkdown', 'covr', 'lintr'

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

VignetteBuilder packages required for checking but not installed:
  'knitr', 'quarto'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jeffrey A. Dahlke <jeff.dahlke.phd@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Jeffrey", "A."),
                    family = "Dahlke",
                    role = c("aut", "cre"),
                    email = "jeff.dahlke.phd@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc', '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: 'leafpop', 'mapview'

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

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Stuart",
                      family = "Baumann",
                      role = c("aut", "cre"),
                      email = "stuart@stuartbaumann.com"),
               person(given = "Margaryta",
                      family = "Klymak",
                      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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Nathan Taback <nathan.taback@utoronto.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Nathan",
                    family = "Taback",
                    role = c("aut", "cre"),
                    email = "nathan.taback@utoronto.ca")
as necessary.
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.
Maintainer: ‘Ashraf Uddin <mdaakib18@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ashraf",
                    family = "Uddin",
                    role = c("aut", "cre"),
                    email = "mdaakib18@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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ze",
                    family = "Zhang",
                    role = c("aut", "cre"),
                    email = "ze.zhang@utsouthwestern.edu")
as necessary.
Maintainer: ‘Manuel Morales <Manuel.A.Morales@williams.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Manuel",
                      family = "Morales",
                      role = c("aut", "cre"),
                      email = "mmorales@williams.edu"),
               person(given = c("with", "code", "developed", "by", "the", "R", "Development", "Core"),
                      family = "Team",
                      role = "aut"),
               person(given = c("with", "general", "advice", "from", "the", "R-help", "listserv"),
                      family = "community",
                      role = "aut"),
               person(given = c("especially", "Duncan"),
                      family = "Murdoch.",
                      role = "aut"))
as necessary.
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/sciRmdTheme
which should likely be
  https://github.com/oobianom/sciRmdTheme/issues
instead.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Duc Tran <duct@nevada.unr.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?
Package required but not available: ‘ggtree’

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'WGCNA', 'conos', 'pagoda2'

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: 'Seurat', 'gprofiler2'

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: ‘Tamal Kumar De <tamalkumar.de@kuleuven.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Isis",
                      family = "Bulte",
                      role = "aut"),
               person(given = c("Tamal", "Kumar"),
                      family = "De",
                      role = c("aut", "cre"),
                      email = "tamalkumar.de@kuleuven.be"),
               person(given = "Patrick",
                      family = "Onghena",
                      role = "aut"))
as necessary.
Specified C++11: support will be removed soon
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?
Packages required but not available: 'alakazam', 'shazam'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Gabriele Lubatti <gabriele.lubatti@helmholtz-muenchen.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Gabriele",
                    family = "Lubatti",
                    role = c("aut", "cre"),
                    email = "gabriele.lubatti@helmholtz-muenchen.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?
Running ‘testthat.R’ [15s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(scopr)
  Loading required package: behavr
  Loading required package: data.table
  
  Attaching package: 'data.table'
  
  The following object is masked from 'package:base':
  
      %notin%
  
  > 
  > test_check("scopr")
    machine_name       date     time test
  1        E_014 2016-01-25 21:36:04    1
  2        E_014 2016-02-17     <NA>    2
  3        E_029 2016-01-25     <NA>    3
  Failed with error:  'there is no package called 'digest''
  Saving _problems/test-parse_single_roi-24.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 46 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-parse_single_roi.R:24:3'): parse_single_roi works with memosiation ──
  Error in `memoise::cache_filesystem(cache, algo = "md5")`: Package `digest` must be installed for `cache_filesystem()`.
  Backtrace:
      ▆
   1. └─scopr:::parse_single_roi(data, cache = cache, verbose = F) at test-parse_single_roi.R:24:3
   2.   └─memoise::cache_filesystem(cache, algo = "md5")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 46 ]
  Error:
  ! Test failures.
  Execution halted
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pkgdown'

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

VignetteBuilder 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: ‘Wenlong Ren <wenlongren@ntu.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Wenlong",
                    family = "Ren",
                    role = c("aut", "cre"),
                    email = "wenlongren@ntu.edu.cn")
as necessary.
Maintainer: ‘Shota Ochi <shotaochi1990@gmail.com>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘ecgca102.Rd’:
    https://doi.org/10.13026/C2X30H
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jaejoon Song <jjsong2@mdanderson.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jaejoon",
                    family = "Song",
                    role = c("aut", "cre"),
                    email = "jjsong2@mdanderson.org")
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: ‘Ed Merkle <merklee@missouri.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ed",
                    family = "Merkle",
                    role = c("aut", "cre"),
                    email = "merklee@missouri.edu")
as necessary.

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

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

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

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

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Debsurya De <debsurya001@gmail.com>’

The Description field contains
  <arXiv:1909.04024> .
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Chakkrit Tantithamthavorn <kla@chakkrit.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Chakkrit",
                    family = "Tantithamthavorn",
                    role = c("aut", "cre"),
                    email = "kla@chakkrit.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: ‘Daniela M. Witten <dwitten@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Daniela", "M."),
                      family = "Witten",
                      role = c("aut", "cre"),
                      email = "dwitten@uw.edu"),
               person(given = "Robert",
                      family = "Tibshirani",
                      role = "aut"))
as necessary.
Package required but not available: ‘missMDA’

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: ‘Marlene Marchena <marchenamarlene@gmail.com>’

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

The Description field contains
  <arXiv:1009.3977>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Stefan Peidli <stefanpeidli@gmail.com>’

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Julien",
                    family = "Boelaert",
                    role = c("aut", "cre"),
                    email = "jubo.stats@gmail.com")
as necessary.
Maintainer: ‘Qi Zhang <karlmzhang@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Pengsheng",
                      family = "Ji",
                      role = "aut"),
               person(given = "Jiashun",
                      family = "Jin",
                      role = "aut"),
               person(given = "Qi",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "karlmzhang@gmail.com"))
as necessary.
Maintainer: ‘Elad Romanov <elad.romanov@gmail.com>’

The Description field contains
  appear). <arXiv:2009.12297>.
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', '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: ‘Holger Schwender <holger.schw@gmx.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Holger",
                      family = "Schwender",
                      role = c("aut", "cre"),
                      email = "holger.schw@gmx.de"),
               person(given = c("with", "a", "contribution", "of", "Arno"),
                      family = "Fritsch",
                      role = "aut"))
as necessary.
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
Maintainer: ‘Sagie Gur-Ari <sagiegurari@gmail.com>’

Found the following (possibly) invalid file URIs:
  URI: docs/api.md
    From: README.md
  URI: .github/CONTRIBUTING.md
    From: README.md
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'lintr', 'devtools', 'roxygen2', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently 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’
checkRd: (-1) scriptloc.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Get location of script in a fashion analagous to ${BASH_SOURCE[0]}}
       |                                                          ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Raphaël Bonnet <raphael.bonnet@univ-cotedazur.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Raphael",
                      family = "Bonnet",
                      role = c("aut", "cre")),
               person(given = "Marion",
                      family = "Guernoté",
                      role = "ctb"),
               person(given = "Terry",
                      family = "Gouin",
                      role = "ctb"),
               person(given = "Maxime",
                      family = "Laurens",
                      role = "ctb"),
               person(given = "Thibault",
                      family = "Meekel",
                      role = "ctb"),
               person(given = "Jean-François",
                      family = "Peyron",
                      role = c("aut", "ths")),
               person(given = "Raphaël",
                      family = "Bonnet",
                      role = "cre",
                      email = "raphael.bonnet@univ-cotedazur.fr"))
as necessary.
Package required but not available: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Andrew Heiss <andrew@andrewheiss.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?
Package required but not available: ‘Seurat’

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Qian",
                    family = "Yang",
                    role = c("aut", "cre"),
                    email = "bioqianyang@163.com")
as necessary.
Packages required but not available: 'TPEA', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Conor Neilson <condwanaland@gmail.com>’

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

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

VignetteBuilder package required 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: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Tamal Kumar De <tamalkumar.de@kuleuven.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Isis",
                      family = "Bulte",
                      role = "aut"),
               person(given = c("Tamal", "Kumar"),
                      family = "De",
                      role = c("aut", "cre"),
                      email = "tamalkumar.de@kuleuven.be"),
               person(given = "Patrick",
                      family = "Onghena",
                      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:
  'covr', 'knitr', 'rmarkdown'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Daniel Osorio <dcosorioh@utexas.edu>’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Tamal Kumar De <tamalkumar.de@kuleuven.be>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Isis",
                      family = "Bulte",
                      role = "aut"),
               person(given = c("Tamal", "Kumar"),
                      family = "De",
                      role = c("aut", "cre"),
                      email = "tamalkumar.de@kuleuven.be"),
               person(given = "Patrick",
                      family = "Onghena",
                      role = "aut"))
as necessary.
Packages required but not available: 'ggExtra', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Tobias Verbeke <tobias.verbeke@openanalytics.eu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tobias",
                    family = "Verbeke",
                    role = c("aut", "cre"),
                    email = "tobias.verbeke@openanalytics.eu")
as necessary.
Maintainer: ‘Lilun Du <dulilun@ust.hk>’

The Description field contains
  Aggregation", <arXiv:2002.11992>.
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) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                  ^
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                                         ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) geom_flat_violin.Rd:7: Lost braces
     7 | url{https://gist.github.com/dgrtwo/eb7750e74997891d7c20}
       |    ^
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: ‘John R. Ortiz <jrortizt@unal.edu.co>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘plot.Rd’:
    https://doi.org/10.25573/data.13118426.v2
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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', 'plotly'

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

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

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:
  'cffr', 'knitr', 'rmarkdown', 'skimr', '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:
  'rmarkdown', 'knitr', 'rhandsontable', 'DT', 'prettydoc'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) sdc_extabs.Rd:59: Lost braces
    59 | (including ]code{forcelist} variables) that can be used to form tables.}
       |                 ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: 'sdcHierarchies', '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: 'optiSolve', 'deaR'

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?
Maintainer: ‘Stefano Maria Iacus <siacus@iq.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Stefano", "Maria"),
                    family = "Iacus",
                    role = c("aut", "cre"),
                    email = "siacus@iq.harvard.edu")
as necessary.
File ‘sde/libs/sde.so’:
  Found non-API call to R: ‘SET_TYPEOF’
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.
Maintainer: ‘Eduardo García-Portugués <edgarcia@est-econ.uc3m.es>’

The BugReports field in DESCRIPTION has
  https://github.com/egarpor/sdetorus
which should likely be
  https://github.com/egarpor/sdetorus/issues
instead.
Maintainer: ‘Takahiro Shimada <taka.shimada@gmail.com>’

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

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Junyue Wu <wu.junyue.p1@dc.tohoku.ac.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Junyue",
                    family = "Wu",
                    role = c("aut", "cre"),
                    email = "wu.junyue.p1@dc.tohoku.ac.jp")
as necessary.
Package required but not available: ‘rJava’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) hyperpar.Rd:17: Lost braces
    17 | \item{c}{denotes the expected range of eqn{f} .}
       |                                           ^
Maintainer: ‘Benjamin Baumgartner <benjamin@baumgrt.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?
Packages required but not available: 'DT', 'surveydown'

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

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

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.
Maintainer: ‘Ali Uenlue <ali.uenlue@icloud.com>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘SDT-package.Rd’:
    https://doi.org/10.1007/978-1-4899-2271-7
    https://doi.org/10.1207/S15327965PLI1104_01
    https://doi.org/10.3389/fpsyg.2016.00272
    https://doi.org/10.2466/14.PR0.117c25z1
  File ‘internalization.Rd’:
    https://doi.org/10.2466/14.PR0.117c25z1
  File ‘plot.sdi.Rd’:
    https://doi.org/10.3389/fpsyg.2016.00272
  File ‘plot.share.Rd’:
    https://doi.org/10.2466/14.PR0.117c25z1
  File ‘print.sdi.Rd’:
    https://doi.org/10.3389/fpsyg.2016.00272
  File ‘print.share.Rd’:
    https://doi.org/10.2466/14.PR0.117c25z1
  File ‘sdi.Rd’:
    https://doi.org/10.3389/fpsyg.2016.00272
  File ‘simplex.Rd’:
    https://doi.org/10.2466/14.PR0.117c25z1
  File ‘summary.sdi.Rd’:
    https://doi.org/10.3389/fpsyg.2016.00272
Maintainer: ‘Boxiang Wang <boxiang-wang@uiowa.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Boxiang",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "boxiang-wang@uiowa.edu"),
               person(given = "Hui",
                      family = "Zou",
                      role = "aut"))
as necessary.
Maintainer: ‘Jocelyn Chi <jocetchi@gmail.com>’

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

The Description field contains
  Hsiao, Lin, Wang, Lee, Lu, and Tzeng. (2021+) <arXiv:2105.03228>.
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?
Packages required but not available:
  'leaflet', 'leaflet.minicharts', 'leaflet.extras2'

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.
Packages required but not available:
  'plotly', 'DT', 'rmarkdown', 'htmlwidgets'

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: ‘Wei Qian <weiqian@stat.umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Wei",
                    family = "Qian",
                    role = c("aut", "cre"),
                    email = "weiqian@stat.umn.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'flexdashboard', 'plotly', 'DT', 'rmarkdown', 'knitr',
  'revtools'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Gabriel Becker <gabembecker@gmail.com>’

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

VignetteBuilder package required 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’

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Isabella Bitetto <bitetto@coispa.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Isabella",
                      family = "Bitetto",
                      role = c("aut", "cre"),
                      email = "bitetto@coispa.it",
                      comment = "COISPA"),
               person(given = "Loretta",
                      family = "Malvarosa",
                      role = "aut",
                      comment = "NISEA"),
               person(given = c("Maria", "Teresa"),
                      family = "Spedicato",
                      role = "aut",
                      comment = "COISPA"),
               person(given = "Ralf",
                      family = "Doering",
                      role = "aut",
                      comment = "THUENEN"),
               person(given = "Joerg",
                      family = "Berkenhagen",
                      role = "aut",
                      comment = "THUENEN"))
as necessary.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Pavel V. Moskalev <moskalefff@gmail.com>’

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

The Description field contains
  <arXiv:1105.2334v1>.
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: ‘Danielle Quinn <danielle.quinn@mun.ca>’

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

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

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Jae Keun Yoo <peter.yoo@ewha.ac.kr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Jae", "Keun"),
                      family = "Yoo",
                      role = c("aut", "cre"),
                      email = "peter.yoo@ewha.ac.kr"),
               person(given = "Bo-Young",
                      family = "Kim",
                      role = "aut"))
as necessary.
checkRd: (-1) seedCCA.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{u}{numeric, maximum number of projections. The default is 10. This is used for \code{type="seed1"}, \code{type="seed2"} and {tyepe="pls"}.}
       |                                                                                                                                   ^
Package required but not available: ‘quanteda’

Package suggested but not available for checking: ‘spelling’

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

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

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

Found the following URLs which should use \doi (with the DOI name only):
  File ‘SE.EQ-package.Rd’:
    http://dx.doi.org/10.1080/10543406.2014.920344
    https://doi.org/10.1002/bimj.201700257
    http://dx.doi.org/10.1208/s12248-020-00458-9
  File ‘SE.EQ.Rd’:
    http://dx.doi.org/10.1080/10543406.2014.920344
  File ‘SE.EQ.dissolution.profiles.Rd’:
    http://dx.doi.org/10.1080/10543406.2014.920344
    https://doi.org/10.1002/bimj.201700257
    http://dx.doi.org/10.1208/s12248-020-00458-9
  File ‘ex_data_JoBS.Rd’:
    http://dx.doi.org/10.1080/10543406.2014.920344
Packages required but not available: 'rgl', 'demography'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'dygraphs', 'leaflet', 'devtools', '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: ‘Eleni Ioanna Delatola <eldelatola@yahoo.gr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Eleni", "Ioanna"),
                      family = "Delatola",
                      role = c("aut", "cre"),
                      email = "eldelatola@yahoo.gr"),
               person(given = "Emilie",
                      family = "Lebarbier",
                      role = "aut"),
               person(given = "Tristan",
                      family = "Mary-Huard",
                      role = "aut"),
               person(given = "Francois",
                      family = "Radvanyi",
                      role = "aut"),
               person(given = "Stephane",
                      family = "Robin",
                      role = "aut"),
               person(given = "Jennifer",
                      family = "Wong",
                      role = "aut"))
as necessary.
Package required but not available: ‘modeest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Rainer Machne <raim@tbi.univie.ac.at>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rainer",
                      family = "Machne",
                      role = c("aut", "cre"),
                      email = "raim@tbi.univie.ac.at"),
               person(given = c("Douglas", "B."),
                      family = "Murray",
                      role = "aut"),
               person(given = c("Peter", "F."),
                      family = "Stadler",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

The Description field contains
  Leonardi (2018) <arXiv:1501.01756>. The Berlin weather sample dataset
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: ‘Michelle Picoli <mipicoli@gmail.com>’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Danilo C Vieira <vieiradc@yahoo.com.br>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Danilo", "C"),
                      family = "Vieira",
                      role = c("aut", "cre"),
                      email = "vieiradc@yahoo.com.br"),
               person(given = "Gustavo",
                      family = "Fonseca",
                      role = "aut",
                      email = "gfonseca.unifesp@gmail.com"),
               person(given = c("Fabio", "Cop"),
                      family = "Ferreira",
                      role = "aut",
                      email = "fabiocferreira.unifesp@gmail.com"),
               person(given = c("with", "contributions", "from", "Marco", "Colossi"),
                      family = "Brustolin.",
                      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:
  '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: 'pedtools', 'pedprobr'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: polymapr_test
> ### Title: Run segregation distortion tests as implemented in the polymapR
> ###   package.
> ### Aliases: polymapr_test
> 
> ### ** Examples
> 
> g1 <- 0
> g2 <- 1
> x <- c(4, 16, 0, 0, 0)
> polymapr_test(x = x, g1 = g1, g2 = g2, type = "segtest")
$p_value
[1] 0.007290358

$best_fit
[1] 5.000000e-01 5.000000e-01 4.440892e-17 4.440892e-17 4.440892e-17

$frq_invalid
[1] 0

$p_invalid
[1] 1

> polymapr_test(x = x, g1 = g1, g2 = g2, type = "polymapR")
Error in polymapr_test(x = x, g1 = g1, g2 = g2, type = "polymapR") : 
  polymapr_test:
polymapR needs to be installed to use type = 'polymapR'.
You can install it with install.packages('polymapR')
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?
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/SEI_vignette.Rnw’
(Is a VignetteBuilder field missing?)

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.
Maintainer: ‘Qingyuan Zhao <qingyzhao@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hera",
                      family = "He",
                      role = "aut"),
               person(given = "Murat",
                      family = "Erdogdu",
                      role = "aut"),
               person(given = "Qingyuan",
                      family = "Zhao",
                      role = c("aut", "cre"),
                      email = "qingyzhao@gmail.com"))
as necessary.
Package required but not available: ‘factoextra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Heewon Jeon <madjakarta@gmail.com>’

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

The Description field contains
  Sejong(http://www.sejong.or.kr/) corpus and
  Hannanum(http://semanticweb.kaist.ac.kr/home/index.php/HanNanum)
Please enclose URLs in angle brackets (<...>).
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘selcorr.R’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'table1', 'rmarkdown'

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xuefei",
                      family = "Mi",
                      role = c("aut", "cre"),
                      email = "mi_xue_fei@hotmail.com"),
               person(given = "Jose",
                      family = "Marulanda",
                      role = "aut"),
               person(given = c("H.", "Friedrich"),
                      family = "Utz",
                      role = "aut"),
               person(given = c("Albrecht", "E."),
                      family = "Melchinger",
                      role = "aut",
                      comment = "Project contact person: Melchinger@uni-hohenheim.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?
Maintainer: ‘Rob Tibshirani <tibs@stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ryan",
                      family = "Tibshirani",
                      role = "aut"),
               person(given = "Rob",
                      family = "Tibshirani",
                      role = c("aut", "cre"),
                      email = "tibs@stanford.edu"),
               person(given = "Jonathan",
                      family = "Taylor",
                      role = "aut"),
               person(given = "Joshua",
                      family = "Loftus",
                      role = "aut"),
               person(given = "Stephen",
                      family = "Reid",
                      role = "aut"),
               person(given = "Jelena",
                      family = "Markovic",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'RSelenium', 'shinytest2', 'wdman'

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:
    ‘as.list.selenider_elements.Rd’ ‘elem_ancestors.Rd’ ‘elem_attr.Rd’
    ‘elem_cache.Rd’ ‘elem_click.Rd’ ‘elem_css_property.Rd’
    ‘elem_equal.Rd’ ‘elem_expect.Rd’ ‘elem_expect_all.Rd’
    ‘elem_filter.Rd’ ‘elem_flatten.Rd’ ‘elem_hover.Rd’ ‘elem_name.Rd’
    ‘elem_scroll_to.Rd’ ‘elem_select.Rd’ ‘elem_size.Rd’ ‘elem_text.Rd’
    ‘find_each_element.Rd’ ‘find_element.Rd’ ‘find_elements.Rd’
    ‘get_actual_element.Rd’ ‘s.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'DatabaseConnector', 'SqlRender', 'ResultModelManager'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jie Qiao <qiaojie2004@vip.qq.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: ‘Bjoern Bornkamp <bbnkmp@mail.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Bjoern",
                    family = "Bornkamp",
                    role = c("aut", "cre"),
                    email = "bbnkmp@mail.de")
as necessary.
Package required but not available: ‘htmlwidgets’

Package suggested but not available for checking: ‘shiny.semantic’

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

Packages suggested but not available for checking:
  'lintr', '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: ‘textstem’

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: ‘Divyansh Agarwal <divyansh@upenn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Divyansh", "Agarwal", "Nancy", "R.", "Zhang"),
                      family = "<nzh@wharton.upenn.edu>",
                      role = "aut",
                      email = "nzh@wharton.upenn.edu"),
               person(given = "Divyansh",
                      family = "Agarwal",
                      role = "cre",
                      email = "divyansh@upenn.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.
Package required but not available: ‘semPlot’

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Marko Robnik-Sikonja <marko.robnik@fri.uni-lj.si>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Marko",
                    family = "Robnik-Sikonja",
                    role = c("aut", "cre"),
                    email = "marko.robnik@fri.uni-lj.si")
as necessary.
Maintainer: ‘Yiran Zhang <yiz038@health.ucsd.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yiran",
                    family = "Zhang",
                    role = c("aut", "cre"),
                    email = "yiz038@health.ucsd.edu")
as necessary.

The Description field contains
  Zhang, Y. and Xu, R. (2022) <arXiv:2204.10426>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Kyu Ha Lee <klee15239@gmail.com>’

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 = "klee15239@gmail.com"),
               person(given = "Catherine",
                      family = "Lee",
                      role = "aut"),
               person(given = "Danilo",
                      family = "Alvares",
                      role = "aut"),
               person(given = "Sebastien",
                      family = "Haneuse",
                      role = "aut"))
as necessary.
Maintainer: ‘Jinhua Su <944866518@qq.com>’

The Description field contains
  method<arXiv:2108.07928> is an improved method of two-step NR iteration
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’
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?
Maintainer: ‘Agnieszka Listwon-Krol <krol@lunenfeld.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Agnieszka",
                      family = "Listwon-Krol",
                      role = c("aut", "cre"),
                      email = "krol@lunenfeld.ca"),
               person(given = "Philippe",
                      family = "Saint-Pierre",
                      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: ‘seminr’

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: 'knitr', 'rmarkdown', 'DiagrammeR'

Packages which this enhances but not available for checking:
  'semPlot', 'seminrExtras'

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?
Package required but not available: ‘leaflet’

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:
  'DT', 'easycsv', 'htmlTable', 'knitr', 'rmarkdown'

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

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

Package suggested but not available for checking: ‘NetworkToolbox’

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: ‘qgraph’

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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’
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?
Problems with news in ‘NEWS.md’:
No news entries found.
Packages required but not available: 'usethis', 'emayili', 'keyring'

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', 'Hmisc', '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’
checkRd: (-1) sendmail_options.Rd:32-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:38-39: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory 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: ‘Giancarlo Vercellino <giancarlo.vercellino@gmail.com>’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Gustavo Paterno <paternogbc@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’
checkRd: (-1) match_dataphy.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_dataphy.Rd:39-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_dataphy.Rd:42-44: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Paul R. Rosenbaum <rosenbaum@wharton.upenn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Paul", "R."),
                      family = "Rosenbaum",
                      role = c("aut", "cre"),
                      email = "rosenbaum@wharton.upenn.edu"),
               person(given = c("Dylan", "S."),
                      family = "Small",
                      role = "aut"))
as necessary.
Maintainer: ‘Bo Zhang <bozhan@wharton.upenn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Bo",
                    family = "Zhang",
                    role = c("aut", "cre"),
                    email = "bozhan@wharton.upenn.edu")
as necessary.

The Description field contains
  B., Small, D. S. (2018). <arXiv:1812.00215>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Dylan Small <dsmall@wharton.upenn.edu>’

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

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Paul", "R."),
                    family = "Rosenbaum",
                    role = c("aut", "cre"),
                    email = "rosenbaum@wharton.upenn.edu")
as necessary.
Maintainer: ‘Ibtihel Rebhi <ibtihel.rebhi@enit.utm.tn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ibtihel",
                      family = "Rebhi",
                      role = c("aut", "cre"),
                      email = "ibtihel.rebhi@enit.utm.tn"),
               person(given = "Dhafer",
                      family = "Malouche",
                      role = "ctb"))
as necessary.
Packages required but not available:
  'FactoMineR', 'factoextra', 'glmulti', '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'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Brian C. Franczak <bfrancza@math.mcmaster.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Brian", "C."),
                      family = "Franczak",
                      role = c("aut", "cre"),
                      email = "bfrancza@math.mcmaster.ca"),
               person(given = c("Ryan", "P."),
                      family = "Browne",
                      role = "aut"),
               person(given = c("Paul", "D."),
                      family = "McNicholas",
                      role = "aut"))
as necessary.
Maintainer: ‘Yijian Huang <yhuang5@emory.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yijian",
                    family = "Huang",
                    role = c("aut", "cre"),
                    email = "yhuang5@emory.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: ‘Kjetil B Halvorsen <kjetil1001@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Kjetil", "B"),
                    family = "Halvorsen",
                    role = c("aut", "cre"),
                    email = "kjetil1001@gmail.com")
as necessary.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘E1.19.Rd’:
    \concept{Data on Book Prices, Pages and Type of Bi [TRUNCATED]
  File ‘E2.9.Rd’:
    \concept{Data on Capital, Labour and Value Added f [TRUNCATED]
  File ‘E4.11.Rd’:
    \concept{ Data on Cost of Repairing Starters, Ring [TRUNCATED]
  File ‘E7.2.Rd’:
    \concept{Prices of Crude Oil, Natural Gas, Bitumin [TRUNCATED]
  File ‘E9.3.Rd’:
    \concept{ Areas, lengths and widths of rectangles  [TRUNCATED]
  File ‘E9.8.Rd’:
    \concept{ Data on monthly rent, annual income and  [TRUNCATED]
Maintainer: ‘Paul R. Rosenbaum <rosenbaum@wharton.upenn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Paul", "R."),
                    family = "Rosenbaum",
                    role = c("aut", "cre"),
                    email = "rosenbaum@wharton.upenn.edu")
as necessary.
Packages required but not available: 'tensorflow', 'tfhub'

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

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

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

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

Package suggested but not available for checking: ‘covr’

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

Packages suggested but not available for checking:
  'plotly', 'covr', 'stm', 'seededlda', 'keyATM', 'sentometrics',
  'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Brian Greenhill <bgreenhill@albany.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Brian", "D."),
                      family = "Greenhill",
                      role = "aut"),
               person(given = c("Michael", "D."),
                      family = "Ward",
                      role = "aut"),
               person(given = "Audrey",
                      family = "Sacks",
                      role = "aut"),
               person(given = "Brian",
                      family = "Greenhill",
                      role = "cre",
                      email = "bgreenhill@albany.edu"))
as necessary.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Author field differs from that derived from Authors@R
  Author:    ‘Inder Tecuapetla-Gómez [cre, aut] (0000-0001-6251-972X), Fanny Galicia-Gómez [ctb], Francisco Rosales-Marticorena [ctb]’
  Authors@R: ‘Inder Tecuapetla-Gómez [cre, aut] (ORDIC: 0000-0001-6251-972X), Fanny Galicia-Gómez [ctb], Francisco Rosales-Marticorena [ctb]’
Maintainer: ‘Lewis A. Jones <LewisA.Jones@outlook.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Xiaoshu Zhu <xiaoshuzhu@westat.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xiaoshu",
                      family = "Zhu",
                      role = c("aut", "cre"),
                      email = "xiaoshuzhu@westat.com"),
               person(given = "Sharon",
                      family = "Lohr",
                      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/seqDesignInstructions.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Dalibor Krleža <dalibor.krleza@fer.hr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Dalibor",
                    family = "Krleža",
                    role = c("aut", "cre"),
                    email = "dalibor.krleza@fer.hr")
as necessary.
Specified C++14: support will be removed soon
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
Maintainer: ‘Bettina Budeus <bettina.budeus@stud.uni-due.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Bettina",
                    family = "Budeus",
                    role = c("aut", "cre"),
                    email = "bettina.budeus@stud.uni-due.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.
Found the following files/directories:
  ‘assocpointpair_result.csv’ ‘foundereffectfinder_result.csv’
  ‘getfreqs_result.csv’ ‘getfreqs_result.png’ ‘orPlot.pdf1_1.pdf’
  ‘orPlot.pdf2_1.pdf’ ‘orPlot.pdf3_1.pdf’ ‘orPlot.pdf4_1.pdf’
  ‘orPlot.pdf5_1.pdf’ ‘orPlot.pdf6_1.pdf’ ‘orPlot.pdf7_1.pdf’
  ‘orPlot.pdf8_1.pdf’ ‘q-values_result.csv’ ‘rewritetuple_result.csv’
  ‘tartan_plot.pdf’ ‘vispair_plot.pdf’ ‘vispairfeat_plot.pdf’
  ‘volcano_plot.pdf’
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 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/seqHMM.Rnw’
   ‘inst/doc/seqHMM_algorithms.Rnw’
   ‘inst/doc/seqHMM_estimation.Rnw’
   ‘inst/doc/seqHMM_visualization.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Niklas Pfister <pfister@stat.math.ethz.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Niklas",
                      family = "Pfister",
                      role = c("aut", "cre"),
                      email = "pfister@stat.math.ethz.ch"),
               person(given = "Jonas",
                      family = "Peters",
                      role = "aut"))
as necessary.
Package required but not available: ‘rms’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Paul C. Boutros <pboutros@mednet.ucla.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Fouad",
                      family = "Yousif",
                      role = "aut"),
               person(given = "Xihui",
                      family = "Lin",
                      role = "aut"),
               person(given = "Fan",
                      family = "Fan",
                      role = "aut"),
               person(given = "Christopher",
                      family = "Lalansingh",
                      role = "aut"),
               person(given = "John",
                      family = "Macdonald",
                      role = "aut"),
               person(given = c("Paul", "C."),
                      family = "Boutros",
                      role = "cre",
                      email = "pboutros@mednet.ucla.edu"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder packages required for checking but not installed:
  'rmarkdown', 'knitr'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Mingli Lei<leimingli2013@sjtu.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mingli",
                      family = "Lei",
                      role = c("aut", "cre"),
                      email = "leimingli2013@sjtu.edu.cn"),
               person(given = "Jia",
                      family = "Xu",
                      role = "aut"),
               person(given = "Li-Ching",
                      family = "Huang",
                      role = "aut"),
               person(given = "Lily",
                      family = "Wang",
                      role = "aut"),
               person(given = "Jing",
                      family = "Li",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc'

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:
    ‘consensus.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Hui Zheng <hzheng1@mgh.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("David", "A"),
                      family = "Schoenfeld",
                      role = "aut"),
               person(given = "Hui",
                      family = "Zheng",
                      role = c("aut", "cre"),
                      email = "hzheng1@mgh.harvard.edu"))
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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently 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', 'kinship2'

VignetteBuilder package required for checking but not installed: ‘knitr’
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: ‘Edward Schuberg <eschu003@ucr.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Edward",
                    family = "Schuberg",
                    role = c("aut", "cre"),
                    email = "eschu003@ucr.edu")
as necessary.
Package required but not available: ‘mixtools’

Packages suggested but not available for checking:
  'bookdown', 'DT', 'knitr', 'pak', 'quarto', 'rmarkdown', 'spelling',
  'tidyverse'

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

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'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', '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: ‘Matt Moores <mmoores@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.

The Description field contains
  <arXiv:1604.07299>. Multivariate observations of SERRS are highly
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', '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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Oisín Ryan <o.ryan@uu.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Oisín",
                    family = "Ryan",
                    role = c("aut", "cre"),
                    email = "o.ryan@uu.nl")
as necessary.

The BugReports field in DESCRIPTION has
  https://github.com/ryanoisin/SEset
which should likely be
  https://github.com/ryanoisin/SEset/issues
instead.
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
Running examples in ‘SEset-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: network_to_SEset
> ### Title: SE-set from precision matrix
> ### Aliases: network_to_SEset
> 
> ### ** Examples
> 
> # first estimate the precision matrix
> data(riskcor)
> omega <- (qgraph::EBICglasso(riskcor, n = 69, returnAllResults = TRUE))$optwi
Error in loadNamespace(x) : there is no package called ‘qgraph’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
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: ‘Rakshitha Godahewa <rakshithagw@gmail.com>’

The Description field contains
  in Godahewa et al. (2022) <arXiv:2211.08661v1>. The model uses the
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Zhi Jin <nalanchongxuan@163.com>’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Paul Gilbert <pgilbert.ttv9z@ncf.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Paul",
                    family = "Gilbert",
                    role = c("aut", "cre"),
                    email = "pgilbert.ttv9z@ncf.ca")
as necessary.
Maintainer: ‘Hong Zhang <hzhang@wpi.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hong",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "hzhang@wpi.edu"),
               person(given = "Zheyang",
                      family = "Wu",
                      role = "aut"))
as necessary.
Maintainer: ‘Mark van der Loo <mark.vanderloo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mark",
                    family = "van der Loo",
                    role = c("aut", "cre"),
                    email = "mark.vanderloo@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:
  'Seurat', 'DT', 'colourpicker', 'shinyjqui'

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

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

Packages suggested but not available for checking:
  'BPCells', 'mixtools', 'presto', 'rtracklayer'

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', 'pkgdown'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 ‘sfaendog.Rd’:
    https://doi.org/10.1016/0304-4076(87)90015-7
    https://doi.org/10.1093/ajae/aaw077
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

Packages suggested but not available for checking:
  'knitr', 'pkgdown', 'rmarkdown', 'tidyverse', 'networkD3'

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', 'rgl'

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:
    ‘h_curve.Rd’ ‘sfc_4x4_meander.Rd’ ‘sfc_generator.Rd’
    ‘spacefilling.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:
  '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: ‘gam’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Collin Erickson <collinberickson@gmail.com>’

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

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?
Maintainer: ‘Kevin Titeca <sfinxinteractomics@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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'mapview', '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: ‘Utz-Uwe Haus <uhaus@cray.com>’

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

Found the following (possibly) invalid file URIs:
  URI: github
    From: README.md
  URI: Win-Builder
    From: README.md
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: ‘Mohamed Laib <laib.med@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mohamed",
                      family = "Laib",
                      role = c("aut", "cre"),
                      email = "laib.med@gmail.com"),
               person(given = "Mikhail",
                      family = "Kanevski",
                      role = "aut"))
as necessary.
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: ‘Monique Graf <monique.p.n.graf@bluewin.ch>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Monique",
                    family = "Graf",
                    role = c("aut", "cre"),
                    email = "monique.p.n.graf@bluewin.ch")
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/vignette.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 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: ‘Youngki Shin <shiny11@mcmaster.ca>’

The Description field contains
  <arXiv:2209.14502> "Fast Inference for Quantile Regression with Tens of
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: ‘Gregory Vaughan <gvaughan@bentley.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gregory",
                      family = "Vaughan",
                      role = c("aut", "cre"),
                      email = "gvaughan@bentley.edu"),
               person(given = "Kun",
                      family = "Chen",
                      role = "ctb"),
               person(given = "Jun",
                      family = "Yan",
                      role = "ctb"))
as necessary.
checkRd: (-1) bisee.Rd:127: Lost braces
   127 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) hisee.Rd:101: Lost braces
   101 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) isee.Rd:116: Lost braces
   116 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) see.Rd:98: Lost braces
    98 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
Maintainer: ‘Albrecht Gebhardt <albrecht.gebhardt@aau.at>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("S", "original", "by", "James", "J.", "Majure", "Iowa", "State"),
                      family = "University",
                      role = "aut",
                      email = "majure@iastate.edu"),
               person(given = c("R", "port", "+", "extensions", "by", "Albrecht"),
                      family = "Gebhardt",
                      role = "aut",
                      email = "albrecht.gebhardt@aau.at"),
               person(given = "Albrecht",
                      family = "Gebhardt",
                      role = "cre",
                      email = "albrecht.gebhardt@aau.at"))
as necessary.
Maintainer: ‘Luigi Augugliaro <luigi.augugliaro@unipa.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Luigi",
                    family = "Augugliaro",
                    role = c("aut", "cre"),
                    email = "luigi.augugliaro@unipa.it")
as necessary.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Noah Simon <nrsimon@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Noah",
                      family = "Simon",
                      role = c("aut", "cre"),
                      email = "nrsimon@uw.edu"),
               person(given = "Jerome",
                      family = "Friedman",
                      role = "aut"),
               person(given = "Trevor",
                      family = "Hastie",
                      role = "aut"),
               person(given = "Rob",
                      family = "Tibshirani",
                      role = "aut"))
as necessary.
Maintainer: ‘Balasubramanian Narasimhan <naras@stat.stanford.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Balasubramanian",
                    family = "Narasimhan",
                    role = c("aut", "cre"),
                    email = "naras@stat.stanford.edu",
                    comment = "with input from Tze Lai and Mei-Chiung Shih")
as necessary.
Maintainer: ‘Thomas Vigie <vigiethomas@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thomas",
                    family = "Vigie",
                    role = c("aut", "cre"),
                    email = "vigiethomas@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?
Maintainer: ‘Irene Castro Conde <irene.castro@uvigo.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Irene", "Castro"),
                      family = "Conde",
                      role = c("aut", "cre"),
                      email = "irene.castro@uvigo.es"),
               person(given = c("Jacobo", "de", "Una"),
                      family = "Alvarez",
                      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:
  'gt', '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?
Package required but not available: ‘mixOmics’

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

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

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: ‘Massimiliano Pastore <massimiliano.pastore@unipd.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Massimiliano", "Pastore", "&", "Luigi"),
                      family = "Lombardi",
                      role = "aut"),
               person(given = "Massimiliano",
                      family = "Pastore",
                      role = "cre",
                      email = "massimiliano.pastore@unipd.it"))
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', 'roxygen2', 'covr', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Carter Davis <cdavis40@chicagobooth.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Carter",
                    family = "Davis",
                    role = c("aut", "cre"),
                    email = "cdavis40@chicagobooth.edu")
as necessary.
checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                   ^
checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                                                                                                                                        ^
Maintainer: ‘Jon Clayden <code@clayden.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jon",
                    family = "Clayden",
                    role = c("aut", "cre"),
                    email = "code@clayden.org")
as necessary.
Package required but not available: ‘RSelenium’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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: ‘SHAPforxgboost’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Xiyue Liao <xliao@sdsu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xiyue",
                      family = "Liao",
                      role = c("aut", "cre"),
                      email = "xliao@sdsu.edu"),
               person(given = c("Mary", "C"),
                      family = "Meyer",
                      role = "aut"))
as necessary.
checkRd: (-1) changept.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) changept.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) changept.Rd:22: Lost braces in \itemize; meant \describe ?
Maintainer: ‘Ben Stabler <benstabler@yahoo.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ben",
                    family = "Stabler",
                    role = c("aut", "cre"),
                    email = "benstabler@yahoo.com")
as necessary.
checkRd: (-1) powerShape.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:32-33: Lost braces in \itemize; meant \describe ?
Maintainer: ‘Karline Soetaert <karline.soetaert@nioz.nl>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Karline",
                    family = "Soetaert",
                    role = c("aut", "cre"),
                    email = "karline.soetaert@nioz.nl")
as necessary.
Package required but not available: ‘rgl’

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

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: ‘Jingyi Liang <jingyiliang19@163.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jingyi",
                    family = "Liang",
                    role = c("aut", "cre"),
                    email = "jingyiliang19@163.com")
as necessary.
Packages required but not available: 'tidyverse', 'kableExtra'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Szymon Maksymiuk <sz.maksymiuk@gmail.com>’

The Description field contains
  Lundberg, S., et al., (2016) <arXiv:1705.07874> The SHAP method is used
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'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently 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: ‘W.J. Braun <john.braun@ubc.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("W.", "John"),
                      family = "Braun",
                      role = "aut",
                      email = "john.braun@ubc.ca"),
               person(given = "W.J.",
                      family = "Braun",
                      role = "cre",
                      email = "john.braun@ubc.ca"))
as necessary.
Maintainer: ‘Damien Challet <damien.challet@gmail.com>’

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

The Description field contains
  signal-to-noise ratio, for heavy-tailed data (see <arXiv:1505.01333>).
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/AsymptoticMarkowitz.Rnw’
   ‘inst/doc/SharpeR.Rnw’
   ‘inst/doc/SharpeRatio.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Liang He <lianghe@mit.edu>’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Rodrigo F. de Mello <mellorf@gmail.com>’

The Description field contains
  Coefficient of Supervised Learning Algorithms" <arXiv:1911.05461>; de
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘rmarkdown’

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

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.
Packages required but not available:
  'ggExtra', 'Hmisc', 'rmarkdown', 'survminer'

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.
checkRd: (-1) age_corr.Rd:15: Lost braces
    15 | \item{plot}{Should the results be plotted? (/code{TRUE/FALSE})}
       |                                                  ^
checkRd: (-1) age_corr.Rd:17: Lost braces
    17 | \item{agecorrection}{Correct for jumps in age (/code{TRUE}) or
       |                                                     ^
checkRd: (-1) age_corr.Rd:18: Lost braces
    18 | only for starting time (/code{FALSE})}
       |                              ^
Package required but not available: ‘xlsx’

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

Package suggested but not available for checking: ‘keyring’

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.
Package required but not available: ‘plotly’

Package suggested but not available for checking: ‘roxygen2’

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

Package suggested but not available for checking: ‘ggExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Andrew Lee <andrewl@maths.usyd.edu.au>’

The Description field contains
  Peres, Lee and Keich (2020) <arXiv:2004.07429> where it is also shown
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) shiftrPrepare.Rd:37: Lost braces
    37 |     See code{\link{shiftrPermBinary}} function and the respective example.
       |             ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

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

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

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

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

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

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: ‘Swechhya Bista <swechhyabista@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Swechhya",
                    family = "Bista",
                    role = c("aut", "cre"),
                    email = "swechhyabista@gmail.com")
as necessary.
Package required but not available: ‘shinytest2’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Eric Bailey <ebailey@idem.in.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Eric",
                    family = "Bailey",
                    role = c("aut", "cre"),
                    email = "ebailey@idem.in.gov")
as necessary.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Buttons.Rd: actionButton, checkboxInput
  Collapses.Rd: tabsetPanel, shinyServer
  Modals.Rd: tabPanel
  Tooltips_and_Popovers.Rd: renderUI
  bsButton.Rd: icon
  bsExample.Rd: runApp
  popify.Rd: renderUI
  tipify.Rd: renderUI
  updateButton.Rd: icon, submitButton
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package required but not available: ‘htmlwidgets’

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?
Packages required but not available: 'plotly', '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: 'ggiraph', 'htmlwidgets', 'shinyGizmo'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Emi Tanaka <emi.tanaka@sydney.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Emi",
                      family = "Tanaka",
                      role = c("aut", "cre"),
                      email = "emi.tanaka@sydney.edu.au"),
               person(family = "Niichan",
                      role = "aut"))
as necessary.
Package required but not available: ‘htmlwidgets’

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:
  'shinyjqui', 'knitr', 'rmarkdown'

VignetteBuilder package required 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', 'billboarder', 'yaml'

Packages suggested but not available for checking:
  'keyring', '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', 'shinytest2', '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:
    ‘destroyModule.R’ ‘makeModule.R’
Running ‘spelling.R’ [0s/0s]
  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(shiny.destroy)
  > 
  > test_check("shiny.destroy")
  Error in `source_dir()`:
  ! Failed to evaluate './setup-shinytest2.R'.
  Caused by error in `loadNamespace()`:
  ! there is no package called 'shinytest2'
  Backtrace:
       ▆
    1. ├─testthat::test_check("shiny.destroy")
    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::loadNamespace(x) at ./setup-shinytest2.R:2:1
   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>`(`<S3: packageNotFoundError>`)
   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?
Packages required but not available: 'yaml', 'DT', 'knitr'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Running ‘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(shiny.emptystate)
  > library(shinytest2)
  Error in library(shinytest2) : there is no package called 'shinytest2'
  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?
Packages required but not available:
  'config', 'yaml', 'iheatmapr', 'vegawidget', 'DT'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'r2d3', 'kableExtra'

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

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

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shinyGovstyle)
  > 
  > test_check("shinyGovstyle")
  Saving _problems/test-backlink_Input-7.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 125 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-backlink_Input.R:4:3'): backlink works ───────────────────────
  Expected `backlink_check$children[[1]][[2]]` to be identical to "Back".
  Differences:
  target is NULL, current is character
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 125 ]
  Error:
  ! Test failures.
  Execution halted
Packages required but not available: 'heatmaply', 'plotly', 'rmarkdown'

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: ‘yaml’

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

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:
    ‘continue_sequence.R’ ‘get_exchange_rates.R’
Maintainer: ‘Huseyin Yildiz <huseyinyildiz35@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Huseyin",
                    family = "Yildiz",
                    role = c("aut", "cre"),
                    email = "huseyinyildiz35@gmail.com")
as necessary.
Package required but not available: ‘htmlwidgets’

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

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) shinyjs-defunct.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shinyjs-defunct.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shinyjs-defunct.Rd:20: Lost braces in \itemize; meant \describe ?
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: ‘Joe Wandy <joe.wandy@glasgow.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Joe",
                    family = "Wandy",
                    role = c("aut", "cre"),
                    email = "joe.wandy@glasgow.ac.uk")
as necessary.
Packages required but not available: 'config', 'DT', 'golem', 'htmlwidgets'

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', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) store_googledrive.Rd:19: Lost braces; missing escapes or markup?
    19 | See the {gargle} package to manage authentication, and especially
       |         ^
checkRd: (-1) store_googledrive.Rd:20: Lost braces; missing escapes or markup?
    20 | \href{https://gargle.r-lib.org/articles/articles/managing-tokens-securely.html}{this vignette from {gargle} package} to manage the process.
       |                                                                                                    ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from 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:
    ‘lottie_addEventListener.Rd’ ‘lottie_button.Rd’
    ‘lottie_removeEventListener.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'DT', 'billboarder'

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.
Maintainer: ‘Andreas Neudecker <andreas.neudecker@inwt-statistics.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Andreas",
                    family = "Neudecker",
                    role = c("aut", "cre"),
                    email = "andreas.neudecker@inwt-statistics.de")
as necessary.
Package required but not available: ‘reactable’

Packages suggested but not available for checking: 'learnr', 'shinytest'

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

Packages suggested but not available for checking:
  'nlmixr2', 'nlmixr2plot', 'xpose.nlmixr2', 'shinytest2', 'knitr',
  'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jean Bertin <jean.bertin@mines-paris.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jean",
                    family = "Bertin",
                    role = c("aut", "cre"),
                    email = "jean.bertin@mines-paris.org")
as necessary.
Packages required but not available: 'dygraphs', 'plotly', 'sparklyr', 'DT'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'apexcharter', 'shinytest2'

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:
    ‘fabs.Rd’
Running examples in ‘shinyMobile-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: f7SplitLayout
> ### Title: Framework7 split layout
> ### Aliases: f7SplitLayout
> 
> ### ** Examples
> 
> library(shiny)
> library(ggplot2)
> library(shinyMobile)
> library(apexcharter)
Error in library(apexcharter) : there is no package called ‘apexcharter’
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shinyMobile)
  > library(shinytest2)
  Error in library(shinytest2) : there is no package called 'shinytest2'
  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: 'DT', 'plotly'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Reneé González-Guzmán <rguzman@geociencias.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?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', '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?
Package required but not available: ‘knitr’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Alex Pickering <alexvpickering@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alex",
                    family = "Pickering",
                    role = c("aut", "cre"),
                    email = "alexvpickering@gmail.com")
as necessary.
Problems with news in ‘NEWS.md’:
No news entries found.
Packages required but not available: 'pivottabler', 'colourpicker'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Jari Haukka <jari.haukka@helsinki.fi>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jari",
                    family = "Haukka",
                    role = c("aut", "cre"),
                    email = "jari.haukka@helsinki.fi")
as necessary.
Problems with news in ‘NEWS.md’:
No news entries found.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'leaflet', 'lintr', '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: ‘Alberto Almuiña <albertogonzalezalmuinha@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alberto",
                    family = "Almuiña",
                    role = c("aut", "cre"),
                    email = "albertogonzalezalmuinha@gmail.com")
as necessary.
Packages required but not available: 'sortable', 'DT', 'esquisse'

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', 'DT', 'devtools', 'emayili', 'knitr', '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: ‘Jeff Allen <jeff@trestletech.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Trestle",
                      family = "Technology",
                      role = "aut"),
               person(family = "LLC.",
                      role = "aut"),
               person(given = "Jeff",
                      family = "Allen",
                      role = "cre",
                      email = "jeff@trestletech.com"))
as necessary.
Package required but not available: ‘rgl’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'colourpicker', 'config', 'DT', 'flextable', 'golem', 'rmarkdown',
  'visNetwork'

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

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

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

Packages suggested but not available for checking:
  'DT', 'leaflet.extras', 'rmarkdown', 'shinybusy', 'shinytest2'

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

Packages suggested but not available for checking:
  'covr', 'DT', 'knitr', 'leaflet', 'lintr', 'plotly', 'rmarkdown',
  'shinytest2'

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', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shinyShortcut)
  > 
  > test_check("shinyShortcut")
  Saving _problems/test-shinyShortcut-31.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-shinyShortcut.R:5:3'): ShinyShorcut returns the correct files ──
  <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-shinyShortcut.R:5:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
Maintainer: ‘Sinead E. Morris <sinead.morris@columbia.edu>’

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

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

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

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: ‘pins’

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

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

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

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

VignetteBuilder package required 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: 'ggpmisc', 'ggtree', 'golem'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Amit Kohli <amit@amitkohli.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Amit",
                    family = "Kohli",
                    role = c("aut", "cre"),
                    email = "amit@amitkohli.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: ‘htmlwidgets’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) run_shinytitle_example.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) run_shinytitle_example.Rd:19: Lost braces in \itemize; meant \describe ?
Maintainer: ‘Gábor Csárdi <csardi.gabor@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "John",
                      family = "Papa",
                      role = "aut"),
               person(given = "Tim",
                      family = "Ferrell",
                      role = "aut"),
               person(given = "Hans",
                      family = "Fjällemark",
                      role = "aut"),
               person(given = "Gábor",
                      family = "Csárdi",
                      role = c("aut", "cre"),
                      email = "csardi.gabor@gmail.com"))
as necessary.
Package required but not available: ‘htmlwidgets’

Package suggested but not available for checking: ‘shinytest’

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:
    ‘slimSelectInput.Rd’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > shinytest2::test_app()
  Error in loadNamespace(x) : there is no package called 'shinytest2'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘José Carlos Del Valle <jcval94@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("José", "Carlos", "Del"),
                    family = "Valle",
                    role = c("aut", "cre"),
                    email = "jcval94@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/shotGroups.Rnw’
(Is a VignetteBuilder field missing?)

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.
Maintainer: ‘Yixuan Qiu <yixuan.qiu@cos.name>’

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yixuan",
                      family = "Qiu",
                      role = c("aut", "cre"),
                      email = "yixuan.qiu@cos.name"),
               person(given = c("authors/contributors", "of", "the", "included", "software.", "See", "file", "AUTHORS", "for"),
                      family = "details.",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Binbin Lu <binbinlu@whu.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Binbin",
                    family = "Lu",
                    role = c("aut", "cre"),
                    email = "binbinlu@whu.edu.cn")
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: ‘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: ‘Carlos Mercado <carlos.mercado@flipsidecrypto.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Carlos",
                    family = "Mercado",
                    role = c("aut", "cre"),
                    email = "carlos.mercado@flipsidecrypto.com")
as necessary.
Maintainer: ‘Kyle Caudle <kyle.caudle@sdsmt.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kyle",
                    family = "Caudle",
                    role = c("aut", "cre"),
                    email = "kyle.caudle@sdsmt.edu")
as necessary.
Maintainer: ‘Yuval Benjamini <yuvalbenj@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yuval",
                    family = "Benjamini",
                    role = c("aut", "cre"),
                    email = "yuvalbenj@gmail.com")
as necessary.
Maintainer: ‘Siddhanta Phuyal <siddhantaphuyal7159@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Siddhanta", "Phuyal", "Jyotirmoy", "Sarkar", "<jsarkar@iupui.edu>", "Mamunur", "Rashid"),
                      family = "<mrashid@depauw.edu>",
                      role = "aut",
                      email = "mrashid@depauw.edu"),
               person(given = "Siddhanta",
                      family = "Phuyal",
                      role = "cre",
                      email = "siddhantaphuyal7159@gmail.com"))
as necessary.
checkRd: (-1) shutterplot.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.'
       |                       ^
Packages required but not available: 'DT', 'plotly', 'yaml'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Marie-Karelle Riviere <eldamjh@gmail.com>’

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

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

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: ‘Noé Palmerin  <sie@banxico.org.mx>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("DGIE", "-", "Banco"),
                      family = "de México",
                      role = "aut"),
               person(given = "Noé",
                      family = "Palmerin",
                      role = "cre",
                      email = "sie@banxico.org.mx"))
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: ‘Ruiyan Luo <rluo@gsu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(family = "Ruiyan",
                      role = c("aut", "cre"),
                      email = "rluo@gsu.edu"),
               person(given = "Xin",
                      family = "Qi",
                      role = "aut"))
as necessary.
Maintainer: ‘Tianyu Zhang <tianyuz3@andrew.cmu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tianyu",
                    family = "Zhang",
                    role = c("aut", "cre"),
                    email = "tianyuz3@andrew.cmu.edu")
as necessary.

The Description field contains
  methods can be found in: <arXiv:2206.02994>
  <arXiv:2104.00846><arXiv:2310.12140>.
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 ‘Sieve-package.Rd’:
    \keyword{sieve estimation; estimation using orthog [TRUNCATED]
Maintainer: ‘Petr Matousu <pmatousu@more-praha.cz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Petr",
                    family = "Matousu",
                    role = c("aut", "cre"),
                    email = "pmatousu@more-praha.cz")
as necessary.
checkRd: (-1) drr.Rd:36: Lost braces; missing escapes or markup?
    36 |   \code{drr} {is Rosin - Rammler probability density function}\cr
       |              ^
checkRd: (-1) drr.Rd:37: Lost braces; missing escapes or markup?
    37 |   \code{urr} {is Rosin - Rammler cumulative distribution function (CDF) representing undersize mass fraction}\cr
       |              ^
checkRd: (-1) drr.Rd:38: Lost braces
    38 |   \code{orr} {is Rosin - Rammler complementary CDF representing oversize mass fraction ie. relative remainder on the sieve with the mesh size \code{x}}\cr
       |              ^
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
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: ‘Hanwen Huang <hanwenh.unc@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hanwen",
                      family = "Huang",
                      role = c("aut", "cre"),
                      email = "hanwenh.unc@gmail.com"),
               person(given = c("Yufeng", "Liu", "&", "J.", "S."),
                      family = "Marron",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
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:
  'BSgenome', 'BSgenome.Hsapiens.UCSC.hg19', 'covr', 'knitr',
  'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘show_group_enrichment.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:
  '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: ‘Mathew Chamberlain <chamberlainphd@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: ‘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.
Maintainer: ‘Michal Burdukiewicz <michalburdukiewicz@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) add_k_mer_state.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
Maintainer: ‘Furkan Gursoy <furkan.gursoy@boun.edu.tr>’

The Description field contains
  Networks. <arXiv:2012.05216>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Louis-Marvin Sander <louis.sander@web.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Louis-Marvin",
                      family = "Sander",
                      role = c("aut", "cre"),
                      email = "louis.sander@web.de"),
               person(given = c("master", "of", "ecology", "student", "from"),
                      family = "Bayreuth",
                      role = "aut"),
               person(family = "DE",
                      role = "aut"))
as necessary.
Maintainer: ‘Adriano Zanin Zambom <adriano.zambom@csun.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jongwook",
                      family = "Kim",
                      role = "aut"),
               person(given = c("Adriano", "Zanin"),
                      family = "Zambom",
                      role = c("aut", "cre"),
                      email = "adriano.zambom@csun.edu"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alexandra",
                    family = "Johnson",
                    role = c("aut", "cre"),
                    email = "alexandra@sigopt.com")
as necessary.
Maintainer: ‘Witold Wolski <wew@fgcz.ethz.ch>’

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) sig.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘p_sie.R’ ‘prp.R’ ‘siie.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Martin Olivier <olivier.martin@inrae.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Carpentier",
                      family = "F.",
                      role = "aut"),
               person(given = "Martin",
                      family = "O.",
                      role = "aut"),
               person(given = "Martin",
                      family = "Olivier",
                      role = "cre",
                      email = "olivier.martin@inrae.fr"))
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) siland.Rd:64: Lost braces; missing escapes or markup?
    64 | \item x_{l,i}, local variable l,
       |         ^
checkRd: (-1) siland.Rd:70: Lost braces; missing escapes or markup?
    70 | \item d_{r,i} the distance between the center of pixel r and the observation at site i.
       |         ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Rong Zhang <roz16@pitt.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rong",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "roz16@pitt.edu"),
               person(given = "Zhao",
                      family = "Ren",
                      role = "aut"),
               person(given = "Wei",
                      family = "Chen",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'factoextra', 'drclust', 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Xianyang Zhang <zhangxiany@stat.tamu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Xianyang",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "zhangxiany@stat.tamu.edu"),
               person(given = "Guang",
                      family = "Cheng",
                      role = "aut"),
               person(given = "Jincheng",
                      family = "Bai",
                      role = "aut"))
as necessary.
Maintainer: ‘Justin Leach <jleach@uab.edu>’

The BugReports field in DESCRIPTION has
  https://github.com/jmleach-bst/sim2Dpredictr
which should likely be
  https://github.com/jmleach-bst/sim2Dpredictr/issues
instead.
checkRd: (-1) sim_Y_Binary_X.Rd:51: Lost braces
    51 |     \item \code{dist = "binomial"} is drawn from eqn{Bin(XB, XB(1-XB))}
       |                                                     ^
Package required but not available: ‘knitr’

Packages suggested but not available for checking:
  'devtools', 'pkgdown', 'spelling', 'lintr', 'ggExtra'

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:
  'gt', 'quarto', 'tidyverse'

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘Allison Cynthia Fialkowski <allijazz@uab.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Allison", "Cynthia"),
                    family = "Fialkowski",
                    role = c("aut", "cre"),
                    email = "allijazz@uab.edu")
as necessary.

Found the following (possibly) invalid file URIs:
  URI: corr_bounds.html
    From: inst/doc/method_comp.html
  URI: variable_types
    From: inst/doc/workflow.html
  URI: errorloop.html
    From: inst/doc/workflow.html

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘intercorr_cont.Rd’:
    \keyword{Fleishman,}
    \keyword{continuous,}
    \keyword{correlation,}
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'printr', '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:
  'qtl', 'knitr', 'rmarkdown', 'devtools', 'roxygen2'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert2geno_allchr
> ### Title: Convert continuous allele information into marker genotypes for
> ###   multiple chromosomes
> ### Aliases: convert2geno_allchr
> ### Keywords: utilities
> 
> ### ** Examples
> 
> library(qtl)
Error in library(qtl) : there is no package called ‘qtl’
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Axel Gandy <a.gandy@imperial.ac.uk>’

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', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but 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’
File ‘Sim.DiffProc/libs/Sim.DiffProc.so’:
  Found non-API call to R: ‘SET_TYPEOF’
This entry point may be removed soon.

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Kathrin Moellenhoff <kathrin.moellenhoff@rub.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kathrin",
                    family = "Moellenhoff",
                    role = c("aut", "cre"),
                    email = "kathrin.moellenhoff@rub.de")
as necessary.
Package required but not available: ‘pedprobr’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SimEUCartelLaw.Rcheck/00install.out’ for details.
Maintainer: ‘Waldir Leoncio <waldir.leoncio@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Waldir",
                    family = "Leoncio",
                    role = c("aut", "cre"),
                    email = "waldir.leoncio@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'kinship2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently 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: ‘Andreas Alfons <alfons@ese.eur.nl>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
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: ‘Wolfgang Rolke <wolfgang.rolke@upr.edu>’

The Description field contains
  value.  Details can be found in <arXiv:2007.04727>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Nusrat Rabbee <rabbee@berkeley.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Danyi",
                      family = "Xiong",
                      role = "aut"),
               person(given = "Teeranan",
                      family = "Pokaprakarn",
                      role = "aut"),
               person(given = "Hiroto",
                      family = "Udagawa",
                      role = "aut"),
               person(given = "Nusrat",
                      family = "Rabbee",
                      role = c("aut", "cre"),
                      email = "rabbee@berkeley.edu"))
as necessary.
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pkgdown', 'covr', 'kableExtra'

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

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

VignetteBuilder package required for 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 Toohey <kevintoohey@live.com>’

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) internal.statistics.one.lm.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) internal.statistics.one.lm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Luke Miratrix <lmiratrix@g.harvard.edu>’

The Description field contains
  <arXiv:2002.05746>. This package provides methods for fitting ITS
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: ‘Charlie Wusuo Liu <liuwusuo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Charlie", "Wusuo"),
                    family = "Liu",
                    role = c("aut", "cre"),
                    email = "liuwusuo@gmail.com")
as necessary.
Packages required but not available: 'htmlwidgets', '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: 'plotly', 'Sie2nts'

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: ‘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:
  'simmer.plot', '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: ‘Rex Parsons <Rex.Parsons94@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Hyung Park <parkh15@nyu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hyung",
                      family = "Park",
                      role = c("aut", "cre"),
                      email = "parkh15@nyu.edu"),
               person(given = "Eva",
                      family = "Petkova",
                      role = "aut"),
               person(given = "Thaddeus",
                      family = "Tarpey",
                      role = "aut"),
               person(given = c("R.", "Todd"),
                      family = "Ogden",
                      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: ‘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.
Package required but not available: ‘randomForestSRC’

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

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

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

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

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:
    ‘si_calculate.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Rami Yaari <ramiyaari@gmail.com>’

The Description field contains
  & Yaari (2018) <arXiv:1807.04202>.  Dattner et al. (2017)
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:
  '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: ‘rJava’

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:
    ‘anon.R’ ‘anonymise.Rd’
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.
Maintainer: ‘Nathan Sheffield <nathan@code.databio.org>’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'devtools', '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: ‘Stephen Wisser <swisser98@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Stephen", "C"),
                      family = "Wisser",
                      role = "aut"),
               person(given = "Stephen",
                      family = "Wisser",
                      role = "cre",
                      email = "swisser98@gmail.com"))
as necessary.
Maintainer: ‘Gabor Csardi <csardi.gabor@gmail.com>’

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Augustin Luna <lunaa@cbio.mskcc.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Augustin",
                      family = "Luna",
                      role = c("aut", "cre"),
                      email = "lunaa@cbio.mskcc.org"),
               person(given = "Vinodh",
                      family = "Rajapakse",
                      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: ‘rstanarm’

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:
    ‘markdown_block.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', 'pkgdown', 'tidyverse'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: simpleUpSet
> ### Title: Make simple UpSet plots
> ### Aliases: simpleUpSet
> 
> ### ** Examples
> 
> ## Use a modified version of the movies data provided with the package UpSetR
> library(tidyverse)
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
Running ‘testthat.R’ [2s/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(SimpleUpset)
  Loading required package: ggplot2
  Loading required package: patchwork
  > 
  > test_check("SimpleUpset")
  Error in `source_dir()`:
  ! Failed to evaluate './setup.R'.
  Caused by error in `library()`:
  ! there is no package called 'tidyverse'
  Backtrace:
       ▆
    1. ├─testthat::test_check("SimpleUpset")
    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(tidyverse) at ./setup.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?
Specified C++11: support will be removed soon
checkRd: (-1) simplex_tree.Rd:24: height/width attributes should be in pixels
Maintainer: ‘Abbas Parchami <parchami@uk.ac.ir>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Abbas",
                    family = "Parchami",
                    role = c("aut", "cre"),
                    email = "parchami@uk.ac.ir",
                    comment = "Department of Statistics, Faculty of Mathematics and Computer, Shahid Bahonar University of Kerman, Kerman, Iran")
as necessary.
Maintainer: ‘John P. Nolan  <jpnolan@american.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("John", "P."),
                      family = "Nolan",
                      role = c("aut", "cre"),
                      email = "jpnolan@american.edu"),
               person(given = c("with", "parts", "adapted", "from"),
                      family = "Fortran",
                      role = "aut"),
               person(given = c("matlab", "code", "by", "Alan"),
                      family = "Genz",
                      role = "aut"))
as necessary.
Maintainer: ‘Alexander Mercier <amercier@g.harvard.edu>’

The Description field contains
  (2009)<arXiv:0803.0929>.  Koutis I., Levin, A., Peng, R.
  (2013)<arXiv:1209.5821>. Toivonen, H., Mahler, S., Zhou, F.
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: '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’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘glimpse_na.Rd’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘RDS’

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', '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: ‘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?
No examples, no tests, no vignettes
Cannot process vignettes
Packages suggested but not available for checking: 'covr', '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?
Maintainer: ‘Samuel Benidt <sgbenidt@gmail.com>’

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

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Hyung Park <parkh15@nyu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hyung",
                      family = "Park",
                      role = c("aut", "cre"),
                      email = "parkh15@nyu.edu"),
               person(given = "Eva",
                      family = "Petkova",
                      role = "aut"),
               person(given = "Thaddeus",
                      family = "Tarpey",
                      role = "aut"),
               person(given = c("R.", "Todd"),
                      family = "Ogden",
                      role = "aut"))
as necessary.

The Description field contains
  dose rules" <arXiv:2006.00267v2> for detail of the method. The model
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', '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', 'covr', 'badger'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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', 'gtsummary', 'survminer', '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 required but not available: ‘plotly’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++14: support will be removed soon
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
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.

The Description field contains
  Van Aelst and Zamar (2019) <arXiv:1812.05678>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Adrian Staempfli <adrian.staempfli@fhsg.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@fhsg.ch"),
               person(given = "Christoph",
                      family = "Strauss",
                      role = "aut"),
               person(given = "Michael",
                      family = "Schmid",
                      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: ‘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 = "Kristopher",
                      family = "Kapphahn",
                      role = "aut"),
               person(given = "Ariadna",
                      family = "Garcia",
                      role = "aut"),
               person(given = "Manisha",
                      family = "Desai",
                      role = "aut"),
               person(given = c("Maria", "E."),
                      family = "Montez-Rath",
                      role = "aut"))
as necessary.

The Description field contains
  the main wrapper function. See Montez-Rath et al. <arXiv:1709.10074>
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) make_one_dataset.Rd:67: Lost braces; missing escapes or markup?
    67 |  \code{within.SD} to be extremely small (e.g., $1 * 10^{-7}$) and all corresponding correlations in matrix
       |                                                        ^
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'lintr', '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:
  '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:
  'covr', 'gsDesign', 'gsDesign2', 'gt', 'knitr', 'rmarkdown',
  'survMisc'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as_gt
> ### Title: Convert summary table to a gt object
> ### Aliases: as_gt as_gt.simtrial_gs_wlr
> 
> ### ** Examples
> 
> 
> # Parameters for enrollment
> enroll_rampup_duration <- 4 # Duration for enrollment ramp up
> enroll_duration <- 16 # Total enrollment duration
> enroll_rate <- gsDesign2::define_enroll_rate(
+   duration = c(
+     enroll_rampup_duration, enroll_duration - enroll_rampup_duration),
+  rate = c(10, 30))
Error in loadNamespace(x) : there is no package called ‘gsDesign2’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'kableExtra', '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: ‘Jacob Bien <jbien@usc.edu>’

The Description field contains
  <arXiv:1607.00021>.
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) add_bold.Rd:15: Lost braces; missing escapes or markup?
    15 | For example, in latex it would take "2" and output "{\\bf 2}"; in html
       |                                                     ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Beilun Wang <bw4mw@virginia.edu>’

The BugReports field in DESCRIPTION has
  https://github.com/QData/SIMULE
which should likely be
  https://github.com/QData/SIMULE/issues
instead.
Cannot process vignettes
Packages suggested but not available for checking:
  'epicontacts', '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: ‘Martin Nahuel Garcia <garcia.martin@inta.gob.ar>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Martin", "Nahuel"),
                    family = "Garcia",
                    role = c("aut", "cre"),
                    email = "garcia.martin@inta.gob.ar")
as necessary.
Maintainer: ‘Nikos Sidiropoulos <nikos.sidiro@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?
Maintainer: ‘Rick Dale <racdale@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rick",
                      family = "Dale",
                      role = c("aut", "cre"),
                      email = "racdale@gmail.com"),
               person(given = c("Harish", "S."),
                      family = "Bhat",
                      role = "aut"))
as necessary.
Package required but not available: ‘yaml’

Packages suggested but not available for checking:
  'usethis', 'details', 'roxygen2', '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', '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:
  'spelling', 'knitr', 'rmarkdown', 'cleanrmd', 'kableExtra', 'covr'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown', 'cleanrmd'
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘calculate-effect-sizes.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘Seurat’

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?
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?
Package required but not available: ‘gam’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Boxiang Liu <jollier.liu@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Boxiang",
                    family = "Liu",
                    role = c("aut", "cre"),
                    email = "jollier.liu@gmail.com")
as necessary.
Maintainer: ‘Federico Vivaldi <federico-vivaldi@virgilio.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Federico", "Vivaldi;", "Tommaso"),
                      family = "Lomonaco",
                      role = "aut"),
               person(given = "Federico",
                      family = "Vivaldi",
                      role = "cre",
                      email = "federico-vivaldi@virgilio.it"))
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) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Oscar Garcia <garcia@dasometrics.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Oscar",
                    family = "Garcia",
                    role = c("aut", "cre"),
                    email = "https://orcid.org/0000-0002-8995-1341")
as necessary.

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Maintainer: ‘Jedrzej S. Bojanowski <jedrzej.bojanowski@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Jedrzej", "S."),
                    family = "Bojanowski",
                    role = c("aut", "cre"),
                    email = "jedrzej.bojanowski@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: ‘F Scott Dahlgren <fdahlgr@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("F", "Scott"),
                      family = "Dahlgren",
                      role = c("aut", "cre"),
                      email = "fdahlgr@gmail.com"),
               person(given = c("Ivo", "M"),
                      family = "Foppa",
                      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: ‘Clement Benard <clement.benard5@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Clement",
                      family = "Benard",
                      role = c("aut", "cre"),
                      email = "clement.benard5@gmail.com"),
               person(given = c("Marvin", "N."),
                      family = "Wright",
                      role = c("ctb", "cph")))
as necessary.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sirus.Rcheck/00install.out’ for details.
Package required but not available: ‘mixOmics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Mélanie Huchon <melanie.huchon@u-bordeaux.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Boris",
                      family = "Hejblum",
                      role = "aut"),
               person(given = "Mélanie",
                      family = "Huchon",
                      role = c("aut", "cre"),
                      email = "melanie.huchon@u-bordeaux.fr"))
as necessary.
Maintainer: ‘Hyunseung Kang <hyunseung@stat.wisc.edu>’

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) rawCCD.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{distr.type}{school district type (constructed for illustration purposes; (values={"A", "B", "C", "D"})).}
       |                                                                                          ^
checkRd: (-1) selectMatch.Rd:61: Lost braces; missing escapes or markup?
    61 | \item{replacementUnitsFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "replacementUnits.csv"}
       |                                                                    ^
checkRd: (-1) selectMatch.Rd:63: Lost braces; missing escapes or markup?
    63 | \item{subUnitTableFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "subUnitTable.csv"}
       |                                                                ^
checkRd: (-1) selectMatch.Rd:66: Lost braces; missing escapes or markup?
    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                  ^
checkRd: (-1) selectMatch.Rd:66: Lost braces; missing escapes or markup?
    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                                                                                  ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'ymlthis', 'yaml', 'rmarkdown', 'rlist'

Packages suggested but not available for checking:
  'knitr', 'spelling', 'pkgdown', 'roxygen2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Phillip B. Nicol <philnicol740@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Phillip", "B."),
                    family = "Nicol",
                    role = c("aut", "cre"),
                    email = "philnicol740@gmail.com")
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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for 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 Stein <news@jonasstein.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jonas",
                      family = "Stein",
                      role = c("aut", "cre"),
                      email = "news@jonasstein.de"),
               person(given = "Ben",
                      family = "Tupper",
                      role = "aut"))
as necessary.
Malformed Description field: should contain one or more complete sentences.
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: 'yaml', 'leafgl', 'leaflet', 'tmap'

Packages suggested but not available for checking:
  'covr', 'DiagrammeR', 'randomForestExplainer'

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?
checkRd: (-1) ss.cc.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ss.ci.Rd:26: Lost braces
    26 | \item{alpha}{The eqn{\\alpha} error used to compute the \eqn{100*(1-\\alpha)\%} confidence interval}
       |                     ^
checkRd: (-1) ss.rr.Rd:84: Lost braces; missing escapes or markup?
    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |     ^
checkRd: (-1) ss.rr.Rd:84: Lost braces; missing escapes or markup?
    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |                 ^
checkRd: (-1) ss.rr.Rd:87: Lost braces; missing escapes or markup?
    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                            ^
checkRd: (-1) ss.rr.Rd:87: Lost braces; missing escapes or markup?
    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                                        ^
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxyglobals', 'vcr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Author field differs from that derived from Authors@R
  Author:    ‘Sean Kross [aut], Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Fred Hutchinson Cancer Center [fnd] (007ps6h72)’
  Authors@R: ‘Sean Kross [aut], Scott Chamberlain [aut, cre] (ORCID: <https://orcid.org/0000-0003-1444-9135>), Fred Hutchinson Cancer Center [fnd] (ROR: <https://ror.org/007ps6h72>)’
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sixtyfour)
  > 
  > test_check("sixtyfour")
  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("sixtyfour")
    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?
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:
    ‘SiZer.R’
Maintainer: ‘Joe Roberts <jorobert@tibco.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("TIBCO", "Software"),
                      family = "Inc.",
                      role = "aut"),
               person(given = "Joe",
                      family = "Roberts",
                      role = "cre",
                      email = "jorobert@tibco.com"))
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:
  'sjPlot', 'knitr', 'rmarkdown'

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

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

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

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: ‘kableExtra’

Packages suggested but not available for checking:
  'lintr', 'quarto', 'sjPlot'

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: ‘kinship2’

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: ‘Seunggeun (Shawn) Lee <lee7801@snu.ac.kr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Seunggeun",
                      family = "Lee",
                      role = "aut",
                      comment = "Shawn"),
               person(given = "Zhangchen",
                      family = "Zhao",
                      role = "aut"),
               person(given = c("with", "contributions", "from", "Larisa"),
                      family = "Miropolsky",
                      role = "aut"),
               person(given = "Michael",
                      family = "Wu",
                      role = "aut"),
               person(given = "Seunggeun",
                      family = "Lee",
                      role = "cre",
                      email = "lee7801@snu.ac.kr",
                      comment = "Shawn"))
as necessary.
Packages required but not available: 'DT', '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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Chun Fung Kwok <jkwok@svi.edu.au>’

The BugReports field in DESCRIPTION has
  https://github.com/kcf-jackson/sketch
which should likely be
  https://github.com/kcf-jackson/sketch/issues
instead.
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:
    ‘ext-annotate_expr.R’
Running examples in ‘sketch-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: eng_sketch
> ### Title: A language engine for 'sketch'
> ### Aliases: eng_sketch
> 
> ### ** Examples
> 
> # The following line makes `sketch::eng_sketch` available to `knitr::knit_engines`.
> # It is usually used in the 'setup' code chunk of an R Markdown document
> knitr::knit_engines$set(sketch = sketch::eng_sketch)
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?
Packages required but not available: 'knitr', 'xaringanExtra', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘David Scott <d.scott@auckland.ac.nz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "David",
                      family = "Scott",
                      role = c("aut", "cre"),
                      email = "d.scott@auckland.ac.nz"),
               person(given = "Fiona",
                      family = "Grimson",
                      role = "aut"))
as necessary.
Maintainer: ‘Hanmo Li <hanmo@pstat.ucsb.edu>’

The Description field contains
  Mengyang Gu (2023), <arXiv:2310.18611>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘rgl’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Patchanok Srisuradetchai <s.patchanok@gmail.com>’

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

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘Ski.Mack.Rd’:
    \keyword{block designs, missing values}
Package required but not available: ‘knitr’

Package suggested but not available for checking: ‘rmarkdown’

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

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

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', 'covr', '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: 'BayesianTools', 'plotly', 'mapview'

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: ‘Matt Kaye <mrkaye97@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Bob",
                      family = "Rudis",
                      role = c("aut", "cre")),
               person(given = "Jay",
                      family = "Jacobs",
                      role = "ctb"),
               person(given = "David",
                      family = "Severski",
                      role = "ctb"),
               person(given = "Quinn",
                      family = "Weber",
                      role = "ctb"),
               person(given = "Konrad",
                      family = "Karczewski",
                      role = "ctb"),
               person(given = "Shinya",
                      family = "Uryu",
                      role = "ctb"),
               person(given = "Gregory",
                      family = "Jefferis",
                      role = "ctb"),
               person(given = "Ed",
                      family = "Niles",
                      role = "ctb"),
               person(given = "Rick",
                      family = "Saporta",
                      role = "ctb"),
               person(given = "Jonathan",
                      family = "Sidi",
                      role = c("aut", "ctb")),
               person(given = "Matt",
                      family = "Kaye",
                      role = c("aut", "ctb", "cre"),
                      email = "mrkaye97@gmail.com"),
               person(given = "Xinye",
                      family = "Li",
                      role = "ctb"),
               person(given = "Andrie",
                      family = "de Vries",
                      role = c("aut", "ctb")))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'texPreview'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Fabio Centofanti <fabio.centofanti@unina.it>’

The Description field contains
  <arXiv:2007.00529>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

The BugReports field in DESCRIPTION has
  https://github.com/unina-sfere/slasso
which should likely be
  https://github.com/unina-sfere/slasso/issues
instead.
Package required but not available: ‘fda.usc’

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

Package in Depends/Imports which should probably only be in LinkingTo: ‘RcppArmadillo’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ilana Trumble <itrumble@unc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Michael",
                      family = "Hudgens",
                      role = "aut"),
               person(given = "Ilana",
                      family = "Trumble",
                      role = c("aut", "cre"),
                      email = "itrumble@unc.edu"),
               person(given = "Andrew",
                      family = "Allmon",
                      role = "aut"))
as necessary.
Maintainer: ‘Muntashir-Al-Arefin <sheen4783@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(family = "Muntashir-Al-Arefin",
                      role = c("aut", "cre"),
                      email = "sheen4783@gmail.com"),
               person(given = c("Prof.", "Md.", "Ayub"),
                      family = "Al.",
                      role = "aut"))
as necessary.
Maintainer: ‘Christine Blume <christine.blume@sbg.ac.at>’

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', '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: ‘Berwin A Turlach <Berwin.Turlach@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Original", "by", "F.L."),
                      family = "Ramsey",
                      role = "aut"),
               person(given = c("D.W.", "Schafer;", "modifications", "by", "Daniel", "W."),
                      family = "Schafer",
                      role = "aut"),
               person(given = "Jeannie",
                      family = "Sifneos",
                      role = "aut"),
               person(given = c("Berwin", "A.", "Turlach;", "vignettes", "contributed", "by", "Nicholas"),
                      family = "Horton",
                      role = "aut"),
               person(given = "Kate",
                      family = "Aloisio",
                      role = "aut"),
               person(given = "Ruobing",
                      family = "Zhang",
                      role = "aut"),
               person(given = c("with", "corrections", "by", "Randall"),
                      family = "Pruim",
                      role = "aut"),
               person(given = c("Berwin", "A"),
                      family = "Turlach",
                      role = "cre",
                      email = "Berwin.Turlach@gmail.com"))
as necessary.
Packages suggested but not available for checking: 'knitr', 'mosaic'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/chapter01-HortonMosaic.Rnw’
   ‘inst/doc/chapter02-HortonMosaic.Rnw’
   ‘inst/doc/chapter03-HortonMosaic.Rnw’
   ‘inst/doc/chapter04-HortonMosaic.Rnw’
   ‘inst/doc/chapter05-HortonMosaic.Rnw’
   ‘inst/doc/chapter06-HortonMosaic.Rnw’
   ‘inst/doc/chapter07-HortonMosaic.Rnw’
   ‘inst/doc/chapter08-HortonMosaic.Rnw’
   ‘inst/doc/chapter09-HortonMosaic.Rnw’
   ‘inst/doc/chapter10-HortonMosaic.Rnw’
   ‘inst/doc/chapter11-HortonMosaic.Rnw’
   ‘inst/doc/chapter12-HortonMosaic.Rnw’
   ‘inst/doc/chapter13-HortonMosaic.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Berwin A Turlach <Berwin.Turlach@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Original", "by", "F.L."),
                      family = "Ramsey",
                      role = "aut"),
               person(given = c("D.W.", "Schafer;", "modifications", "by", "Daniel", "W."),
                      family = "Schafer",
                      role = "aut"),
               person(given = "Jeannie",
                      family = "Sifneos",
                      role = "aut"),
               person(given = c("Berwin", "A.", "Turlach;", "vignettes", "contributed", "by", "Nicholas"),
                      family = "Horton",
                      role = "aut"),
               person(given = "Linda",
                      family = "Loi",
                      role = "aut"),
               person(given = "Kate",
                      family = "Aloisio",
                      role = "aut"),
               person(given = "Ruobing",
                      family = "Zhang",
                      role = "aut"),
               person(given = c("with", "corrections", "by", "Randall"),
                      family = "Pruim",
                      role = "aut"),
               person(given = c("Berwin", "A"),
                      family = "Turlach",
                      role = "cre",
                      email = "Berwin.Turlach@gmail.com"))
as necessary.
Packages suggested but not available for checking:
  'Hmisc', 'knitr', 'mosaic'

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

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/chapter01-HortonMosaic.Rnw’
   ‘inst/doc/chapter02-HortonMosaic.Rnw’
   ‘inst/doc/chapter03-HortonMosaic.Rnw’
   ‘inst/doc/chapter04-HortonMosaic.Rnw’
   ‘inst/doc/chapter05-HortonMosaic.Rnw’
   ‘inst/doc/chapter06-HortonMosaic.Rnw’
   ‘inst/doc/chapter07-HortonMosaic.Rnw’
   ‘inst/doc/chapter08-HortonMosaic.Rnw’
   ‘inst/doc/chapter09-HortonMosaic.Rnw’
   ‘inst/doc/chapter10-HortonMosaic.Rnw’
   ‘inst/doc/chapter11-HortonMosaic.Rnw’
   ‘inst/doc/chapter12-HortonMosaic.Rnw’
   ‘inst/doc/chapter13-HortonMosaic.Rnw’
(Is a VignetteBuilder field missing?)

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

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: ‘Shan Ba <shanbatr@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Shan",
                    family = "Ba",
                    role = c("aut", "cre"),
                    email = "shanbatr@gmail.com")
as necessary.
Packages required but not available: 'DT', 'golem'

Packages suggested but not available for checking:
  'bookdown', 'colourpicker', 'esquisse', 'flextable', 'kableExtra',
  'knitr', 'openMSE', 'shiny.i18n', 'rmarkdown'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Everaldo Freitas Guedes <efgestatistico@gmail.com>’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) fit_slim.Rd:24: Lost braces; missing escapes or markup?
    24 | sum(x' V^{-1} (y - x beta)) = 0 as the covariance V tends from V[, , 1] +
       |          ^
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.
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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Emmanuel Caron <emmanuelcaron3@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Emmanuel",
                      family = "Caron",
                      role = c("aut", "cre"),
                      email = "emmanuelcaron3@gmail.com"),
               person(given = "Jérôme",
                      family = "Dedecker",
                      role = "aut"),
               person(given = "Bertrand",
                      family = "Michel",
                      role = "aut"))
as necessary.

The Description field contains
  <arXiv:1906.06583>.
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', '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', 'bookdown', 'covr', 'tmap', 'leaflet'

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

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

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

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: ‘Wesley Burr <wesley.burr@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Wesley",
                      family = "Burr",
                      role = c("aut", "cre"),
                      email = "wesley.burr@gmail.com"),
               person(given = c("with", "contributions", "from", "Karim"),
                      family = "Rahim",
                      role = "aut"))
as necessary.
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
Running examples in ‘slp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: slp.gam
> ### Title: Generate a Basis Matrix for Discrete Prolate Spheroidal
> ###   (Slepian) Sequences
> ### Aliases: slp.gam slp
> ### Keywords: models smooth regression Slepian gam
> 
> ### ** Examples
> 
>     # Examples using pkg:gam
>     library("gam")
Error in library("gam") : there is no package called ‘gam’
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', 'covr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Author field differs from that derived from Authors@R
  Author:    ‘George Vega Yon [aut, cre] (<https://orcid.org/0000-0002-3171-0844>), Paul Marjoram [ctb, ths] (<https://orcid.org/0000-0003-0824-7449>), National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02), Michael Schubert [rev] (JOSS reviewer, <https://orcid.org/0000-0002-6862-5221>), Michel Lang [rev] (JOSS reviewer, <https://orcid.org/0000-0001-9754-0393>)’
  Authors@R: ‘George Vega Yon [aut, cre] (ORCID: <https://orcid.org/0000-0002-3171-0844>), Paul Marjoram [ctb, ths] (ORCID: <https://orcid.org/0000-0003-0824-7449>), National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02), Michael Schubert [rev] (what: JOSS reviewer, ORCID: <https://orcid.org/0000-0002-6862-5221>), Michel Lang [rev] (what: JOSS reviewer, ORCID: <https://orcid.org/0000-0001-9754-0393>)’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'Hmisc', 'weights'

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/smacof.Rnw’
(Is a VignetteBuilder field missing?)

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

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: ‘Abhishek Nandy <nandy006@umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Abhishek",
                    family = "Nandy",
                    role = c("aut", "cre"),
                    email = "nandy006@umn.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'kableExtra', 'sdcHierarchies'

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

Package suggested but not available for checking: ‘gurobi’

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.
Maintainer: ‘William Artman <William_Artman@URMC.Rochester.edu>’

The Description field contains
  outcomes. Please see Artman (2020) <arXiv:2008.02341>.
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’

Package suggested but not available for checking: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘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.
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.
checkRd: (-1) cities_lon_lat.Rd:6: Lost braces
     6 | A subset of world.cities{maps}. Extracted in order to shink number of dependencies. 
       |                         ^
Packages required but not available: 'devtools', 'usethis', 'rmarkdown'

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

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Dipankar Bandyopadhyay <bandyopd@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jing",
                      family = "Xu",
                      role = "aut"),
               person(given = "Dipankar",
                      family = "Bandyopadhyay",
                      role = c("aut", "cre"),
                      email = "bandyopd@gmail.com"),
               person(given = "Douglas",
                      family = "Azevedo",
                      role = "aut"),
               person(given = "Bibhas",
                      family = "Chakraborty",
                      role = "aut"))
as necessary.

The Description field contains
  <arXiv:1902.09386>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘covr’

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jun Chen <Chen.Jun2@mayo.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jun",
                      family = "Chen",
                      role = c("aut", "cre"),
                      email = "Chen.Jun2@mayo.edu"),
               person(given = "Ehsan",
                      family = "Behnam",
                      role = "aut",
                      email = "behnamgh@usc.edu"))
as necessary.
Package required but not available: ‘smarter’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Remko Duursma <remkoduursma@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "David",
                      family = "Warton",
                      role = "aut",
                      email = "David.Warton@unsw.edu.au"),
               person(given = "Remko",
                      family = "Duursma",
                      role = c("aut", "cre"),
                      email = "remkoduursma@gmail.com"),
               person(given = "Daniel",
                      family = "Falster",
                      role = "aut"),
               person(given = "Sara",
                      family = "Taskinen.",
                      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: ‘Herman Jopia <hjopia@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Herman",
                    family = "Jopia",
                    role = c("aut", "cre"),
                    email = "hjopia@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: ‘Tobias Verbeke <tobias.verbeke@openanalytics.eu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Tobias",
                      family = "Verbeke",
                      role = c("aut", "cre"),
                      email = "tobias.verbeke@openanalytics.eu"),
               person(given = c("based", "on", "datasets", "provided", "on", "the", "book's"),
                      family = "website",
                      role = "aut"))
as necessary.
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
Maintainer: ‘Ed Merkle <merklee@missouri.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ed",
                      family = "Merkle",
                      role = c("aut", "cre"),
                      email = "merklee@missouri.edu"),
               person(given = "Michael",
                      family = "Smithson",
                      role = "aut"))
as necessary.
checkRd: (-1) trlong.Rd:17: Lost braces
    17 |     \item{\code{resp}}{a factor indicating the transport mode choice, and \code{B} denotes taking the bus, code{D} denotes driving one's own vehicle, \code{F} denotes getting a ride with a friend, \code{O} denotes other, and \code{W} denotes walking}
       |                                                                                                                ^
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.
Package required but not available: ‘gt’

Packages suggested but not available for checking:
  'gtsummary', 'knitr', 'reactable', 'rmarkdown', 'survminer',
  'usethis'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) smdocker_log.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:35-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:19: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from 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) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                  ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                            ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                          ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                                    ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                              ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                        ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                      ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                                ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Qian Zhu <zqian@jimmy.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Qian",
                      family = "Zhu",
                      role = c("aut", "cre"),
                      email = "zqian@jimmy.harvard.edu"),
               person(given = "Guo-Cheng",
                      family = "Yuan",
                      role = "aut"))
as necessary.
Maintainer: ‘Darren Wilkinson <darrenjwilkinson@btinternet.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Darren",
                    family = "Wilkinson",
                    role = c("aut", "cre"),
                    email = "darrenjwilkinson@btinternet.com")
as necessary.
Maintainer: ‘Paul Walter <paul.w@gmx.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Paul",
                    family = "Walter",
                    role = c("aut", "cre"),
                    email = "paul.w@gmx.net")
as necessary.
Packages required but not available: 'Hmisc', 'weights'

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', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(smidm)
  > library(covr)
  Error in library(covr) : there is no package called 'covr'
  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: ‘Alexey Shipunov <dactylorhiza@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alexey",
                    family = "Shipunov",
                    role = c("aut", "cre"),
                    email = "dactylorhiza@gmail.com",
                    comment = "with help of Eugenij Altshuler")
as necessary.
Packages required but not available: 'htmlwidgets', 'yaml'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Siddharth Jain <siddharthjain242@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Siddharth",
                      family = "Jain",
                      role = c("aut", "cre"),
                      email = "siddharthjain242@gmail.com"),
               person(given = "Prabhanjan",
                      family = "Tattar",
                      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: ‘Adam Lund <adam.lund@math.ku.dk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Adam",
                    family = "Lund",
                    role = c("aut", "cre"),
                    email = "adam.lund@math.ku.dk")
as necessary.

The Description field contains
  Mogensen and Hansen (2019) <arXiv:1805.02407>. Currently Lasso and SCAD
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Specified C++11: support will be removed soon
checkRd: (-1) SMMA.Rd:115: Lost braces
   115 |  is the empirical explained variance from \cite{Meinshausen and B{u}hlmann, 2015}.  See \cite{Lund et al., 2020} for more details and references.
       |                                                                  ^
checkRd: (-1) SMMA.Rd:170: Lost braces
   170 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
Specified C++11: support will be removed soon
Maintainer: ‘Nicolas Vergne <nicolas.vergne@univ-rouen.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Vlad", "Stefan"),
                      family = "Barbu",
                      role = "aut"),
               person(given = "Caroline",
                      family = "Berard",
                      role = "aut"),
               person(given = "Dominique",
                      family = "Cellier",
                      role = "aut"),
               person(given = "Mathilde",
                      family = "Sautreuil",
                      role = "aut"),
               person(given = "Nicolas",
                      family = "Vergne",
                      role = c("aut", "cre"),
                      email = "nicolas.vergne@univ-rouen.fr"))
as necessary.
checkRd: (-1) estimMk.Rd:44: Lost braces; missing escapes or markup?
    44 | estimMk returns the transition probability matrix of size (S^{k})xS (with S = length(E)) 
       |                                                              ^
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxytest'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Aldo M. Garay <medina_garay@yahoo.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Aldo", "M."),
                      family = "Garay",
                      role = c("aut", "cre"),
                      email = "medina_garay@yahoo.com"),
               person(given = c("Monique", "Bettio"),
                      family = "Massuia",
                      role = "aut",
                      email = "moniquemassuia@gmail.com"),
               person(given = "Victor",
                      family = "Lachos",
                      role = "aut",
                      email = "hlachos@ime.unicamp.br"))
as necessary.
Maintainer: ‘Qingan Sun <quinsun@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Qingan",
                      family = "Sun",
                      role = c("aut", "cre"),
                      email = "quinsun@gmail.com"),
               person(given = "Xiaojun",
                      family = "Li",
                      role = "aut"),
               person(given = c("James", "C"),
                      family = "Sacchettini",
                      role = "aut"))
as necessary.
checkRd: (-1) getGlobalOptimum.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smoof_function.Rd:10: Lost braces
    10 | or code{smoof_multi_objective_function}. Both single- and multi-objective functions share the following attributes.
       |        ^
Maintainer: ‘Georg Hahn <ghahn@hsph.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Georg",
                      family = "Hahn",
                      role = c("aut", "cre"),
                      email = "ghahn@hsph.harvard.edu"),
               person(given = c("Sharon", "M."),
                      family = "Lutz",
                      role = "ctb"),
               person(given = "Nilanjana",
                      family = "Laha",
                      role = "ctb"),
               person(given = "Christoph",
                      family = "Lange",
                      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?
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.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  smoother.Rd: TTR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Christian Hennig <christian.hennig@unibo.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Christian",
                    family = "Hennig",
                    role = c("aut", "cre"),
                    email = "christian.hennig@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?
Maintainer: ‘Chanwoo Lee <chanwoo.lee@wisc.edu>’

The Description field contains
  estimation with unknown permutations" <arXiv:2111.04681>.
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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Found the following files/directories:
  ‘my_new_social_media_plot.png’
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Adrian Bowman <adrian.bowman@glasgow.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Adrian",
                      family = "Bowman",
                      role = c("aut", "cre"),
                      email = "adrian.bowman@glasgow.ac.uk"),
               person(given = c("Adelchi", "Azzalini.", "Ported", "to", "R", "by", "B.", "D.", "Ripley", "up", "to", "version"),
                      family = "2.0",
                      role = "aut",
                      email = "ripley@stats.ox.ac.uk"),
               person(given = c("version", "2.1", "by", "Adrian"),
                      family = "Bowman",
                      role = "aut"),
               person(given = "Adelchi",
                      family = "Azzalini",
                      role = "aut"),
               person(given = c("version", "2.2", "by", "Adrian"),
                      family = "Bowman.",
                      role = "aut"))
as necessary.
Running examples in ‘sm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sm.surface3d
> ### Title: Adding a regression surface to an rgl plot.
> ### Aliases: sm.surface3d
> ### Keywords: nonparametric regression smooth
> 
> ### ** Examples
> 
> with(trawl, {
+    Zone93    <- (Year == 1 & Zone == 1)
+    Position  <- cbind(Longitude - 143, Latitude)
+    model1 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.1, 0.1), display = "rgl", xlab="Longitude - 143")
+    model2 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.2, 0.2), display = "none")
+    sm.surface3d(model2$eval.points, model2$est, model1$scaling, col = "red")
+ })
Error in sm.surface3d(model2$eval.points, model2$est, model1$scaling,  : 
  a scaling must be specified.
Calls: with -> with.default -> eval -> eval -> sm.surface3d
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: ‘Dimitris Kavroudakis <dimitris123@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Dimitris",
                    family = "Kavroudakis",
                    role = c("aut", "cre"),
                    email = "dimitris123@gmail.com")
as necessary.
Packages required but not available: 'rms', 'flextable'

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

The Description field contains
  Loewinger et al., (2022) <arXiv:2212.08697>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘JuliaCall’

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:
  'bookdown', '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: ‘Wujuan Zhong <zhongwujuan@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Wujuan",
                    family = "Zhong",
                    role = c("aut", "cre"),
                    email = "zhongwujuan@gmail.com")
as necessary.
Maintainer: ‘Samuel Blanck <samuel.blanck@univ-lille.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Guillemette",
                      family = "Marot",
                      role = c("aut", "cre")),
               person(given = "Samuel",
                      family = "Blanck",
                      role = "cre",
                      email = "samuel.blanck@univ-lille.fr"))
as necessary.
Package required but not available: ‘sortable’

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

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: ‘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.
checkRd: (-1) SnakesAndLaddersGame.Rd:25: Lost braces; missing escapes or markup?
    25 | {Hector Haffenden} {haffendenh@cardiff.ac.uk}
       |                    ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from 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:
    ‘sk.R’ ‘sk_export.R’ ‘sk_index.R’ ‘sk_pars.R’ ‘sk_plot.R’
    ‘sk_plot.Rd’ ‘sk_sub.Rd’ ‘sk_var.Rd’ ‘sk_var_mult.Rd’
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                  ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                           ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                                      ^
checkRd: (-1) sk_GLS.Rd:40: Lost braces; missing escapes or markup?
    40 | Operations with V^{-1} are computed using the factorization \code{fac} (see \code{sk_var}), or
       |                   ^
checkRd: (-1) sk_LL.Rd:37: Lost braces; missing escapes or markup?
    37 | \code{quad_form} is z^T V^{-1} z, for the observed response vector z, which is constructed
       |                           ^
checkRd: (-1) sk_var.Rd:41: Lost braces; missing escapes or markup?
    41 | returns the quadratic form X^T V^{-1} X.
       |                                  ^
checkRd: (-1) sk_var.Rd:33: Lost braces; missing escapes or markup?
    33 | either matrix \code{V}, or X^T V^{-1} X, or a factorization ('chol' or 'eigen')
       |                                  ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Giancarlo Vercellino <giancarlo.vercellino@gmail.com>’

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

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.
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'knitr', 'kableExtra'

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: ‘Takayuki Kawashima <kawashima@c.titech.ac.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Toshihiro",
                      family = "Abe",
                      role = "aut",
                      email = "abetosh@ss.nanzan-u.ac.jp"),
               person(given = "Hironori",
                      family = "Fujisawa",
                      role = "aut",
                      email = "fujisawa@ism.ac.jp"),
               person(given = "Takayuki",
                      family = "Kawashima",
                      role = c("aut", "cre"),
                      email = "kawashima@c.titech.ac.jp"))
as necessary.
Maintainer: ‘Benjamin Brew <goldenberglab@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Bo",
                      family = "Wang",
                      role = "aut"),
               person(given = "Aziz",
                      family = "Mezlini",
                      role = "aut"),
               person(given = "Feyyaz",
                      family = "Demir",
                      role = "aut"),
               person(given = "Marc",
                      family = "Fiume",
                      role = "aut"),
               person(given = "Zhuowen",
                      family = "Tu",
                      role = "aut"),
               person(given = "Michael",
                      family = "Brudno",
                      role = "aut"),
               person(given = "Benjamin",
                      family = "Haibe-Kains",
                      role = "aut"),
               person(given = "Anna",
                      family = "Goldenberg",
                      role = "aut"),
               person(given = "Benjamin",
                      family = "Brew",
                      role = "cre",
                      email = "goldenberglab@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', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Wei Sun <sunweisurrey8@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Wei",
                      family = "Sun",
                      role = c("aut", "cre"),
                      email = "sunweisurrey8@gmail.com"),
               person(given = "Xingye",
                      family = "Qiao",
                      role = "aut"),
               person(given = "Guang",
                      family = "Cheng",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', '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: ‘Jochen Knaus <jo@imbi.uni-freiburg.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jochen",
                    family = "Knaus",
                    role = c("aut", "cre"),
                    email = "jo@imbi.uni-freiburg.de")
as necessary.
Maintainer: ‘Svetlana Eden <svetlana.eden@vanderbilt.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Svetlana",
                    family = "Eden",
                    role = c("aut", "cre"),
                    email = "svetlana.eden@vanderbilt.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: ‘Hana Sevcikova <hanas@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hana",
                      family = "Sevcikova",
                      role = c("aut", "cre"),
                      email = "hanas@uw.edu"),
               person(given = c("A.", "J."),
                      family = "Rossini",
                      role = "aut"))
as necessary.
Package required but not available: ‘yaml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Luke Tierney <luke-tierney@uiowa.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Luke",
                      family = "Tierney",
                      role = c("aut", "cre"),
                      email = "luke-tierney@uiowa.edu"),
               person(given = c("A.", "J."),
                      family = "Rossini",
                      role = "aut"),
               person(given = "Na",
                      family = "Li",
                      role = "aut"),
               person(given = "H.",
                      family = "Sevcikova",
                      role = "aut"))
as necessary.
Package required but not available: ‘yaml’

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'VariantAnnotation',
  'TxDb.Hsapiens.UCSC.hg19.knownGene'

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: ‘Matteo Sesia <msesia@stanford.edu>’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Specified C++11: support will be removed soon
checkRd: (-1) knockoffGenotypes.Rd:32: Lost braces; missing escapes or markup?
    32 | This function efficiently constructs group-knockoffs of {0,1,2} variables distributed
       |                                                         ^
checkRd: (-1) knockoffGenotypes.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{X}{a {0,1,2} matrix of size n-by-p containing the original variables.}
       |            ^
checkRd: (-1) knockoffGenotypes.Rd:29: Lost braces; missing escapes or markup?
    29 | A {0,1,2} matrix of size n-by-p containing the knockoff variables.
       |   ^
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.
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/snplist.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘David Hervas <ddhervas@yahoo.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "David",
                    family = "Hervas",
                    role = c("aut", "cre"),
                    email = "ddhervas@yahoo.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?
checkRd: (-1) plot.selm.Rd:101: Lost braces
   101 | data. Default value for code{which} is \code{2:4} if \code{p>1}, otherwise
       |                             ^
Maintainer: ‘Luis Benavides <luisbv@tec.mx>’

The Description field contains
  (2019) <arXiv:1901.04443>.
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?
Package required but not available: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Alireza Mahani <alireza.s.mahani@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Alireza", "S."),
                      family = "Mahani",
                      role = "aut"),
               person(given = "Asad",
                      family = "Hasan",
                      role = "aut"),
               person(given = "Marshall",
                      family = "Jiang",
                      role = "aut"),
               person(given = c("Mansour", "T.A."),
                      family = "Sharabiani",
                      role = "aut"),
               person(given = "Alireza",
                      family = "Mahani",
                      role = "cre",
                      email = "alireza.s.mahani@gmail.com"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
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("based", "on", "original", "code", "by", "David"),
                      family = "Brahm",
                      role = "aut"))
as necessary.
Found the following calls to attach():
File ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘.R_Test’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Maikol Solís <maikol.solis@ucr.ac.cr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Maikol",
                    family = "Solís",
                    role = c("aut", "cre"),
                    email = "maikol.solis@ucr.ac.cr")
as necessary.

The Description field contains
  M. (2018) <arXiv:1803.03333>.
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?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'roxyglobals'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘PowerRelation.R’ ‘SocialRanking.R’ ‘copeland.R’ ‘doRanking.Rd’
    ‘elementLookup.Rd’ ‘generator.R’ ‘makePowerRelationMonotonic.R’
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.
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:
  'cmdstanr', '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?
Maintainer: ‘Kieran Healy <kjhealy@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) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                          ^
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                                                        ^
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                                                                     ^
Maintainer: ‘Yang Li <yangli.stat@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yang",
                      family = "Li",
                      role = c("aut", "cre"),
                      email = "yangli.stat@gmail.com"),
               person(given = c("Jun", "S."),
                      family = "Liu",
                      role = "aut"))
as necessary.
checkRd: (-1) s_soda_pred.Rd:8: Lost braces; missing escapes or markup?
     8 | S-SODA assumes within each slice the X vector follow multivariate normal distribution. This function predicts the response y by reverting the P(X | slice(y)) to P(slice(y) | X), and estimates the E(y|X) as sum_{h} E(y | slice(y)=h, X) P (slice(y)=h | X)
       |                                                                                                                                                                                                                   ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from 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) db_compact.Rd:41: Lost braces; missing escapes or markup?
    41 | database structure will be set to true. See GET /{db}. You can also obtain a list of
       |                                                  ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Luis Diaz-Garcia <diazgarcia@wisc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Luis",
                    family = "Diaz-Garcia",
                    role = c("aut", "cre"),
                    email = "diazgarcia@wisc.edu")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Maintainer: ‘Jose D. Loera <jose.loera@inegi.org.mx>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Jose", "D."),
                    family = "Loera",
                    role = c("aut", "cre"),
                    email = "jose.loera@inegi.org.mx")
as necessary.
Package required but not available: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘G. Peters <peters.activities@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "G.",
                    family = "Peters",
                    role = c("aut", "cre"),
                    email = "peters.activities@gmail.com",
                    comment = "Ed.")
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: ‘Seungjun Ahn <seungjun.ahn@mountsinai.org>’

The Description field contains
  <arXiv:2303.13702v1>.
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: ‘Hmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Dione Pereira Cardoso <cardoso.dione@gmail.com>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘KFactor.Rd’:
    \keyword{Nomograph; Particle-size; Organic matter; [TRUNCATED]
  File ‘RFactor_calc.Rd’:
    \keyword{Erosivity index; R-Factor; Universal Soil [TRUNCATED]
  File ‘RFactor_est.Rd’:
    \keyword{Erosivity index; R-Factor; Universal Soil [TRUNCATED]
  File ‘SoilConservation.Rd’:
    \keyword{Soil Conservation; Erosivity index; R-Fac [TRUNCATED]
  File ‘SoilLoss.Rd’:
    \keyword{Soil Loss; Water Erosion; R Factor; K Fac [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: '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: ‘Anderson Rodrigo da Silva <anderson.agro@hotmail.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: ‘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.
Maintainer: ‘Yi Yang <yi.yang6@mcgill.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chenglong",
                      family = "Ye",
                      role = "aut",
                      email = "yexxx323@umn.edu"),
               person(given = "Yi",
                      family = "Yang",
                      role = c("aut", "cre"),
                      email = "yi.yang6@mcgill.ca"),
               person(given = "Yuhong",
                      family = "Yang",
                      role = "aut",
                      email = "yyang@stat.umn.edu"))
as necessary.
Maintainer: ‘Carlos A. Sierra <csierra@bgc-jena.mpg.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Carlos", "A."),
                      family = "Sierra",
                      role = c("aut", "cre"),
                      email = "csierra@bgc-jena.mpg.de"),
               person(given = "Markus",
                      family = "Mueller",
                      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?
Package required but not available: ‘nlraa’

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: ‘Emanuele Cordano <emanuele.cordano@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Emanuele",
                      family = "Cordano",
                      role = c("aut", "cre"),
                      email = "emanuele.cordano@gmail.com"),
               person(given = "Daniele",
                      family = "Andreis",
                      role = "aut"),
               person(given = "Fabio",
                      family = "Zottele",
                      role = "aut"))
as necessary.
Maintainer: ‘Zhaoliang He <1024299329@qq.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhaoliang",
                      family = "He",
                      role = c("aut", "cre"),
                      email = "1024299329@qq.com"),
               person(given = "Linsui",
                      family = "Deng",
                      role = "aut",
                      email = "1175520015@qq.com"),
               person(given = "Kaiwen",
                      family = "Tan",
                      role = "aut",
                      email = "913596401@qq.com"))
as necessary.
Maintainer: ‘Jasper Van doninck <vandoninck.jasper@gmail.com>’

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Bijan",
                    family = "Seyednasrollah",
                    role = c("aut", "cre"),
                    email = "bijan.s.nasr@gmail.com")
as necessary.

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 ‘DayOfYear.Rd’:
    \keyword{DOY,}
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) solr_mlt.Rd:70: Lost braces; missing escapes or markup?
    70 | TermVector DEFAULT_FIELD_NAMES = new String[] {"contents"}
       |                                               ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
checkRd: (-1) solve_pH_from_AT.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:93: Lost braces in \itemize; meant \describe ?
Cannot process vignettes
Packages suggested but not available for checking:
  '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: ‘Jon Clayden <code@clayden.org>’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘livio finos <livio@stat.unipd.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "livio",
                    family = "finos",
                    role = c("aut", "cre"),
                    email = "livio@stat.unipd.it")
as necessary.
Packages required but not available: 'rlist', 'colourpicker'

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

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: ‘Andreas Dominik <andreas.dominik@mni.thm.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Andreas",
                    family = "Dominik",
                    role = c("aut", "cre"),
                    email = "andreas.dominik@mni.thm.de")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'Hmisc', 'knitr', 'rmarkdown'

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Charles",
                    family = "Berry",
                    role = c("aut", "cre"),
                    email = "ccberry@ucsd.edu")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'devtools', 'googleCloudStorageR', '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:
    ‘soundSpeed.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?
Maintainer: ‘Willem Daniel Schutte <wd.schutte@nwu.ac.za>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Willem", "Daniel"),
                    family = "Schutte",
                    role = c("aut", "cre"),
                    email = "wd.schutte@nwu.ac.za")
as necessary.
Maintainer: ‘"Zeb Burke-Conte" <zmbc@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zeb",
                      family = "Burke-Conte",
                      role = "aut"),
               person(given = "\"Zeb",
                      family = "Burke-Conte\"",
                      role = "cre",
                      email = "zmbc@uw.edu"))
as necessary.
Found the following HTML validation problems:
sorcering.html:639:1 (sorcering.Rd:26): Warning: <script> anchor "MathJax-script" already defined
Maintainer: ‘Weimin Zhang <zhangwm@hotmail.com>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘asrm.Rd’:
    https://doi.org/10.1111/biom.12997
  File ‘sorocs.Rd’:
    https://doi.org/10.1111/biom.12997
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Aurnov",
                    family = "Chattopadhyay",
                    role = c("aut", "cre"),
                    email = "aurnovcy@gmail.com")
as necessary.
Packages required but not available: 'htmlwidgets', 'learnr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling', '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’
checkRd: (-1) load_sorvi_data.Rd:23: 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: ‘Spencer Graves <spencer.graves@prodsyse.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Spencer",
                      family = "Graves",
                      role = c("cre", "aut", "cph"),
                      email = "spencer.graves@prodsyse.com"),
               person(given = "Sundar",
                      family = "Dorai-Raj",
                      role = "aut"),
               person(given = "Romain",
                      family = "Francois",
                      role = "ctb"))
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: ‘frictionless’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Bruno Silva <bmsasilva@gmail.com>’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Luis J. Villanueva-Rivera <ljvillanueva@coquipr.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Luis", "J."),
                      family = "Villanueva-Rivera",
                      role = c("aut", "cre"),
                      email = "ljvillanueva@coquipr.com"),
               person(given = c("Bryan", "C."),
                      family = "Pijanowski",
                      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: ‘Daniel Marcelino <dmarcelino@live.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Daniel",
                    family = "Marcelino",
                    role = c("aut", "cre"),
                    email = "dmarcelino@live.com")
as necessary.

The BugReports field in DESCRIPTION has
  http://github.com/danielmarcelino/soundexBR
which should likely be
  http://github.com/danielmarcelino/soundexBR/issues
instead.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘soundexBR.Rd’:
    http://dx.doi.org/10.2139/ssrn.2320547
Package required but not available: ‘geomorph’

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: ‘Matthew Daniel Young <my4@sanger.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Matthew", "Daniel"),
                    family = "Young",
                    role = c("aut", "cre"),
                    email = "my4@sanger.ac.uk")
as necessary.
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.
Maintainer: ‘Kevin Ushey <kevinushey@gmail.com>’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sourcoise
> ### Title: sources R script and caches results on disk
> ### Aliases: sourcoise
> 
> ### ** Examples
> 
> ## Don't show: 
> if (rlang::is_installed("insee")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ dir <- tempdir()
+ set_sourcoise_root(dir)
+ fs::file_copy(
+    fs::path_package("sourcoise", "some_data.R"),
+   dir,
+   overwrite = TRUE)
+ # Force execution (root is set explicitly here, it is normally deduced from project)
+ data <- sourcoise("some_data.R", force_exec = TRUE)
+ # The second time cache is used
+ data <- sourcoise("some_data.R")
+ ## Don't show: 
+ }) # examplesIf
> dir <- tempdir()
> set_sourcoise_root(dir)
[1] "/tmp/RtmpDNr9Y9"
> fs::file_copy(fs::path_package("sourcoise", "some_data.R"), dir, overwrite = TRUE)
> data <- sourcoise("some_data.R", force_exec = TRUE)
Error in loadNamespace(x) : there is no package called ‘quarto’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'config', 'golem', 'kableExtra', 'knitr'

Package suggested but not available for checking: ‘gridlayout’

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: ‘Matheus Dalsente Krause <krause.d.matheus@gmail.com>’

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

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

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

The Description field contains
  MCMC algorithm. See D Angelo et al. (2018) <arXiv:1803.07166> and D
  Angelo et al. (2018) <arXiv:1807.03874>.
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:
  '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?
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/isotherms.rnw’
(Is a VignetteBuilder field missing?)

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Alberto Krone-Martins <algol@sim.ul.pt>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alberto",
                    family = "Krone-Martins",
                    role = c("aut", "cre"),
                    email = "algol@sim.ul.pt")
as necessary.
Maintainer: ‘Vilmantas Gegzna <GegznaV@gmail.com>’

Found the following (possibly) invalid file URI:
  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?
Maintainer: ‘Anne Chao <chao@stat.nthu.edu.tw>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Anne",
                      family = "Chao",
                      role = c("aut", "cre"),
                      email = "chao@stat.nthu.edu.tw"),
               person(given = c("K.", "H."),
                      family = "Ma",
                      role = "aut"),
               person(given = c("T.", "C."),
                      family = "Hsieh",
                      role = "aut"),
               person(given = "Chun-Huo",
                      family = "Chiu",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'DiagrammeR', 'knitr', 'NLMR', 'rmarkdown', 'roxygen2'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Running examples in ‘SpaDES.core-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convertToPackage
> ### Title: Convert standard module code into an R package
> ### Aliases: convertToPackage
> 
> ### ** Examples
> 
> if (requireNamespace("ggplot2") && requireNamespace("pkgload") ) {
+   tmpdir <- tempdir2()
+   newModule("test", tmpdir, open = FALSE)
+   convertToPackage("test", path = tmpdir)
+   pkgload::load_all(file.path(tmpdir, "test"))
+   pkgload::unload("test")
+ }
Loading required namespace: pkgload
New module test created at /tmp/Rtmp1X04KI/reproducible/U3C0xYmG
* edit module code in test.R
* write tests for your module code in tests/
* describe and document your module in test.Rmd
* tell others how to cite your module by editing citation.bib
* choose a license for your module; see LICENSE.md
Main module file is: /tmp/Rtmp1X04KI/reproducible/U3C0xYmG/test/test.R
Main documentation file is: /tmp/Rtmp1X04KI/reproducible/U3C0xYmG/test/test.Rmd
Error in convertToPackage("test", path = tmpdir) : 
  requireNamespace("roxygen2", quietly = TRUE) is not TRUE
Calls: convertToPackage -> stopifnot
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Unknown package ‘earlywarnings’ in Rd xrefs
Running ‘testthat.R’ [6s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spaero)
  > 
  > test_check("spaero")
  Saving _problems/test-simulator-8.R
  [ FAIL 1 | WARN 4 | SKIP 7 | PASS 47 ]
  
  ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
  • On CRAN (6): 'test-simulator.R:60:3', 'test-simulator.R:82:3',
    'test-simulator.R:157:3', 'test-simulator.R:190:3', 'test-stats.R:118:3',
    'test-stats.R:237:3'
  • {earlywarnings} is not installed (1): 'test-stats.R:303:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-simulator.R:6:3'): Argument checking works ─────────────────────
  <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-simulator.R:6:3
   2.   └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
   3.     └─lifecycle:::deprecate_stop0(msg)
   4.       └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 4 | SKIP 7 | PASS 47 ]
  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’
Cannot process vignettes
Packages suggested but not available for checking:
  'flowmapblue', 'hexSticker', 'quarto', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jose Manuel Vera Oteo <vera.josemanuel@gmail.com>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘geocode_cadastral.Rd’:
    \keyword{cadastre,}
    \keyword{geocoding,}
    \keyword{latitude,}
    \keyword{longitude,}
  File ‘to_number.Rd’:
    \keyword{currency,}
    \keyword{euros,}
    \keyword{money,}
  File ‘to_words.Rd’:
    \keyword{integers,}
    \keyword{money,}
    \keyword{spanish,}
Packages required but not available: 'DT', 'rmarkdown', 'knitr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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: ‘Daniela Witten <dwitten@u.washington.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Daniela", "M."),
                      family = "Witten",
                      role = "aut"),
               person(given = "Robert",
                      family = "Tibshirani",
                      role = "aut"),
               person(given = "Daniela",
                      family = "Witten",
                      role = "cre",
                      email = "dwitten@u.washington.edu"))
as necessary.
Maintainer: ‘Aki Ariga <chezou@gmail.com>’

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

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

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.
Packages required but not available: 'sparklyr', 'sparklyr.nested'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Ramnath Vaidyanathan <ramnath.vaidya@gmail.com>’

Found the following (possibly) invalid file URI:
  URI: CONDUCT.md
    From: README.md
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking:
  'formattable', '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: ‘sparklyr’

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: 'sparklyr', 'listviewer'

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

Package suggested but not available for checking: ‘r2d3’

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

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: ‘Thomas Leeper <thosjleeper@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: ‘sparklyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Edgar Ruiz <edgar@rstudio.com>’

The BugReports field in DESCRIPTION has
  https://github.com/r-spark/sparkwarc
which should likely be
  https://github.com/r-spark/sparkwarc/issues
instead.
Package required but not available: ‘sparklyr’

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

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

VignetteBuilder package required for 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 Gibberd <a.gibberd@lancaster.ac.uk>’

The Description field contains
  <arXiv:2303.11892>. Options to use classic multivariate Kalman filter
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: ‘Max Kuhn <mxkuhn@gmail.com>’

The Description field contains
  classifier from Ramey et al. (2017) <arXiv:1602.01182>. Other
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Daniel P. Palomar <daniel.p.palomar@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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Jelmer Ypma <uctpjyy@ucl.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Jelmer",
                    family = "Ypma",
                    role = c("aut", "cre"),
                    email = "uctpjyy@ucl.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.
Malformed Description field: should contain one or more complete sentences.
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/sparseHessianFD.Rnw’
(Is a VignetteBuilder field missing?)

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Daniel P. Palomar <daniel.p.palomar@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', 'prettydoc', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Maintainer: ‘Andrew Zammit-Mangion <andrewzm@gmail.com>’

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘Takahashi_Davis.Rd’:
    \keyword{factor,}
  File ‘cholsolve.Rd’:
    \keyword{factor,}
  File ‘cholsolveAQinvAT.Rd’:
    \keyword{factor,}
checkRd: (-1) cholsolveAQinvAT.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Solve the equation X = AQ^{-1}t(A) under permutations}
       |                                  ^
Maintainer: ‘Max Kuhn <mxkuhn@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Line",
                      family = "Clemmensen",
                      role = "aut",
                      email = "lhc@imm.dtu.dk"),
               person(given = c("contributions", "by", "Max"),
                      family = "Kuhn",
                      role = "aut"),
               person(given = "Max",
                      family = "Kuhn",
                      role = "cre",
                      email = "mxkuhn@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: ‘Riccardo Rastelli <riccardoras@gmail.com>’

The Description field contains
  <arXiv:1808.09262>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Adam B Kashlak <kashlak@ualberta.ca>’

The Description field contains
  search method outlined in Kashlak and Kong (2019) <arXiv:1705.02679>
  and in Kashlak (2019) <arXiv:1903.10988>.
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) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |    ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |             ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                      ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                   ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                            ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                                     ^
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: ‘Lax Chan <laxchan77@gmail.com>’

The Description field contains
  W., Vincent, K (2019) <arXiv:1902.05156>. This package explicitly
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', '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?
Maintainer: ‘N. Benjamin Erichson <erichson@uw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("N.", "Benjamin"),
                      family = "Erichson",
                      role = c("aut", "cre"),
                      email = "erichson@uw.edu"),
               person(given = "Peng",
                      family = "Zheng",
                      role = "aut"),
               person(given = "Sasha",
                      family = "Aravkin",
                      role = "aut"))
as necessary.

The Description field contains
  Erichson et al. (2018) <arXiv:1804.00341>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Marc Ratkovic <ratkovic@princeton.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Marc",
                      family = "Ratkovic",
                      role = c("aut", "cre"),
                      email = "ratkovic@princeton.edu"),
               person(given = "Dustin",
                      family = "Tingley",
                      role = "aut"))
as necessary.
checkRd: (-1) plot.sparsereg.Rd:22-23: Lost braces
    22 | \env{main1, main2, main3}{
       |                          ^
checkRd: (-1) plot.sparsereg.Rd:25-27: Lost braces
    25 | \env{xlabel}{
       |             ^
checkRd: (-1) plot.sparsereg.Rd:29-31: Lost braces
    29 | \env{plot.one}{
       |               ^
checkRd: (-1) summary.sparsereg.Rd:27-29: Lost braces
    27 | \env{interval}{
       |               ^
checkRd: (-1) summary.sparsereg.Rd:31-33: Lost braces
    31 | \env{ci}{
       |         ^
checkRd: (-1) summary.sparsereg.Rd:35-37: Lost braces
    35 | \env{order}{
       |            ^
checkRd: (-1) summary.sparsereg.Rd:39-41: Lost braces
    39 | \env{normal}{
       |             ^
checkRd: (-1) summary.sparsereg.Rd:43-45: Lost braces
    43 | \env{select}{
       |             ^
checkRd: (-1) summary.sparsereg.Rd:47-48: Lost braces
    47 | \env{printit}{
       |              ^
checkRd: (-1) summary.sparsereg.Rd:50-52: Lost braces
    50 | \env{stage}{
       |            ^
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'kableExtra', '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: ‘Gertjan van den Burg <gertjanvandenburg@gmail.com>’

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

The Description field contains
  <arXiv:1701.06967>. In the model, a regularization term is added to the
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

The BugReports field in DESCRIPTION has
  https://github.com/GjjvdBurg/SparseStep
which should likely be
  https://github.com/GjjvdBurg/SparseStep/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: '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:
  'FactoMineR', 'plotly', 'shinyjqui', 'htmlwidgets', 'explor',
  'scatterD3', 'leaflet'

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: '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?
Maintainer: ‘Marius Placzek <marius.placzek@med.uni-goettingen.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "T.",
                      family = "Asendorf",
                      role = "aut"),
               person(given = "R.",
                      family = "Gera",
                      role = "aut"),
               person(given = "S.",
                      family = "Islam",
                      role = "aut"),
               person(given = "M.",
                      family = "Harden",
                      role = "aut"),
               person(given = "M.",
                      family = "Placzek",
                      role = "aut"),
               person(given = "Marius",
                      family = "Placzek",
                      role = "cre",
                      email = "marius.placzek@med.uni-goettingen.de"))
as necessary.
Maintainer: ‘Altieri Linda <linda.altieri@unibo.it>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "L.",
                      family = "Altieri",
                      role = "aut"),
               person(given = "D.",
                      family = "Cocchi",
                      role = "aut"),
               person(given = "G.",
                      family = "Roli",
                      role = "aut"),
               person(given = "Altieri",
                      family = "Linda",
                      role = "cre",
                      email = "linda.altieri@unibo.it"))
as necessary.
Maintainer: ‘Fabio Sigrist <fabiosigrist@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Fabio",
                      family = "Sigrist",
                      role = c("aut", "cre"),
                      email = "fabiosigrist@gmail.com"),
               person(given = c("Hans", "R."),
                      family = "Kuensch",
                      role = "aut"),
               person(given = c("Werner", "A."),
                      family = "Stahel",
                      role = "aut"))
as necessary.
Maintainer: ‘Rounak Dey <deyrnk@umich.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rounak",
                      family = "Dey",
                      role = c("aut", "cre"),
                      email = "deyrnk@umich.edu"),
               person(given = "Seunggeun",
                      family = "Lee",
                      role = "aut"))
as necessary.
Packages required but not available: 'plotly', 'fda.usc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Tuomas Rajala <tuomas.rajala@iki.fi>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Tuomas",
                    family = "Rajala",
                    role = c("aut", "cre"),
                    email = "tuomas.rajala@iki.fi")
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?
Packages required but not available: 'leaflet', 'leaflet.extras', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘David Clifford <david.clifford+CRAN@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "David",
                    family = "Clifford",
                    role = c("aut", "cre"),
                    email = "david.clifford+CRAN@gmail.com")
as necessary.
Packages required but not available: 'keras', 'tensorflow'

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

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

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

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Javier Garcia-Pintado <jgarciapintado@marum.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Javier",
                    family = "Garcia-Pintado",
                    role = c("aut", "cre"),
                    email = "jgarciapintado@marum.de")
as necessary.
checkRd: (-1) distSG.Rd:40: Lost braces; missing escapes or markup?
    40 |   matrix and weight matrix (plus a matrix with {eID} identifiers
       |                                                ^
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:
  'tmap', 'knitr', 'rmarkdown'

VignetteBuilder package required 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
Maintainer: ‘Nobin Chandra Paul<ncp375@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Nobin", "Chandra"),
                    family = "Paul",
                    role = c("aut", "cre"),
                    email = "ncp375@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

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

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

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

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', 'devtools', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Joshua French <joshua.french@ucdenver.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Joshua",
                    family = "French",
                    role = c("aut", "cre"),
                    email = "joshua.french@ucdenver.edu")
as necessary.
Maintainer: ‘Yili Hong <yilihong@vt.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yili",
                      family = "Hong",
                      role = c("aut", "cre"),
                      email = "yilihong@vt.edu"),
               person(given = "Li",
                      family = "Xu",
                      role = "aut"),
               person(given = "Yimeng",
                      family = "Xie",
                      role = "aut"),
               person(given = "Zhongnan",
                      family = "Jin",
                      role = "aut"))
as necessary.

The Description field contains
  al. (2018, <arXiv:1809.06418>). The package also contains the Lyme
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

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

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Benjamin", "M."),
                      family = "Taylor",
                      role = c("aut", "cre"),
                      email = "benjamin.taylor.software@gmail.com"),
               person(given = c("Barry", "S.", "Rowlingson", "Additional", "contributions", "Ziyu"),
                      family = "Zheng",
                      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: 'knitr', 'rmarkdown'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Francesco Pantalone <pantalone.fra@gmail.com>’

The Description field contains
  <arXiv:1710.09116>. The implementation has been done in C++ through the
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Axel Gandy <a.gandy@imperial.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Axel",
                      family = "Gandy",
                      role = c("aut", "cre"),
                      email = "a.gandy@imperial.ac.uk"),
               person(given = c("Jan", "Terje"),
                      family = "Kvaloy.",
                      role = "aut",
                      email = "jan.t.kvaloy@uis.no"))
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
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: ‘Ning Hao <nhao@math.arizona.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Yue", "S."),
                      family = "Niu",
                      role = "aut"),
               person(given = "Ning",
                      family = "Hao",
                      role = c("aut", "cre"),
                      email = "nhao@math.arizona.edu"),
               person(given = "Bin",
                      family = "Dong",
                      role = "aut"))
as necessary.
Maintainer: ‘Milana Gataric <m.gataric@statslab.cam.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Milana",
                      family = "Gataric",
                      role = c("aut", "cre"),
                      email = "m.gataric@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
  T. and Samworth, R. J. (2018) <arXiv:1712.05630>. The algorithm is
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘David A. Schoenfeld <dschoenfeld@mgh.harvard.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("David", "A."),
                    family = "Schoenfeld",
                    role = c("aut", "cre"),
                    email = "dschoenfeld@mgh.harvard.edu")
as necessary.
Maintainer: ‘Ziang Zhang <aguero.zhang@mail.utoronto.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ziang",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "aguero.zhang@mail.utoronto.ca"),
               person(given = "Lei",
                      family = "Sun",
                      role = "aut"))
as necessary.

The Description field contains
  Accounting for Covariate Effects" <arXiv:2203.15641>.
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: ‘rJava’

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

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

VignetteBuilder package required 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: ‘Shuichi Kawano <skawano@math.kyushu-u.ac.jp>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Shuichi",
                    family = "Kawano",
                    role = c("aut", "cre"),
                    email = "skawano@math.kyushu-u.ac.jp")
as necessary.
Package required but not available: ‘rcarbon’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from 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:
    ‘federov.R’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Rasheed AM <a.rasheed@qut.edu.au>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rasheed",
                      family = "AM",
                      role = c("aut", "cre"),
                      email = "a.rasheed@qut.edu.au"),
               person(given = "Egodawatta",
                      family = "P",
                      role = "aut"),
               person(given = "Goonetilleke",
                      family = "A",
                      role = "aut"),
               person(given = "McGree",
                      family = "J",
                      role = "aut"))
as necessary.
Maintainer: ‘Alexios Ghalanos <alexios@4dscape.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alexios",
                    family = "Ghalanos",
                    role = c("aut", "cre"),
                    email = "alexios@4dscape.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: ‘separationplot’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Javier",
                      family = "Martinez-Lopez",
                      role = c("aut", "cre"),
                      email = "javi.martinez.lopez@gmail.com"),
               person(given = "Babak",
                      family = "Naimi",
                      role = "aut",
                      email = "naimi.b@gmail.com"),
               person(given = "Julia",
                      family = "Martinez-Fernandez",
                      role = "aut",
                      email = "juliamf@um.es"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'roxygen2'

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

VignetteBuilder package required 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: ‘quarto’

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: ‘Charlie Beirnaert <charlie_beirnaert@icloud.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Charlie",
                      family = "Beirnaert",
                      role = c("aut", "cre"),
                      email = "charlie_beirnaert@icloud.com"),
               person(given = c("Trung", "Nghia"),
                      family = "Vu",
                      role = "aut"),
               person(given = "Pieter",
                      family = "Meysman",
                      role = "aut"),
               person(given = "Kris",
                      family = "Laukens",
                      role = "aut"),
               person(given = "Dirk",
                      family = "Valkenborg",
                      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) findRef.Rd:39: Lost braces
    39 | Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemi\`{e}re F, Verschoren A, Goethals B, Laukens K. (2011) An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics. 2011 Oct 20;12:405.
       |                                                              ^
checkRd: (-1) hClustAlign.Rd:70: Lost braces
    70 | Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemi\`{e}re F, Verschoren A, Goethals B, Laukens K. (2011) An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics. 2011 Oct 20;12:405.
       |                                                              ^
Package has ‘vignettes’ subdirectory 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: ‘Denis Rastegaev <drastega@gmail.com>’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘Seurat’

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

VignetteBuilder package required for 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', 'tidyverse', 'rmarkdown'

VignetteBuilder package required 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) FitAkdParameters.Rd:23: Lost braces; missing escapes or markup?
    23 |       p(y|ens) = 1 / K * sum {dnorm(y, z.i, s)} \cr
       |                              ^
Package required but not available: ‘epiR’

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:
  'calendR', 'knitr', 'rmarkdown'

VignetteBuilder package required for 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 Paciorek <paciorek@alumni.cmu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Chris",
                    family = "Paciorek",
                    role = c("aut", "cre"),
                    email = "paciorek@alumni.cmu.edu")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
Maintainer: ‘Martin Seilmayer <martin.seilmayer@gmail.com>’

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

Package suggested but not available for checking: ‘covr’

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

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Christopher R John <chris.r.john86@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Christopher", "R"),
                      family = "John",
                      role = c("aut", "cre"),
                      email = "chris.r.john86@gmail.com"),
               person(given = "David",
                      family = "Watson",
                      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?
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘innprod.R’ ‘utils.R’
Maintainer: ‘Castor Guisande Gonzalez <castor@uvigo.es>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Castor", "Guisande"),
                    family = "Gonzalez",
                    role = c("aut", "cre"),
                    email = "castor@uvigo.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: ‘Charles J. Geyer <charlie@stat.umn.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Charles", "J."),
                      family = "Geyer",
                      role = c("aut", "cre"),
                      email = "charlie@stat.umn.edu"),
               person(given = c("Elizabeth", "A."),
                      family = "Thompson",
                      role = "aut",
                      email = "eathomp@u.washington.edu"))
as necessary.
checkRd: (-1) speech_recompiler.Rd:25: Lost braces; missing escapes or markup?
    25 | The default compilation is that of \ code {speech_build (., compiler = TRUE}).
       |                                           ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘import_qiime2_tax_table.R’ ‘import_sintax_tax_table.R’
Maintainer: ‘Michal Juraska <mjuraska@fredhutch.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Michal",
                      family = "Juraska",
                      role = c("aut", "cre"),
                      email = "mjuraska@fredhutch.org"),
               person(given = c("with", "contributions", "from", "Peter", "B."),
                      family = "Gilbert",
                      role = "aut",
                      email = "pgilbert@scharp.org"),
               person(given = "Xiaomin",
                      family = "Lu",
                      role = "aut",
                      email = "xlu2@phhp.ufl.edu"),
               person(given = "Min",
                      family = "Zhang",
                      role = "aut",
                      email = "mzhangst@umich.edu"),
               person(given = "Marie",
                      family = "Davidian",
                      role = "aut",
                      email = "davidian@stat.ncsu.edu"),
               person(given = c("Anastasios", "A."),
                      family = "Tsiatis",
                      role = "aut",
                      email = "tsiatis@stat.ncsu.edu"))
as necessary.
Maintainer: ‘Selva Prabhakaran <selva86@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Selva",
                    family = "Prabhakaran",
                    role = c("aut", "cre"),
                    email = "selva86@gmail.com")
as necessary.
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: '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?
Found the following files/directories:
  ‘.neig’
Maintainer: ‘Maximilian Lange <maximilian-lange@t-online.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Maximilian",
                      family = "Lange",
                      role = c("aut", "cre"),
                      email = "maximilian-lange@t-online.de"),
               person(given = "Sven",
                      family = "Lautenbach",
                      role = "aut"),
               person(given = "Claudia",
                      family = "Raedig",
                      role = "aut"))
as necessary.
Maintainer: ‘Alexander Brenning <alexander.brenning@uni-jena.de>’

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 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: ‘Yang Liu <yliu87@umd.edu>’

The Description field contains
  <arXiv:2303.10079>. Both the conditional densities of observed
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: ‘Xingche Guo <xguo@iastate.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Xingche",
                    family = "Guo",
                    role = c("aut", "cre"),
                    email = "xguo@iastate.edu")
as necessary.
Specified C++11: support will be removed soon
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
    61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc}, 
       |                                                   ^
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Yijun Xie <yijun.xie@uwaterloo.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yijun",
                    family = "Xie",
                    role = c("aut", "cre"),
                    email = "yijun.xie@uwaterloo.ca")
as necessary.
Maintainer: ‘Jongmin Lee <jongminlee9218@gmail.com>’

The Description field contains
  H.-S. (2020) <arXiv:2003.02578>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Packages required but not available: 'rgl', 'sphereplot'

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.
Package required but not available: ‘rgl’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: piecewise_geodesic
> ### Title: Piecewise Geodesic
> ### Aliases: piecewise_geodesic
> 
> ### ** Examples
> 
> # `rgl` package and `sphereplot` pacakges are needed for the visualizaiton of the following example.
> # Define control points and knots
> library(rgl)
Error in library(rgl) : there is no package called ‘rgl’
Execution halted
Maintainer: ‘John P. Nolan <jpnolan@american.edu>’

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

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', 'roxyglobals'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Bob Rudis <bob@rud.is>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Bob",
                      family = "Rudis",
                      role = c("aut", "cre"),
                      email = "bob@rud.is",
                      comment = "bob@rud.is"),
               person(family = "SEOmoz"),
               person(family = "Inc",
                      role = "aut"))
as necessary.
Maintainer: ‘Iván Ayala-Bizarro <ivan.ayala@unh.edu.pe>’

The Description field contains
  http://drought.unl.edu/monitoringtools/downloadablespiprogram.aspx.
Please enclose URLs in angle brackets (<...>).
Found the following files/directories:
  ‘AlphaGA_3.txt’ ‘AlphaML_3.txt’ ‘BetaGA_3.txt’ ‘BetaML_3.txt’
  ‘Performance_GA_ML_ 3 .pdf’ ‘SPIGA_3Pmon.Pm_St1.pdf’
  ‘SPIGA_3Pmon.Pm_St2.pdf’ ‘SPI_AG_3.txt’ ‘SPI_ML_3.txt’
  ‘SPI_ML_3Pm_St1.pdf’ ‘SPI_ML_3Pm_St2.pdf’ ‘SPI_ML_3Pm_St3.pdf’
  ‘SPI_ML_3Pm_St4.pdf’ ‘SPI_PARAM_3.txt’ ‘SPI_PARAM_3Pm_St1.pdf’
  ‘SPI_PARAM_3Pm_St2.pdf’ ‘SPI_PARAM_3Pm_St3.pdf’
  ‘SPI_PARAM_3Pm_St4.pdf’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘Udaya B. Kogalur <ubk@kogalur.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Hemant",
                      family = "Ishwaran",
                      role = "aut",
                      email = "hemant.ishwaran@gmail.com"),
               person(given = c("Udaya", "B."),
                      family = "Kogalur",
                      role = "cre",
                      email = "ubk@kogalur.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: ‘Arturas Rozenas <ar199@nyu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Arturas",
                    family = "Rozenas",
                    role = c("aut", "cre"),
                    email = "ar199@nyu.edu")
as necessary.
Maintainer: ‘Jilber Urbina <JilberUrbina@gmail.com>’

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

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: ‘Johannes W. Dietrich <johannes.dietrich@ruhr-uni-bochum.de>’

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?
Maintainer: ‘Sam Levin <levisc8@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gudrun",
                      family = "Carl",
                      role = c("cre", "aut")),
               person(given = "Ingolf",
                      family = "Kuehn",
                      role = "aut"),
               person(given = "Sam",
                      family = "Levin",
                      role = c("aut", "cre"),
                      email = "levisc8@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', '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: 'quarto', 'knitr'

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: 'plotly', 'Rdimtools'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Julien Chiquet <julien.chiquet@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Charles",
                      family = "Bouveyron",
                      role = "aut"),
               person(given = "Julien",
                      family = "Chiquet",
                      role = c("aut", "cre"),
                      email = "julien.chiquet@gmail.com"),
               person(given = "Pierre",
                      family = "Latouche",
                      role = "aut"),
               person(given = "Pierre-Alexandre",
                      family = "Mattei",
                      role = "aut"))
as necessary.

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently 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?
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: ‘Roberto Villegas-Diaz <r.villegas-diaz@outlook.com>’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Melantha Wang <wang.melantha@gmail.com>’

The Description field contains
  Cost Experience Simulator" <arXiv:2109.04058>.
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', '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
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  'knitr', 'rmarkdown', 'covr', 'pkgdown'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Collin Erickson <collinberickson@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Collin",
                    family = "Erickson",
                    role = c("aut", "cre"),
                    email = "collinberickson@gmail.com")
as necessary.
Maintainer: ‘Sam Parsons <sam.parsons@radboudumc.nl>’

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

The BugReports field in DESCRIPTION has
  https://github.com/sdparsons/splithalf
which should likely be
  https://github.com/sdparsons/splithalf/issues
instead.
Cannot process vignettes
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VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) speedtestdata.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:23: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

VignetteBuilder package required 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
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.

The Description field contains
  Christidis, Van Aelst and Zamar (2019) <arXiv:1812.05678>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Ananda Mahto <mrdwab@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ananda",
                    family = "Mahto",
                    role = c("aut", "cre"),
                    email = "mrdwab@gmail.com")
as necessary.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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 >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘addlearn_local.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', '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:
  'kableExtra', 'rgl', 'tmap', '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: ‘ridigbio’

Packages suggested but not available for checking: 'taxize', 'vcr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Vincent Guyader <vincent@thinkr.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Vincent",
                    family = "Guyader",
                    role = c("aut", "cre"),
                    email = "vincent@thinkr.fr")
as necessary.
Maintainer: ‘Giancarlo Vercellino <giancarlo.vercellino@gmail.com>’

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

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

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: ‘Feiyu Yue <yuefyopals@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zihao",
                      family = "Zheng",
                      role = "aut"),
               person(given = "Feiyu",
                      family = "Yue",
                      role = c("aut", "cre"),
                      email = "yuefyopals@gmail.com"))
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'

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Lennard",
                    family = "van Wanrooij",
                    role = c("aut", "cre"),
                    email = "lennardvanwanrooij@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
Package required but not available: ‘ggExtra’

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

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

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

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

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: ‘Ming Wang <willnju@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ming",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "willnju@gmail.com"),
               person(given = "Yongtao",
                      family = "Guan",
                      role = "aut"),
               person(given = "Kun",
                      family = "Xu",
                      role = "aut"))
as necessary.
Maintainer: ‘Nobin Chandra Paul<nobin.niasm@outlook.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Nobin", "Chandra"),
                      family = "Paul",
                      role = c("aut", "cre"),
                      email = "nobin.niasm@outlook.com"),
               person(given = "Anil",
                      family = "Rai",
                      role = "aut"),
               person(given = "Ankur",
                      family = "Biswas",
                      role = "aut"),
               person(given = "Tauqueer",
                      family = "Ahmad",
                      role = "aut"),
               person(given = c("Prachi", "Misra"),
                      family = "Sahoo",
                      role = "aut"))
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: ‘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', 'mapview', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Maintainer: ‘DongHyuk Lee <leedhyuk@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "DongHyuk",
                      family = "Lee",
                      role = c("aut", "cre"),
                      email = "leedhyuk@gmail.com"),
               person(given = "Samiran",
                      family = "Sinha",
                      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: ‘swfscMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Fei Zhou <fei.zhou@outlook.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Fei",
                      family = "Zhou",
                      role = c("aut", "cre"),
                      email = "fei.zhou@outlook.com"),
               person(given = "Yuwen",
                      family = "Liu",
                      role = "aut"),
               person(given = "Xi",
                      family = "Lu",
                      role = "aut"),
               person(given = "Jie",
                      family = "Ren",
                      role = "aut"),
               person(given = "Cen",
                      family = "Wu",
                      role = "aut"))
as necessary.
Maintainer: ‘Adrienne M. Wootten <amwootte@ou.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Adrienne", "M."),
                    family = "Wootten",
                    role = c("aut", "cre"),
                    email = "amwootte@ou.edu",
                    comment = "University of Oklahoma")
as necessary.
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Guo Yu <gy63@uw.edu>’

The Description field contains
  <arXiv:1907.08414>.
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’
Specified C++11: support will be removed soon
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Lauren",
                      family = "Grant",
                      role = c("aut", "cre"),
                      email = "pacele@vcu.edu"),
               person(given = "David",
                      family = "Wheeler",
                      role = "aut"))
as necessary.
Maintainer: ‘Pavel V. Moskalev <moskalefff@gmail.com>’

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

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking:
  '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:
  'bookdown', '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?
Maintainer: ‘Renato Panaro <renatovp@ime.usp.br>’

The Description field contains
  right-censored data. RV Panaro (2020) <arXiv:2003.10548>.
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', 'devtools', 'roxygen2'

VignetteBuilder package required for checking but not installed: ‘knitr’
Author field differs from that derived from Authors@R
  Author:    ‘Renato Panaro [aut, cre] (<https://orcid.org/0000-0002-1903-2091>, https://rvpanaro.github.io/), Fábio Demarqui [aut] (<https://orcid.org/0000-0001-9236-1986>), Vinícius Mayrink [aut] (<https://orcid.org/0000-0002-5683-8326>)’
  Authors@R: ‘Renato Panaro [aut, cre] (ORCID: <https://orcid.org/0000-0002-1903-2091>, URL: https://rvpanaro.github.io/), Fábio Demarqui [aut] (ORCID: <https://orcid.org/0000-0001-9236-1986>), Vinícius Mayrink [aut] (ORCID: <https://orcid.org/0000-0002-5683-8326>)’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'knitr', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Matthew E. Aiello-Lammens <matt.lammens@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: ‘knitr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'library' or 'require' calls not declared from:
  ‘MBA’ ‘akima’ ‘colorspace’ ‘fields’ ‘maps’
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'prettydoc'

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "G.",
                    family = "Grothendieck",
                    role = c("aut", "cre"),
                    email = "ggrothendieck@gmail.com")
as necessary.
checkRd: (-1) sqldf.Rd:248: Lost braces
   248 | and code{port} arguments of sqldf.
       |         ^
Package required but not available: ‘yaml’

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

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', 'covr', 'lintr'

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

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: 'tarchetypes', 'targets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Fernando Puente-Sánchez <fernando.puente.sanchez@slu.se>’

Found the following (possibly) invalid URLs:
  URL: http://eggnogdb.embl.de/#/app/results?seqid=P0A7G6&target_nogs=COG0468#COG0468_datamenu
    From: man/RecA.Rd
    Message: Invalid URL: '#' not allowed in fragment
Maintainer: ‘Martin Aryee <martin.aryee@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhijin",
                      family = "Wu",
                      role = "aut",
                      comment = "Jean"),
               person(given = "Martin",
                      family = "Aryee",
                      role = c("aut", "cre"),
                      email = "martin.aryee@gmail.com"))
as necessary.
Maintainer: ‘Mike Lee <random.deviate@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mike",
                    family = "Lee",
                    role = c("aut", "cre"),
                    email = "random.deviate@gmail.com")
as necessary.
Maintainer: ‘Ravi Varadhan <ravi.varadhan@jhu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Ravi",
                    family = "Varadhan",
                    role = c("aut", "cre"),
                    email = "ravi.varadhan@jhu.edu")
as necessary.
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{ - a small, positive scalar that determines when iterations 
       |               ^
checkRd: (-1) fpiter.Rd:60-61: Lost braces
    60 |     \code{maxiter}{ - an integer denoting the maximum limit on the number of 
       |                   ^
checkRd: (-1) fpiter.Rd:63-65: Lost braces
    63 |     \code{trace}{ - a logical variable denoting whether some of the intermediate 
       |                 ^
checkRd: (-1) fpiter.Rd:67-70: Lost braces
    67 |     \code{intermed}}{ - a logical variable denoting whether the intermediate 
       |                     ^
checkRd: (-1) squarem.Rd:134: Lost braces
   134 |       along with the corresponding log-likelihood value.  When the code{objfn} is not specified it will return the fixed-point residual instead of the objective function values. 
       |                                                                        ^
'library' or 'require' call not declared from: ‘interval’
Maintainer: ‘Aron C. Eklund <aroneklund@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Aron", "C."),
                    family = "Eklund",
                    role = c("aut", "cre"),
                    email = "aroneklund@gmail.com")
as necessary.
Packages required but not available: 'plotly', 'rlist'

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

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
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: ‘Arnaud Le Rouzic <arnaud.le-rouzic@universite-paris-saclay.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Arnaud",
                    family = "Le Rouzic",
                    role = c("aut", "cre"),
                    email = "arnaud.le-rouzic@universite-paris-saclay.fr")
as necessary.
Package required but not available: ‘devtools’

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

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
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.
checkRd: (-1) plot.SRCS.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:56-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:77-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:87-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:143-144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:145: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:146-148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:149: Lost braces in \itemize; meant \describe ?
Maintainer: ‘Attila Csala <a@csala.me>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘sRDA.Rd’:
    https://doi.org/10.1093/bioinformatics/btx374
Maintainer: ‘Harriet Jane Goers <hgoers@umd.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Harriet", "Jane"),
                    family = "Goers",
                    role = c("aut", "cre"),
                    email = "hgoers@umd.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: ‘Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Steffen",
                      family = "Nestler",
                      role = "aut"),
               person(given = "Alexander",
                      family = "Robitzsch",
                      role = c("aut", "cre"),
                      email = "robitzsch@ipn.uni-kiel.de"),
               person(given = "Oliver",
                      family = "Luedtke",
                      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'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘testthat.R’ [5s/8s]
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(srppp)
  Loading required package: dm
  
  Attaching package: 'dm'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("srppp")
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Lukas Beule <lukas.beule@julius-kuehn.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: 'DT', 'shinybusy'

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

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

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:
  'spelling', '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: ‘Kelli F. Johnson <kelli.johnson@noaa.gov>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
Package required but not available: ‘r4ss’

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) ssaBSS-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
Maintainer: ‘Michael P. Fay <mfay@niaid.nih.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Michael", "P."),
                    family = "Fay",
                    role = c("aut", "cre"),
                    email = "mfay@niaid.nih.gov")
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?
Packages required but not available:
  'config', 'golem', 'htmlwidgets', 'rhandsontable', 'rmarkdown',
  'shinybusy'

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

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

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

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: 'spThin', 'leaflet'

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: ‘Yang Liu <zjubioly@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yang",
                      family = "Liu",
                      role = c("aut", "cre"),
                      email = "zjubioly@gmail.com"),
               person(given = "Francesca",
                      family = "Chiaromonte",
                      role = "aut"),
               person(given = "Bing",
                      family = "Li",
                      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?
Package required but not available: ‘MESS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Christiana Kartsonaki <christiana.kartsonaki@gmail.com>’

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

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

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

VignetteBuilder package required 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’

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', 'spelling'

VignetteBuilder package required for checking but not installed: ‘knitr’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/1s]
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'

VignetteBuilder package required 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: ‘Sebastien Thonnard <sebastien.thonnard@icloud.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sebastien",
                    family = "Thonnard",
                    role = c("aut", "cre"),
                    email = "sebastien.thonnard@icloud.com")
as necessary.
Maintainer: ‘Megan Orr <megan.orr@ndsu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Megan",
                      family = "Orr",
                      role = c("aut", "cre"),
                      email = "megan.orr@ndsu.edu"),
               person(given = "Peng",
                      family = "Liu",
                      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/ssizeRNA.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Luis Benites Sanchez <lbenitesanchez@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Luis", "Benites"),
                      family = "Sanchez",
                      role = c("aut", "cre"),
                      email = "lbenitesanchez@gmail.com"),
               person(given = c("Clecio", "da", "Silva"),
                      family = "Ferreira",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'kableExtra', 'kfigr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
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: ‘Peter Curtis <peterrobertcurtis@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’
checkRd: (-1) new.distance.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:35-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:30-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:38-40: Lost braces in \itemize; meant \describe ?
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Mikhail Zhelonkin <Mikhail.Zhelonkin@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Mikhail",
                      family = "Zhelonkin",
                      role = c("aut", "cre"),
                      email = "mikhail.zhelonkin@gmail.com"),
               person(given = c("Marc", "G."),
                      family = "Genton",
                      role = "aut"),
               person(given = "Elvezio",
                      family = "Ronchetti",
                      role = "aut"))
as necessary.
Maintainer: ‘Luis Benites <lbenitesanchez@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rocio",
                      family = "Maehara",
                      role = "aut"),
               person(given = "Luis",
                      family = "Benites",
                      role = c("aut", "cre"),
                      email = "lbenitesanchez@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: '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: ‘Edgar Santos-Fernandez <santosfe@qut.edu.au>’

The Description field contains
  <arXiv:2103.03538>. In these models, spatial dependence is captured
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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

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

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

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

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

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Dave",
                    family = "Zes",
                    role = c("aut", "cre"),
                    email = "zesdave@gmail.com")
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: ‘Kevin Matlock <kevin.matlock@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Kevin",
                      family = "Matlock",
                      role = c("aut", "cre"),
                      email = "kevin.matlock@gmail.com"),
               person(given = "Raziur",
                      family = "Rahman",
                      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 in Depends/Imports which should probably only be in LinkingTo: ‘RcppArmadillo’
Package required but not available: ‘gsDesign’

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'

VignetteBuilder package required for 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 Hernando Vanegas <hvanegasp@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Luis", "Hernando"),
                      family = "Vanegas",
                      role = c("aut", "cre"),
                      email = "hvanegasp@gmail.com"),
               person(given = c("Gilberto", "A."),
                      family = "Paula",
                      role = "aut"))
as necessary.
Packages required but not available: 'knitr', 'Hmisc', 'expss'

Package suggested but not available for checking: ‘rmarkdown’

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

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

Package suggested but not available for checking: ‘shinytest2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Niklas Pfister <np@math.ku.dk>’

The Description field contains
  <arXiv:1911.01850>. The procedure uses averaging to estimate a
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
checkRd: (-1) SRanalysis.Rd:100: Lost braces
   100 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
checkRd: (-1) StabilizedRegression.Rd:109: Lost braces
   109 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
Package required but not available: ‘fBasics’

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

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

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Benjamin Hofner <benjamin.hofner@pei.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'

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) stabsel_parameters.Rd:42: Lost braces
    42 |     always use code{"none"}.}
       |                    ^
checkRd: (-1) stabsel_stabsel.Rd:25: Lost braces
    25 |     always use code{"none"}.}
       |                    ^
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Running examples in ‘staccuracy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: reg_aucroc
> ### Title: Area under the ROC curve for regression target outcomes
> ### Aliases: reg_aucroc
> 
> ### ** Examples
> 
> # Remove rows with missing values from airquality dataset
> airq <- airquality |>
+   na.omit()
> 
> # Create binary version where the target variable 'Ozone' is dichotomized based on its median
> airq_bin <- airq
> airq_bin$Ozone <- airq_bin$Ozone >= median(airq_bin$Ozone)
> 
> # Create a generic regression model; use autogam
> req_aq   <- autogam::autogam(airq, 'Ozone', family = gaussian())
Error in loadNamespace(x) : there is no package called ‘autogam’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

The Description field contains
  stacking” <arXiv:2101.07954>.
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) stackExample.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stackExample.Rd:11: 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:
  '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: ‘Gherardo Varando <gherardo.varando@gmail.com>’

The Description field contains
  Smith J. Q. (2018) <arXiv:1705.09457>.  Thwaites P. A., Smith, J. Q.
  (2017) <arXiv:1510.00186>.  Barclay L. M., Hutton J. L. and Smith J. Q.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘David Nutter <david.nutter@bioss.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Helen",
                      family = "Kettle",
                      role = "aut"),
               person(given = "David",
                      family = "Nutter",
                      role = "cre",
                      email = "david.nutter@bioss.ac.uk"))
as necessary.
Maintainer: ‘LW Pembleton <lwpembleton@gmail.com>’

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

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) stamppFst.Rd:20: Lost braces
    20 | \code{Fsts}{a matrix of pairwise Fst values between populations}
       |            ^
checkRd: (-1) stamppFst.Rd:21: Lost braces
    21 | \code{Pvalues}{a matrix of p-values for each of the pairwise Fst values containined in the 'Fsts' matrix}
       |               ^
checkRd: (-1) stamppFst.Rd:22: Lost braces
    22 | \code{Bootstraps}{a dataframe of each Fst value generated during Bootstrapping and the associated confidence intervals}
       |                  ^
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘stamp.direction.r’
Maintainer: ‘Christopher D. Eager <eager.stats@gmail.com>’

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

VignetteBuilder package required for checking but not installed: ‘knitr’
checkRd: (-1) standardize.Rd:94: Lost braces; missing escapes or markup?
    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                ^
checkRd: (-1) standardize.Rd:94: Lost braces; missing escapes or markup?
    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                                           ^
Package has ‘vignettes’ subdirectory 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:
    ‘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:
  'rmarkdown', 'kableExtra', '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: ‘E. P. Adams <eric.adams@orau.org>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("E.", "L."),
                      family = "Frome",
                      role = "aut",
                      email = "fromeEL@ornl.gov"),
               person(given = c("D.", "P."),
                      family = "Frome",
                      role = "aut"),
               person(given = c("E.", "P."),
                      family = "Adams",
                      role = "cre",
                      email = "eric.adams@orau.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?
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'covr', 'spelling', 'rmarkdown'

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

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

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Marek Hlavac <marek.hlavac@gmail.com>’

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

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
checkRd: (-1) stargazer.Rd:229: Lost braces
   229 |   \item{report}{a character string containing only elements of {\code{"v"}, \code{"c"}, \code{"s"},\code{"t"}, \code{"p"}, \code{"*"}} that determines whether, and in which order, variable names (\code{"v"}), coefficients (\code{"c"}), standard errors/confidence intervals (\code{"s"}), test statistics (\code{"t"}) and p-values (\code{"p"}) should be reported in regression tables. If one of the aforementioned letters is followed by an asterisk (\code{"*"}), significance stars will be reported next to the corresponding statistic.}
       |                                                                ^
checkRd: (-1) stargazer.Rd:246: Lost braces
   246 |   \item{table.placement}{a character string containing only elements of {\code{"h"}, \code{"t"},\code{"b"}, \code{"p"}, \code{"!"}, \code{"H"}} that determines the table placement in its LaTeX floating environment.}
       |                                                                         ^
Maintainer: ‘Felix Cheysson <felix@cheysson.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Felix",
                    family = "Cheysson",
                    role = c("aut", "cre"),
                    email = "felix@cheysson.fr")
as necessary.
Maintainer: ‘Yannis Barboni <yannis.barboni1@gmail.com>’

The Description field contains
  to local spread of plant diseases." 2019. <arXiv:1811.06782>, using a
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’
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required 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:
    ‘stat_frequency.R’
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:
    ‘character_dimensions.Rd’ ‘constellation_as_multistar.Rd’
    ‘constellation_as_tibble_list.Rd’ ‘define_dimension.Rd’
    ‘define_fact.Rd’ ‘dm_mrs_age.Rd’ ‘dm_mrs_cause.Rd’
    ‘filter_dimension.Rd’ ‘filter_fact_rows.Rd’
    ‘get_conformed_dimension.Rd’ ‘get_conformed_dimension_names.Rd’
    ‘get_dimension.Rd’ ‘get_dimension_attribute_names.Rd’
    ‘get_dimension_names.Rd’ ‘get_measure_names.Rd’ ‘get_star_schema.Rd’
    ‘get_star_schema_names.Rd’ ‘incremental_refresh_constellation.Rd’
    ‘incremental_refresh_star_schema.Rd’ ‘match_records.Rd’
    ‘modify_conformed_dimension_records.Rd’ ‘modify_dimension_records.Rd’
    ‘ms_mrs.Rd’ ‘ms_mrs_test.Rd’ ‘multistar_as_flat_table.Rd’
    ‘purge_dimensions_constellation.Rd’ ‘purge_dimensions_star_schema.Rd’
    ‘rename_dimension.Rd’ ‘rename_dimension_attributes.Rd’
    ‘rename_fact.Rd’ ‘rename_measures.Rd’ ‘role_playing_dimension.Rd’
    ‘run_query.Rd’ ‘select_dimension.Rd’ ‘select_fact.Rd’ ‘snake_case.Rd’
    ‘st_mrs_age.Rd’ ‘st_mrs_age_test.Rd’ ‘st_mrs_age_w10.Rd’
    ‘st_mrs_age_w11.Rd’ ‘st_mrs_age_w_test.Rd’ ‘st_mrs_cause.Rd’
    ‘st_mrs_cause_test.Rd’ ‘st_mrs_cause_w10.Rd’ ‘st_mrs_cause_w11.Rd’
    ‘st_mrs_cause_w_test.Rd’ ‘star_schema_as_flat_table.Rd’
    ‘star_schema_as_multistar.Rd’ ‘star_schema_as_tibble_list.Rd’
    ‘update_record.Rd’ ‘update_selection.Rd’
    ‘update_selection_general.Rd’ ‘updates_st_mrs_age.Rd’
    ‘updates_st_mrs_age_test.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?
Cannot process vignettes
Packages suggested but not available for checking:
  'OpenStreetMap', 'PCICt', 'covr', 'knitr', 'rmarkdown', 'starsdata'

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:
    ‘prcomp.Rd’
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', 'leaflet.extras', 'mapview'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Haolun Shi <shl2003@connect.hku.hk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Haolun",
                      family = "Shi",
                      role = c("aut", "cre"),
                      email = "shl2003@connect.hku.hk"),
               person(given = "Guosheng",
                      family = "Yin",
                      role = "aut"))
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'covr', 'knitr', 'pkgdown', 'rmarkdown', 'spelling'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_project
> ### Title: Start a new project
> ### Aliases: create_project
> 
> ### ** Examples
> 
> ## Don't show: 
> if (pkgdown::in_pkgdown()) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ # specifying project folder location (folder does not yet exist)
+ project_path <- file.path(tempdir(), "My Project Folder")
+ 
+ # creating folder where secure data would be stored (typically will be a network drive)
+ secure_data_path <- file.path(tempdir(), "secure_data")
+ dir.create(secure_data_path)
+ 
+ # creating new project folder
+ create_project(project_path, path_data = secure_data_path)
+ ## Don't show: 
+ }) # examplesIf
Error in loadNamespace(x) : there is no package called ‘pkgdown’
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: ‘Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alexander",
                      family = "Robitzsch",
                      role = c("aut", "cre"),
                      email = "robitzsch@ipn.uni-kiel.de",
                      comment = c(ORCID = "0000-0002-8226-3132")),
               person(given = "Oliver",
                      family = "Luedtke",
                      role = "aut",
                      comment = c(ORCID = "0000-0001-9744-3059")))
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: ‘lessR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘yaml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Robin Lock <rlock@stlawu.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ann",
                      family = "Cannon",
                      role = "aut"),
               person(given = "George",
                      family = "Cobb",
                      role = "aut"),
               person(given = "Bradley",
                      family = "Hartlaub",
                      role = "aut"),
               person(given = "Julie",
                      family = "Legler",
                      role = "aut"),
               person(given = "Robin",
                      family = "Lock",
                      role = c("aut", "cre"),
                      email = "rlock@stlawu.edu"),
               person(given = "Thomas",
                      family = "Moore",
                      role = "aut"),
               person(given = "Allan",
                      family = "Rossman",
                      role = "aut"),
               person(given = "Jeffrey",
                      family = "Witmer",
                      role = "aut"))
as necessary.

The BugReports field in DESCRIPTION has
  https://github.com/statmanrobin/Stat2Data
which should likely be
  https://github.com/statmanrobin/Stat2Data/issues
instead.
checkRd: (-1) AutoPollution.Rd:16: Lost braces
    16 |     \code{Side} \tab {Side of vehicle: code{1}=right or \code{2}=left}\cr
       |                                            ^
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', 'Hmisc', 'rpivotTable'

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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘od_list.R’ ‘od_resource.R’ ‘od_utils.R’ ‘other_endpoints.R’
    ‘sc_data.R’ ‘schema.R’ ‘schema_uri.R’ ‘sdmx_table.R’ ‘table.R’
    ‘table_as_data_frame.R’ ‘table_json.R’ ‘table_meta.R’ ‘table_saved.R’
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: ‘Dylan Beijers <dylanbeijers@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', 'covr', 'pkgdown', '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’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'knitr', 'statgenSTA'

Packages suggested but not available for checking: 'asreml', '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:
  'asreml', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
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: 'knitr', 'qtl'

Packages suggested but not available for checking: 'asreml', '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?
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Maintainer: ‘Martina Morris <morrism@uw.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Packages required but not available: 'tergm', 'ergm.count', 'ergm'

Packages suggested but not available for checking:
  'ergm.rank', 'ergm.ego', 'EpiModel', 'latentnet', 'networksis',
  'ndtv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ergm', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Carlos Trucios <ctrucios@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Carlos",
                    family = "Trucios",
                    role = c("aut", "cre"),
                    email = "ctrucios@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: ‘Hossein Azari Soufiani <azari.hossein@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Hossein", "Azari"),
                      family = "Soufiani",
                      role = c("aut", "cre"),
                      email = "azari.hossein@gmail.com"),
               person(given = "William",
                      family = "Chen",
                      role = "aut"))
as necessary.
Maintainer: ‘Kartikeya Bolar <kartikeya.bolar@tapmi.edu.in>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kartikeya",
                    family = "Bolar",
                    role = c("aut", "cre"),
                    email = "kartikeya.bolar@tapmi.edu.in")
as necessary.
Packages required but not available: 'rmarkdown', 'Hmisc', 'rpivotTable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pkgdown', 'kableExtra', 'leaflet', 'tmap',
  '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?
Packages required but not available: 'knitr', 'MVN'

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: 'rmarkdown', 'knitr'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'plotly', 'rhandsontable', 'sortable'

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:
  'DT', 'htmlwidgets', 'leaflet', 'shinyjqui', 'sortable', 'tidyverse',
  'visNetwork'

Package suggested but not available for checking: ‘colourpicker’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Brett Naul <brettnaul@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Brett",
                    family = "Naul",
                    role = c("aut", "cre"),
                    email = "brettnaul@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: ‘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.
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?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for 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 Giuliano <mgiuliano.mail@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Marco",
                    family = "Giuliano",
                    role = c("aut", "cre"),
                    email = "mgiuliano.mail@gmail.com")
as necessary.
Maintainer: ‘Benjamin Risk <bbr28@cornell.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Benjamin", "B."),
                      family = "Risk",
                      role = "aut"),
               person(given = c("Nicholas", "A."),
                      family = "James",
                      role = "aut"),
               person(given = c("David", "S."),
                      family = "Matteson",
                      role = "aut"),
               person(given = "Benjamin",
                      family = "Risk",
                      role = "cre",
                      email = "bbr28@cornell.edu"))
as necessary.
Running examples in ‘steadyICA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dcovICA
> ### Title: ICA via distance covariance for 2 components
> ### Aliases: dcovICA
> ### Keywords: givens distance covariance ICA
> 
> ### ** Examples
> 
> library(JADE)
> library(ProDenICA)
Error in library(ProDenICA) : there is no package called ‘ProDenICA’
Execution halted
Maintainer: ‘David Leiva <dleivaur@ub.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("David", "Leiva", "&", "Han", "de", "Vries"),
                      family = "<J.deVries1@uu.nl>.",
                      role = "aut",
                      email = "J.deVries1@uu.nl"),
               person(given = "David",
                      family = "Leiva",
                      role = "cre",
                      email = "dleivaur@ub.edu"))
as necessary.
Maintainer: ‘Cedric E Ginestet <cedric.ginestet@kcl.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Cedric", "E"),
                    family = "Ginestet",
                    role = c("aut", "cre"),
                    email = "cedric.ginestet@kcl.ac.uk")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'rmarkdown', 'covr', '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: ‘Jean-Baptiste Camps <jbcamps@hotmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Jean-Baptiste", "Camps", ";", "Florian"),
                      family = "Cafiero",
                      role = "aut"),
               person(given = "Jean-Baptiste",
                      family = "Camps",
                      role = "cre",
                      email = "jbcamps@hotmail.com"))
as necessary.

Found the following (possibly) invalid file URIs:
  URI: stemmatology-utils
    From: README.md
  URI: 10.1484/M.LECTIO-EB.5.102565
    From: README.md

Found the following URLs which should use \doi (with the DOI name only):
  File ‘PCC.Exploratory.Rd’:
    http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565
  File ‘PCC.Rd’:
    http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565
  File ‘PCC.Stemma.Rd’:
    http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565
  File ‘PCC.buildGroup.Rd’:
    http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565
  File ‘PCC.conflicts.Rd’:
    http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565
  File ‘PCC.disagreement.Rd’:
    http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565
  File ‘PCC.elimination.Rd’:
    http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565
  File ‘PCC.equipollent.Rd’:
    http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565
  File ‘PCC.overconflicting.Rd’:
    http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565
  File ‘PCC.reconstructModel.Rd’:
    http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565
  File ‘fournival.Rd’:
    http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565
  File ‘heinrichi.Rd’:
    http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565
  File ‘notreBesoin.Rd’:
    http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565
  File ‘parzival.Rd’:
    https://doi.org/10.1016/j.jtbi.2003.11.022
    http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565
  File ‘stemmatology-package.Rd’:
    http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565
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:
  'diffviewer', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory 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: ‘Sergio Garofalo <sergio.garofalo96@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sergio",
                    family = "Garofalo",
                    role = c("aut", "cre"),
                    email = "sergio.garofalo96@gmail.com")
as necessary.
Cannot process vignettes
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Arya Ebadi <aeba3842@uni.sydney.edu.au>’

The Description field contains
  (2020) <arXiv:2011.11939>. Such setups include target-decoy competition
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Maintainer: ‘Leandro A. Pereira <leandro.ap@ufu.br>’

The Description field contains
  hypothesis test. Pinto & Pereira (2021) <arXiv:2109.07978>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Package required but not available: ‘plotly’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Maintainer: ‘Eleni Vradi <vradi.eleni@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Eleni",
                    family = "Vradi",
                    role = c("aut", "cre"),
                    email = "vradi.eleni@gmail.com")
as necessary.
checkRd: (-1) tuneParam.Rd:28: Lost braces; missing escapes or markup?
    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
checkRd: (-1) tuneParamCL2.Rd:28: Lost braces; missing escapes or markup?
    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
Maintainer: ‘Mee Young Park <meeyoung@google.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Mee", "Young"),
                      family = "Park",
                      role = c("aut", "cre"),
                      email = "meeyoung@google.com"),
               person(given = "Trevor",
                      family = "Hastie",
                      role = "aut"))
as necessary.
Maintainer: ‘Wai-ki Yip <yuser86@yahoo.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Wai-ki",
                      family = "Yip",
                      role = c("aut", "cre"),
                      email = "yuser86@yahoo.com"),
               person(given = "Ann",
                      family = "Lazar",
                      role = "ctb"),
               person(given = "David",
                      family = "Zahrieh",
                      role = "ctb"),
               person(given = "Chip",
                      family = "Cole",
                      role = "ctb"),
               person(given = "Ann",
                      family = "Lazar",
                      role = "ctb"),
               person(given = "Marco",
                      family = "Bonetti",
                      role = "ctb"),
               person(given = "Victoria",
                      family = "Wang",
                      role = "ctb"),
               person(given = "William",
                      family = "Barcella",
                      role = "ctb"),
               person(given = "Sergio",
                      family = "Venturini",
                      role = "ctb"))
as necessary.
Packages required but not available: 'flextable', 'survAUC'

Packages suggested but not available for checking:
  'knitr', 'BiocStyle', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'StepReg', 'DT', 'flextable', 'rmarkdown'

Packages suggested but not available for checking: 'knitr', 'BiocStyle'

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/StepR.Rnw’
(Is a VignetteBuilder field missing?)

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: ‘Chu-Lan Michael Kao <chulankao@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chao",
                      family = "Du",
                      role = "aut"),
               person(given = c("Chu-Lan", "Michael"),
                      family = "Kao",
                      role = c("aut", "cre"),
                      email = "chulankao@gmail.com"),
               person(given = "Samuel",
                      family = "Kou",
                      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 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: ‘Kendro Vincent <vincent.kendro@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yu-Chin",
                      family = "Hsu",
                      role = "aut"),
               person(given = "Kendro",
                      family = "Vincent",
                      role = c("aut", "cre"),
                      email = "vincent.kendro@gmail.com"))
as necessary.
Maintainer: ‘Aaron Olsen <aarolsen@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Aaron",
                      family = "Olsen",
                      role = c("aut", "cre"),
                      email = "aarolsen@gmail.com"),
               person(given = "Annat",
                      family = "Haber",
                      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) landmarkMatrixToList.Rd:10: Lost braces
    10 |   \item{semilandmark.pattern}{a regular expression pattern passed to \code{sub()} for identifying and grouping curve points. The default is landmark names ending in one or more numbers. To disable grouping, set to code{''}.}
       |                                                                                                                                                                                                                           ^
Package required but not available: ‘yaml’

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rmarkdown’

Package suggested but not available for checking: ‘knitr’

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.
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘knitr’